Contacts of the helix formed by residues 29 - 67 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 3.7 19.0 - - + +
31A PRO* 3.5 47.3 - - + -
34A LEU* 4.4 15.0 - - + -
27B MET* 3.1 26.4 + - + +
28B ASP* 1.3 73.5 + - - +
30B ALA* 1.3 65.7 + - - +
31B PRO* 3.2 3.6 - - - -
32B GLN* 3.1 31.8 + - - +
33B MET* 2.9 30.2 + - + +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP* 3.2 15.0 + - - +
29B LEU* 1.3 75.8 - - - +
31B PRO* 1.3 64.7 - - + +
33B MET* 3.1 10.6 + - - +
34B LEU* 2.8 32.4 + - - +
29C LEU* 3.9 16.6 - - + +
30C ALA 6.0 0.4 - - - +
33C MET* 4.1 16.5 - - + +
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Residues in contact with PRO 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP* 3.5 26.0 - - - +
29B LEU 3.3 3.8 - - - -
30B ALA* 1.3 96.2 - - + +
32B GLN* 1.3 62.0 + - + +
34B LEU* 3.6 3.5 + - - +
35B ARG* 3.3 41.6 + - - +
29C LEU* 3.5 19.7 - - + -
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.4 31.2 - - + +
38A GLN* 5.1 4.2 + - - -
27B MET* 6.0 1.2 - - - +
28B ASP 4.9 3.4 + - - +
29B LEU* 3.1 30.4 + - - +
31B PRO* 1.3 78.2 - - + +
33B MET* 1.3 67.3 + - - +
35B ARG* 3.2 27.3 + - - +
36B GLU* 3.1 25.3 + - - +
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Residues in contact with MET 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 4.8 10.5 - - - +
33A MET* 3.6 42.6 - - + +
34A LEU* 4.1 21.1 - - + -
37A LEU* 3.8 27.1 - - + +
29B LEU* 2.9 22.9 + - + +
30B ALA* 3.6 6.1 - - - +
32B GLN* 1.3 75.6 - - - +
34B LEU* 1.3 63.8 + - - +
36B GLU* 3.0 4.6 + - - +
37B LEU* 2.9 27.1 + - + +
33C MET* 3.6 27.6 - - + -
33D MET* 6.2 0.7 - - + -
33E MET* 5.6 2.7 - - + -
37E LEU* 5.3 0.9 - - + -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 2.8 15.7 + - - +
31B PRO 3.7 5.6 - - - +
33B MET* 1.3 77.9 - - - +
35B ARG* 1.3 62.6 + - + +
37B LEU* 3.2 3.4 + - + -
38B GLN* 2.9 42.1 + - + +
29C LEU* 4.0 25.8 - - + -
32C GLN* 3.4 39.9 - - + +
33C MET* 4.0 22.6 - - + +
36C GLU* 3.8 26.0 - - + -
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 3.3 24.2 + - - +
32B GLN* 3.2 36.3 + - - +
34B LEU* 1.3 79.0 - - + +
36B GLU* 1.3 62.4 + - - +
38B GLN* 3.3 19.3 + - - +
39B GLU* 2.9 29.3 + - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.7 19.5 - - + +
37A LEU* 3.9 17.7 - - + -
38A GLN* 3.5 35.9 + - + +
41A ASN* 2.8 39.2 + - - +
32B GLN* 3.1 17.5 + - - +
33B MET 3.0 8.6 + - - +
35B ARG* 1.3 79.5 - - - +
37B LEU* 1.3 57.6 + - - +
39B GLU* 3.2 11.5 + - - +
40B THR* 2.9 27.2 + - - -
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Residues in contact with LEU 37 (chain B).
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 31.4 - - + -
37A LEU* 4.0 16.8 - - + -
33B MET* 2.9 18.5 + - + +
34B LEU* 3.2 6.9 + - - +
36B GLU* 1.3 75.5 - - - +
38B GLN* 1.3 62.0 + - - +
40B THR* 3.3 9.4 + - - +
41B ASN* 3.1 26.9 + - - -
33C MET* 3.9 52.5 - - + +
36C GLU* 3.9 15.0 - - + -
37C LEU* 3.9 15.7 - - + -
40C THR* 4.9 3.0 + - - +
33D MET* 5.1 0.7 - - + -
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 2.9 34.0 + - + +
35B ARG* 3.6 22.3 - - - +
37B LEU* 1.3 78.1 - - - +
39B GLU* 1.3 60.9 + - - +
41B ASN* 3.3 3.8 + - - +
42B ALA* 3.0 22.3 + - - +
32C GLN* 3.8 21.1 + - - -
36C GLU* 3.6 28.7 - - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.2 33.8 - - - +
45A GLN* 5.1 6.7 - - - +
48A ARG* 5.5 1.1 + - - +
35B ARG 2.9 13.5 + - - +
36B GLU* 3.5 17.4 - - - +
38B GLN* 1.3 73.5 - - - +
40B THR* 1.3 66.5 + - - +
42B ALA* 3.2 7.7 + - + +
43B ALA* 2.9 25.2 + - + +
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Residues in contact with THR 40 (chain B).
