Contacts of the helix formed by residues 29 - 67 (chain D) in PDB entry 3V2P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 29 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP* 5.8 0.2 - - - +
30C ALA* 3.8 16.2 - - + +
31C PRO* 3.5 45.3 - - + -
34C LEU* 4.1 19.5 - - + -
28D ASP* 1.3 85.5 - - + +
30D ALA* 1.3 61.2 + - - +
31D PRO* 3.3 3.6 - - - -
32D GLN* 3.1 30.3 + - - +
33D MET* 2.8 37.5 + - + +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 2.9 17.9 + - + +
28D ASP* 4.4 0.2 - - - +
29D LEU* 1.3 78.1 - - - +
31D PRO* 1.3 66.9 - - + +
33D MET* 3.1 11.6 + - - +
34D LEU* 2.9 20.8 + - - +
28E ASP* 3.1 34.8 - - - +
29E LEU* 3.4 14.4 - - + +
33E MET* 4.6 5.6 - - - +
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Residues in contact with PRO 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET 3.3 28.9 - - - +
28D ASP 3.8 6.3 - - - +
29D LEU 3.4 3.8 - - - -
30D ALA* 1.3 96.0 - - + +
32D GLN* 1.3 63.6 + - + +
34D LEU* 3.4 4.0 + - + +
35D ARG* 3.2 38.0 + - - +
29E LEU* 3.5 15.9 - - + -
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.6 30.3 - - + +
38C GLN* 5.1 4.0 + - - -
28D ASP 4.6 5.6 + - - +
29D LEU* 3.1 30.7 + - - +
31D PRO* 1.3 77.4 - - + +
33D MET* 1.3 65.6 + - - +
35D ARG* 3.3 20.6 + - - +
36D GLU* 3.1 26.4 + - - +
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Residues in contact with MET 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B MET* 6.2 0.2 - - + -
37B LEU* 5.1 1.6 - - + -
30C ALA* 4.7 11.7 - - - +
33C MET* 3.6 44.2 - - + +
34C LEU* 4.1 19.1 - - + -
37C LEU* 3.6 26.5 - - + +
29D LEU* 2.8 28.9 + - + +
30D ALA* 3.6 7.4 - - - +
32D GLN* 1.3 77.1 - - - +
34D LEU* 1.3 63.9 + - - +
36D GLU* 3.1 4.9 + - - +
37D LEU* 3.0 26.5 + - - +
33E MET* 3.7 24.0 - - + +
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA 2.9 16.7 + - - +
31D PRO* 3.7 4.5 - - + +
33D MET* 1.3 74.5 - - - +
35D ARG* 1.3 63.8 + - - +
37D LEU* 3.2 3.6 + - + +
38D GLN* 3.0 45.4 + - + +
29E LEU* 4.0 20.9 - - + -
32E GLN* 3.7 52.7 - - + +
33E MET* 3.9 16.7 - - + +
36E GLU* 3.7 15.7 - - + +
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PRO* 3.2 23.5 + - - +
32D GLN* 3.5 32.1 + - - +
33D MET 3.2 0.2 - - - -
34D LEU* 1.3 78.3 - - - +
36D GLU* 1.3 63.1 + - - +
38D GLN* 3.3 17.5 + - + +
39D GLU* 3.0 44.6 + - + +
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.8 19.6 - - + +
37C LEU* 3.8 18.4 - - + -
38C GLN* 3.5 34.2 + - + +
41C ASN* 2.7 46.6 + - - +
32D GLN* 3.1 19.4 + - - +
33D MET 3.1 7.4 + - - +
35D ARG* 1.3 77.8 - - - +
37D LEU* 1.3 58.1 + - - +
39D GLU* 3.2 15.8 + - - +
40D THR* 2.9 20.2 + - - -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.5 35.9 - - + -
37C LEU* 3.8 13.9 - - + -
33D MET 3.0 14.5 + - - +
34D LEU* 3.2 7.6 + - - +
36D GLU* 1.3 78.2 - - - +
38D GLN* 1.3 61.3 + - - +
40D THR* 3.3 8.5 + - + +
41D ASN* 3.0 21.8 + - - +
33E MET* 3.5 61.0 - - + +
36E GLU* 3.7 16.1 - - + +
37E LEU* 3.6 14.1 - - + -
40E THR* 4.7 3.1 + - - +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.0 34.8 + - + +
35D ARG* 3.6 22.8 + - + +
37D LEU* 1.3 73.0 - - - +
39D GLU* 1.3 66.3 + - + +
41D ASN* 3.2 4.3 + - - +
42D ALA* 3.0 23.1 + - - +