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 36.9 - - + +
37A LEU* 5.0 2.4 + - - +
40A THR* 4.4 8.1 - - - +
41A ASN* 2.5 26.1 + - - -
44A LEU* 3.6 10.7 - - + +
36B GLU 2.9 13.8 + - - -
37B LEU* 3.4 15.1 - - + +
38B GLN 3.2 0.2 - - - -
39B GLU* 1.3 76.3 - - - +
41B ASN* 1.3 59.3 + - - +
43B ALA* 3.2 4.0 + - - +
44B LEU* 2.9 33.2 + - + +
40C THR* 4.2 12.1 - - - +
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.1 12.7 + - - +
38B GLN 3.8 6.1 - - - +
39B GLU 3.3 0.2 - - - -
40B THR* 1.3 79.5 - - - +
42B ALA* 1.3 56.6 + - - +
44B LEU* 3.3 7.8 + - - +
45B GLN* 2.9 41.1 + - + +
36C GLU* 2.6 50.2 + - - +
39C GLU* 3.6 18.8 - - + +
40C THR* 2.7 35.3 + - - +
43C ALA* 5.0 2.6 - - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 4.7 5.2 + - - +
38B GLN 3.0 13.6 + - - +
39B GLU* 3.2 11.2 + - + +
41B ASN* 1.3 73.0 - - - +
43B ALA* 1.3 66.2 + - - +
45B GLN* 3.3 21.1 + - - +
46B ASP* 3.2 20.3 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 5.2 1.8 - - - +
44A LEU* 3.5 22.0 - - + -
45A GLN* 5.4 0.7 - - - +
48A ARG* 3.5 36.3 - - - +
39B GLU* 2.9 15.9 + - + +
40B THR* 3.4 8.1 - - - +
42B ALA* 1.3 76.9 - - - +
44B LEU* 1.3 58.9 + - - +
46B ASP* 3.1 6.2 + - - +
47B VAL* 2.9 30.6 + - - +
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Residues in contact with LEU 44 (chain B).
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 3.8 38.6 - - + -
44A LEU* 4.2 12.1 - - + -
40B THR* 2.9 25.2 + - + +
41B ASN* 3.7 7.4 - - - +
42B ALA 3.3 0.2 - - - -
43B ALA* 1.3 75.6 - - - +
45B GLN* 1.3 58.1 + - - +
47B VAL* 3.5 11.4 - - + +
48B ARG* 2.8 31.2 + - - +
40C THR* 3.9 38.6 - - + +
43C ALA* 4.3 18.3 - - + +
44C LEU* 4.6 5.6 - - + -
47C VAL* 4.8 11.4 - - + +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASN* 2.9 30.9 + - + +
42B ALA* 3.5 21.4 + - - +
43B ALA 3.2 0.2 - - - -
44B LEU* 1.3 75.4 - - - +
46B ASP* 1.3 63.3 + - - +
48B ARG* 3.3 27.4 + - - +
49B GLU* 3.0 24.5 + - - +
39C GLU* 5.2 9.7 - - - +
43C ALA* 5.6 2.2 - - + +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 2.9 40.0 + - - +
52A ARG* 3.0 22.8 + - - -
42B ALA 3.2 5.8 + - - +
43B ALA 3.1 8.8 + - - +
45B GLN* 1.3 76.8 - - - +
47B VAL* 1.3 64.2 + - - +
49B GLU* 3.2 18.2 + - - +
50B LEU* 2.9 38.8 + - - +
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Residues in contact with VAL 47 (chain B).
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 29.2 - - + -
44A LEU* 4.2 15.0 - - + -
47A VAL* 4.7 3.8 - - + -
48A ARG* 3.5 30.1 - - + +
51A LEU* 3.6 20.7 - - + +
43B ALA 2.9 19.9 + - - +
44B LEU* 3.2 15.9 + - + +
46B ASP* 1.3 75.9 - - - +
48B ARG* 1.3 58.7 + - - +
50B LEU* 3.3 2.5 + - - -
51B LEU* 2.9 29.4 + - + +
47C VAL* 4.7 8.3 - - + -
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Residues in contact with ARG 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU 2.8 18.0 + - - +
45B GLN* 3.6 27.3 + - - +
47B VAL* 1.3 77.4 - - - +
49B GLU* 1.3 57.6 + - - +
51B LEU* 3.3 6.2 + - - +
52B ARG* 2.9 57.1 + - - +
39C GLU* 4.5 11.3 + - - -
42C ALA* 4.8 0.8 - - - +
43C ALA* 3.7 25.2 - - + +
46C ASP* 2.5 49.4 + - + -
47C VAL* 4.4 12.6 - - + -
50C LEU* 3.9 10.2 - - + +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLN 3.0 16.5 + - - +
46B ASP* 3.7 18.3 - - - +
48B ARG* 1.3 76.2 - - - +
50B LEU* 1.3 63.4 + - + +
52B ARG* 3.3 13.2 + - - +
53B GLN* 3.0 30.8 + - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 3.8 23.6 - - - +
51A LEU* 3.6 27.1 - - + -
52A ARG* 4.2 33.0 - - + +
55A VAL* 3.9 8.0 - - + +
46B ASP* 2.9 43.7 + - - +
47B VAL* 4.5 1.3 - - - -
49B GLU* 1.3 75.2 - - + +
51B LEU* 1.3 59.5 + - - +
53B GLN* 2.8 36.3 - - - +
54B GLN* 2.8 29.7 + - - +
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Residues in contact with LEU 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.7 33.7 - - + +
51A LEU* 4.2 6.2 - - + +
47B VAL* 2.9 17.4 + - + +
48B ARG 3.7 4.3 - - - +
50B LEU* 1.3 74.9 - - - +
52B ARG* 1.3 57.7 + - - +
54B GLN* 3.6 7.0 - - - +
55B VAL* 2.9 36.6 + - + +
47C VAL* 3.7 44.0 - - + +
50C LEU* 3.7 21.3 - - + -
51C LEU* 4.2 6.5 - - + +
54C GLN* 3.4 29.8 - - + +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG* 2.9 55.8 + - - +
49B GLU* 3.5 10.3 - - - +
51B LEU* 1.3 77.5 - - - +
53B GLN* 1.3 60.7 + - - +
55B VAL* 3.5 4.1 + - - +
56B LYS* 3.3 19.6 + - - +
46C ASP* 4.0 17.4 + - - +
50C LEU* 3.4 37.6 - - + +
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Residues in contact with GLN 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.5 24.3 - - + +
49B GLU* 3.0 22.3 + - + +
50B LEU* 2.8 53.8 - - - +
52B ARG* 1.3 76.3 - - - +
54B GLN* 1.3 62.9 + - - +
56B LYS* 3.2 9.4 + - - +
57B GLU* 3.1 27.0 + - + +
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Residues in contact with GLN 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.2 14.8 + - - -
51A LEU* 3.7 7.8 - - - +
54A GLN* 2.9 44.1 + - - +
55A VAL* 3.7 23.7 + - + +
58A ILE* 3.3 24.1 - - + +
50B LEU 2.8 16.6 + - - +
51B LEU* 3.2 7.6 + - - +
53B GLN* 1.3 78.9 - - - +
55B VAL* 1.3 61.7 + - - +
57B GLU* 3.2 7.9 + - - +
58B ILE* 3.0 23.6 + - + +
54C GLN* 3.0 23.7 + - - +
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Residues in contact with VAL 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 2.9 27.1 + - + +
52B ARG* 3.8 5.4 - - - +
53B GLN 3.3 0.2 - - - -
54B GLN* 1.3 76.0 - - - +
56B LYS* 1.3 54.3 + - - +
58B ILE* 3.8 5.1 - - - +
59B THR* 2.7 45.8 + - - +
50C LEU* 4.0 22.2 - - + +
53C GLN* 4.8 12.3 - - + -
54C GLN* 3.5 35.0 - - + +
57C GLU* 4.7 11.9 - - + -
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG 3.3 10.2 + - - +
53B GLN* 3.2 12.5 + - - +
54B GLN 3.2 0.6 - - - -
55B VAL* 1.3 81.8 - - - +
57B GLU* 1.3 66.2 + - - +
59B THR* 3.5 7.2 + - - -
60B PHE* 3.1 22.9 + - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.9 4.7 - - + -
58A ILE* 3.8 19.1 - - + -
59A THR* 3.0 38.2 + - - +
62A LYS* 3.1 38.8 + - + +
53B GLN* 3.1 17.4 + - + +
54B GLN* 3.2 8.7 + - - +
56B LYS* 1.3 81.4 - - - +