36E GLU* 3.5 33.8 + - + +
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASN* 3.6 16.4 + - - +
45C GLN* 5.8 2.4 + - - -
35D ARG* 3.0 34.8 + - + +
36D GLU* 3.5 29.6 - - - +
38D GLN* 1.3 77.1 - - + +
40D THR* 1.3 57.5 + - - +
42D ALA* 3.3 7.9 + - - +
43D ALA* 3.0 29.1 + - - +
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Residues in contact with THR 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 4.1 28.8 - - + +
37C LEU* 4.8 2.4 + - - +
40C THR* 4.1 10.8 - - + +
41C ASN* 2.5 28.5 + - - -
44C LEU* 3.7 19.0 - - + +
36D GLU 2.9 11.4 + - - -
37D LEU* 3.5 14.6 - - + +
39D GLU* 1.3 78.7 - - - +
41D ASN* 1.3 57.7 + - - +
43D ALA* 3.4 2.4 + - - +
44D LEU* 3.0 30.0 + - + +
40E THR* 4.3 12.6 - - - +
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Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU 3.0 13.3 + - - +
38D GLN 3.2 7.8 + - - +
40D THR* 1.3 75.8 - - - +
42D ALA* 1.3 63.7 + - - +
44D LEU* 3.4 4.5 + - - +
45D GLN* 3.0 49.6 + - - +
36E GLU* 3.8 15.3 + - - +
39E GLU* 2.8 50.8 + - - +
40E THR* 4.0 14.9 + - - +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ARG* 4.9 3.0 + - - +
38D GLN 3.0 12.7 + - - +
39D GLU* 3.5 11.7 - - - +
40D THR 3.3 0.2 - - - -
41D ASN* 1.3 78.4 - - - +
43D ALA* 1.3 62.0 + - - +
45D GLN* 3.2 11.0 + - - +
46D ASP* 3.2 19.8 + - - +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASN* 5.2 1.6 - - - +
44C LEU* 4.3 29.6 - - + +
45C GLN* 5.4 4.5 - - + +
48C ARG* 4.0 25.9 - - - +
39D GLU 3.0 15.7 + - - +
40D THR* 3.7 5.2 - - - +
42D ALA* 1.3 76.6 - - - +
44D LEU* 1.3 58.4 + - - +
46D ASP* 3.2 5.5 + - - +
47D VAL* 2.9 30.5 + - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.6 38.8 - - + -
44C LEU* 3.5 32.8 - - + -
40D THR* 3.0 18.5 + - + +
41D ASN* 3.6 9.0 - - - +
42D ALA 3.2 0.2 - - - -
43D ALA* 1.3 74.7 - - - +
45D GLN* 1.3 61.4 + - - +
47D VAL* 4.2 10.1 - - + -
48D ARG* 2.8 30.0 + - - +
40E THR* 4.7 9.6 - - + +
43E ALA* 4.4 20.6 - - + +
44E LEU* 4.8 5.6 - - - +
47E VAL* 4.2 22.4 - - + -
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 3.0 43.1 + - - +
42D ALA* 3.4 10.8 - - - +
44D LEU* 1.3 76.5 - - - +
46D ASP* 1.3 58.1 + - - +
48D ARG* 3.2 26.7 + - - +
49D GLU* 3.0 43.3 + - - +
52D ARG* 5.4 2.1 + - - -
39E GLU* 4.8 3.6 + - - +
43E ALA* 3.9 20.2 - - - +
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Residues in contact with ASP 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ARG* 2.6 40.6 - - - +
52C ARG* 3.0 15.2 + - - -
42D ALA 3.2 7.2 + - - +
43D ALA 3.2 9.1 + - - +
44D LEU 3.2 0.2 - - - -
45D GLN* 1.3 77.2 - - - +
47D VAL* 1.3 60.2 + - - +
49D GLU* 3.3 17.1 + - - +
50D LEU* 2.9 44.0 + - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A STE 3.8 29.6 - - + -
44C LEU* 4.3 19.1 - - + -
47C VAL* 4.6 5.6 - - + -
48C ARG* 4.4 24.5 - - + -
51C LEU* 3.7 20.6 - - + +
43D ALA 2.9 20.9 + - - +
44D LEU* 3.2 10.3 + - + +
46D ASP* 1.3 75.4 - - - +
48D ARG* 1.3 58.7 + - - +
50D LEU* 3.4 3.9 + - - +
51D LEU* 2.9 29.8 + - + +
47E VAL* 4.6 9.0 - - + -
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU 2.8 16.9 + - - +
45D GLN* 3.4 29.9 + - - +
46D ASP 3.2 0.2 - - - -
47D VAL* 1.3 77.6 - - - +