58B ILE* 1.3 59.4 + - - +
60B PHE* 3.2 6.9 + - - +
61B LEU* 2.9 27.8 + - - +
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Residues in contact with ILE 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.0 31.6 - - + -
54B GLN* 3.0 14.8 + - - +
55B VAL* 3.9 4.5 - - - +
57B GLU* 1.3 73.2 - - - +
59B THR* 1.3 61.1 + - - +
61B LEU* 3.2 10.0 + - + +
62B LYS* 2.8 27.4 + - + +
54C GLN* 3.6 37.5 - - + +
57C GLU* 3.9 24.5 - - + +
58C ILE* 4.1 26.9 - - + +
61C LEU* 5.1 10.4 - - + +
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Residues in contact with THR 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 2.7 30.3 + - - +
56B LYS* 3.7 8.2 - - - -
58B ILE* 1.3 76.9 - - - +
60B PHE* 1.3 62.7 + - - +
62B LYS* 3.4 7.5 + - - +
63B ASN* 3.1 36.6 + - - +
57C GLU* 3.8 34.9 - - - +
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Residues in contact with PHE 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LYS* 3.4 29.8 - - + +
66A MET* 3.4 35.9 - - + -
56B LYS* 3.1 15.0 + - + +
57B GLU* 3.5 9.2 - - - +
58B ILE 3.2 0.2 - - - -
59B THR* 1.3 75.8 - - - +
61B LEU* 1.3 62.2 - - - +
63B ASN* 3.4 8.1 + - + +
64B THR* 2.9 43.7 + - - -
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Residues in contact with LEU 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 5.1 7.6 - - + +
61A LEU* 3.9 30.3 - - + -
62A LYS* 4.2 19.3 - - + +
65A VAL* 3.6 40.8 - - + -
57B GLU 2.9 16.4 + - - +
58B ILE* 3.5 11.9 - - + +
60B PHE* 1.3 78.2 - - - +
62B LYS* 1.3 61.6 + - - +
64B THR* 3.3 4.5 + - - -
65B VAL* 3.1 34.0 + - + +
61C LEU* 4.0 25.4 - - + -
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Residues in contact with LYS 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE 2.8 13.8 + - - +
59B THR* 3.4 15.3 - - - +
61B LEU* 1.3 76.5 - - - +
63B ASN* 1.3 83.4 + - - +
65B VAL* 3.1 4.7 + - - +
66B MET* 2.9 49.2 + - + +
57C GLU* 2.7 41.0 + - - +
60C PHE* 3.7 36.1 - - + -
61C LEU* 4.1 19.9 - - + +
64C THR* 5.2 0.2 - - - +
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Residues in contact with ASN 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 3.1 32.8 + - - +
60B PHE* 3.9 7.4 - - + +
62B LYS* 1.3 95.7 + - - +
64B THR* 1.3 60.9 + - - +
66B MET* 3.4 16.0 + - - +
67B GLU* 3.2 23.0 + - - +
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Residues in contact with THR 64 (chain B).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 6.2 0.2 - - - -
65A VAL* 4.1 23.1 - - + +
66A MET* 4.3 20.4 - - + -
71A CYS* 5.1 5.5 - - + +
60B PHE* 2.9 42.5 + - - -
61B LEU* 3.6 7.4 - - - -
62B LYS 3.2 0.2 - - - -
63B ASN* 1.3 74.2 - - - +
65B VAL* 1.3 65.2 + - - +
67B GLU* 3.4 6.2 + - - +
68B CYS* 3.4 17.8 + - - +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.1 22.0 - - + -
71A CYS* 5.5 0.2 - - - -
61B LEU* 3.1 21.7 + - + +
62B LYS 3.7 3.8 - - - +
64B THR* 1.3 73.5 - - - +
66B MET* 1.3 66.9 + - - +
68B CYS* 3.1 21.8 + - + +
71B CYS* 4.3 13.7 - - - +
61C LEU* 3.7 17.7 - - + -
64C THR* 3.8 20.7 - - + +
65C VAL* 4.1 23.1 - - + +
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 2.9 36.7 + - + +
63B ASN* 3.6 26.2 - - - +
65B VAL* 1.3 78.2 - - - +
67B GLU* 1.3 57.4 + - + +
68B CYS 3.4 4.5 + - - +
71B CYS* 5.6 2.1 - - - +
60C PHE* 5.4 9.0 - - + -
64C THR* 3.9 34.4 - - + +
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS 4.6 3.3 - - - +
63B ASN 3.2 13.4 + - - +
64B THR* 3.4 7.2 + - - +
65B VAL 3.2 0.2 - - - -
66B MET* 1.3 77.6 - - + +
68B CYS* 1.3 61.2 + - - +
69B ASP 3.6 2.1 + - - -
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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