49D GLU* 1.3 57.2 + - - +
51D LEU* 3.3 3.9 + - - +
52D ARG* 2.9 64.6 + - - +
42E ALA* 3.8 11.7 + - - +
43E ALA* 3.9 21.1 - - + +
46E ASP* 2.4 50.2 + - - +
47E VAL* 4.5 15.2 - - + +
50E LEU* 4.2 8.2 - - + +
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLN* 3.0 25.1 + - - +
46D ASP* 3.3 17.6 + - - +
48D ARG* 1.3 74.1 - - - +
50D LEU* 1.3 63.2 + - + +
52D ARG* 3.3 23.8 + - - +
53D GLN* 3.1 22.5 + - - +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ARG* 4.0 25.1 - - + +
51C LEU* 3.9 19.1 - - + -
52C ARG* 4.2 29.2 - - + +
55C VAL* 3.9 15.3 - - + +
46D ASP* 2.9 44.6 + - - +
47D VAL* 3.6 4.5 - - - +
49D GLU* 1.3 77.4 - - + +
51D LEU* 1.3 56.8 + - - +
53D GLN* 3.2 8.2 + - + +
54D GLN* 2.9 28.7 + - - +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.7 28.0 - - + +
51C LEU* 4.3 6.7 - - + +
47D VAL* 2.9 18.8 + - + +
48D ARG 3.7 4.5 - - - +
50D LEU* 1.3 75.8 - - - +
52D ARG* 1.3 62.8 + - - +
54D GLN* 3.2 11.4 + - - +
55D VAL* 3.0 31.2 + - + +
47E VAL* 3.8 30.5 - - + +
50E LEU* 3.5 33.4 - - + -
51E LEU* 4.2 9.6 - - + +
54E GLN* 3.5 26.2 - - - +
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLN* 5.4 2.6 + - - -
48D ARG* 2.9 49.8 + - - +
49D GLU* 3.6 22.7 + - - +
50D LEU 3.2 0.2 - - - -
51D LEU* 1.3 76.9 - - - +
53D GLN* 1.3 62.0 + - - +
55D VAL* 3.7 4.2 + - - +
56D LYS* 3.4 30.5 + - - +
46E ASP* 2.8 28.9 + - - -
50E LEU* 3.8 26.5 - - + -
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Residues in contact with GLN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C VAL* 4.6 15.5 - - + -
49D GLU 3.1 12.4 + - - +
50D LEU* 3.5 11.0 - - + +
52D ARG* 1.3 75.4 - - - +
54D GLN* 1.3 64.8 + - - +
56D LYS* 3.1 36.4 + - - +
57D GLU* 2.9 45.2 + - - +
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Residues in contact with GLN 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.3 5.5 + - - -
54A GLN* 5.1 0.2 - - - +
51C LEU* 3.3 15.1 - - - +
54C GLN* 2.8 40.2 + - - +
55C VAL* 3.7 15.8 - - + +
58C ILE* 3.3 25.1 - - + +
50D LEU 2.9 16.1 + - - +
51D LEU* 3.2 11.5 + - - +
53D GLN* 1.3 77.9 - - - +
55D VAL* 1.3 62.3 + - - +
57D GLU* 3.2 9.3 + - - +
58D ILE* 3.0 29.4 + - + +
54E GLN* 3.0 34.2 + - - +
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Residues in contact with VAL 55 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.0 27.9 + - + +
52D ARG* 4.0 5.6 - - - +
53D GLN 3.3 0.2 - - - -
54D GLN* 1.3 75.7 - - - +
56D LYS* 1.3 59.6 + - + +
58D ILE* 3.3 5.8 + - + +
59D THR* 2.9 40.2 + - - +
50E LEU* 4.1 20.2 - - + +
53E GLN* 3.5 34.5 - - + +
54E GLN* 3.5 33.9 - - + +
57E GLU* 5.1 2.2 - - + -
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 3.4 19.7 - - - +
53D GLN* 3.1 30.4 + - - +
55D VAL* 1.3 80.4 - - + +
57D GLU* 1.3 59.8 + - - +
59D THR* 3.5 6.3 + - - -
60D PHE* 3.0 27.4 + - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 5.1 3.4 - - + -
58C ILE* 3.8 19.5 - - + +
59C THR* 3.8 25.0 + - - +
62C LYS* 2.9 43.7 + - + +
53D GLN* 2.9 41.4 + - + +
54D GLN* 3.2 8.9 + - - +
56D LYS* 1.3 75.7 - - - +
58D ILE* 1.3 60.7 + - - +
60D PHE* 3.4 4.0 + - - +
61D LEU* 3.0 28.5 + - - +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 4.2 27.8 - - + -
54D GLN 3.0 17.9 + - - +
55D VAL* 3.8 5.6 - - - +
57D GLU* 1.3 76.1 - - - +
59D THR* 1.3 59.4 + - - +
61D LEU* 3.3 8.6 + - + +
62D LYS* 2.8 27.9 + - - +
54E GLN* 3.5 39.3 - - + +
57E GLU* 3.9 19.3 - - + -
58E ILE* 3.9 31.6 - - + +
61E LEU* 5.1 8.6 - - + +
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Residues in contact with THR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 2.9 30.1 + - - +
56D LYS* 3.8 7.1 - - - -
58D ILE* 1.3 73.8 - - - +
60D PHE* 1.3 64.8 + - - +
62D LYS* 3.2 12.5 + - - +
63D ASN* 2.8 44.8 + - - +
53E GLN* 4.7 1.6 + - - -
57E GLU* 2.9 29.0 + - - +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS* 3.3 29.4 - - + -
66C MET* 3.2 43.3 - - + -
56D LYS 3.0 18.5 + - - +
57D GLU* 3.7 5.8 - - - +
59D THR* 1.3 76.7 - - - +
61D LEU* 1.3 54.0 + - - +
63D ASN* 3.3 11.2 + - + +
64D THR* 2.8 52.2 + - - -
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 5.1 8.3 - - + -
61C LEU* 3.6 28.9 - - + +
62C LYS* 3.7 29.4 - - + +
65C VAL* 3.8 28.3 - - + -
57D GLU 3.0 18.4 + - - +
58D ILE* 3.5 10.8 - - + +
59D THR 3.2 0.2 - - - -
60D PHE* 1.3 80.2 - - - +
62D LYS* 1.3 61.8 + - - +
64D THR* 3.3 5.3 + - - -
65D VAL* 3.1 32.7 + - + +
61E LEU* 3.9 25.4 - - + -
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ILE 2.8 17.9 + - - +
59D THR* 3.4 9.6 - - - +
60D PHE 3.2 0.2 - - - -
61D LEU* 1.3 77.7 - - - +
63D ASN* 1.3 86.2 + - - +
65D VAL* 3.6 1.6 + - - +
66D MET* 3.0 57.3 + - + +
57E GLU* 2.8 59.1 + - + +
60E PHE* 4.2 14.9 - - + -
61E LEU* 3.9 19.2 - - + +
64E THR* 5.3 1.0 + - - +
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Residues in contact with ASN 63 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D THR* 2.8 41.4 + - - +
60D PHE* 3.8 9.9 - - + +
62D LYS* 1.3 93.5 - - - +
64D THR* 1.3 60.9 + - - +
66D MET* 3.5 8.7 - - - +
67D GLU* 2.9 51.9 + - - +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS* 5.5 0.2 - - - +
65C VAL* 3.6 35.0 - - + +
66C MET* 4.6 9.3 - - + +
71C CYS* 5.5 5.3 - - + +
60D PHE* 2.8 46.5 + - - -
61D LEU* 3.5 9.2 - - + -
63D ASN* 1.3 76.5 - - - +
65D VAL* 1.3 63.1 + - - +
67D GLU* 3.2 6.4 + - - +
68D CYS* 3.2 19.8 + - - +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 4.3 20.9 - - + -
71C CYS* 6.1 0.7 - - - -
61D LEU* 3.1 21.9 + - + +
62D LYS 4.2 0.2 - - - +
64D THR* 1.3 76.4 - - - +
66D MET* 1.3 62.2 + - - +
68D CYS* 3.2 20.2 + - + +
71D CYS* 4.2 17.5 - - - +
61E LEU* 3.7 19.3 - - + -
64E THR* 3.8 19.4 - - + +
65E VAL* 3.9 23.1 - - + +
----------------------------------------------------------
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Residues in contact with MET 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LYS* 3.0 49.2 + - + +
63D ASN* 3.5 10.3 - - - +
65D VAL* 1.3 79.5 - - - +
67D GLU* 1.3 61.4 - - + +
68D CYS 3.3 3.0 + - - +
71D CYS* 6.1 0.3 - - - +
60E PHE* 4.7 11.0 - - + -
64E THR* 3.6 32.0 - - + +
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C CYS* 5.2 0.2 - - - +
63D ASN* 2.9 35.0 + - + +
64D THR* 3.5 6.1 - - - +
65D VAL 3.2 0.2 - - - -
66D MET* 1.3 81.3 - - + +
68D CYS* 1.3 63.9 + - - +
69D ASP* 3.7 9.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il