Contacts of the helix formed by residues 41 - 67 (chain D) in PDB entry 1R5I
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 THR 41 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER* 3.9 13.6 + - - -
38D LYS* 2.9 17.8 + - + +
39D GLU 3.0 1.4 - - - -
40D GLU* 1.3 91.4 - - + +
42D LYS* 1.3 65.6 + - - +
43D GLU 3.3 2.7 - - - -
44D VAL* 3.2 10.1 - - - +
45D LEU* 3.0 23.5 + - - +
94D ALA 4.7 2.2 - - - -
95D ASN* 2.9 58.6 + - + +
97D VAL* 4.1 12.8 - - + -
100D ILE* 6.1 0.4 - - - -
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Residues in contact with LYS 42 (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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36D SER 5.8 3.8 - - - +
37D ASN 5.7 2.0 - - - +
38D LYS 3.7 7.4 + - - +
39D GLU* 3.0 23.0 + - + +
40D GLU 3.5 0.2 - - - -
41D THR* 1.3 78.9 + - - +
43D GLU* 1.3 62.2 + - - +
45D LEU* 3.5 10.3 + - + +
46D LYS* 3.4 30.4 + - - +
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLU 4.8 0.4 + - - -
40D GLU 4.4 13.9 + - - +
42D LYS* 1.3 76.9 - - - +
44D VAL* 1.3 77.7 + - + +
46D LYS* 3.3 13.6 + - - +
47D LEU* 2.8 25.9 - - + +
97D VAL* 6.0 1.1 - - + -
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER* 6.5 0.2 - - - -
41D THR* 3.2 18.8 + - - +
43D GLU* 1.3 84.1 - - + +
45D LEU* 1.3 65.7 + - - +
47D LEU* 3.0 13.7 + - + +
48D PHE* 2.9 26.3 + - - +
97D VAL* 4.1 22.4 - - + +
100D ILE* 3.3 40.2 - - + -
101D LYS* 3.6 32.5 - - + +
104D ILE* 4.5 5.4 - - + -
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TYR* 4.0 23.8 - - + +
36D SER* 3.6 36.6 - - - +
41D THR 3.0 14.3 + - - +
42D LYS* 3.6 11.7 - - + +
43D GLU 3.3 0.2 - - - -
44D VAL* 1.3 84.4 - - + +
46D LYS* 1.3 65.6 + - + +
48D PHE* 3.4 12.7 + - + +
49D LYS* 3.1 55.6 + - + +
90D GLN* 5.3 0.2 - - - +
100D ILE* 5.2 1.3 - - + -
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Residues in contact with LYS 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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42D LYS* 3.4 20.4 - - - +
43D GLU* 3.4 10.5 - - - +
44D VAL 3.0 0.4 - - - -
45D LEU* 1.3 80.4 - - + +
47D LEU* 1.3 70.8 + - + +
49D LYS* 3.2 8.0 + - - +
50D LEU* 3.0 31.2 + - + +
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Residues in contact with LEU 47 (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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43D GLU* 2.8 30.3 - - + +
44D VAL* 3.0 12.1 + - + +
46D LYS* 1.3 80.3 - - + +
48D PHE* 1.3 62.0 + - - +
50D LEU* 3.4 12.8 + - + +
51D LYS* 3.0 24.4 + - - +
101D LYS* 6.3 1.1 - - + -
104D ILE* 3.7 17.9 - - + +
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Residues in contact with PHE 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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32D ILE* 4.9 1.3 - - + -
33D TYR* 3.7 33.9 - + - -
44D VAL 2.9 12.1 + - - +
45D LEU* 3.5 16.2 - - + +
46D LYS 3.1 0.2 - - - -
47D LEU* 1.3 74.9 - - - +
49D LYS* 1.3 64.4 + - - +
51D LYS* 3.0 5.0 + - - +
52D VAL* 2.9 33.6 + - + +
86D VAL* 5.3 2.5 - - + -
87D PHE* 3.7 26.9 - + - -
90D GLN* 3.4 44.2 - - + -
100D ILE* 4.0 16.4 - - + -
103D ASN* 4.4 12.1 - - + -
104D ILE* 3.6 21.9 - - + +
107D LEU* 4.6 12.6 - - + -
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Residues in contact with LYS 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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30D GLU* 4.6 8.3 + - - -
33D TYR* 3.3 59.5 - - + +
45D LEU* 3.1 38.6 + - + +
46D LYS* 3.2 8.7 + - - +
48D PHE* 1.3 77.3 - - - +
50D LEU* 1.3 67.7 + - + +
52D VAL* 3.2 1.4 + - - +
53D ASN* 3.0 33.2 + - - +
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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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46D LYS* 3.0 16.8 + - + +
47D LEU* 3.6 15.9 - - + +
49D LYS* 1.3 79.8 - - + +
51D LYS* 1.3 57.8 + - - +
53D ASN* 3.3 14.4 + - + +
54D GLN* 2.9 28.3 + - - +
57D ARG* 4.3 5.2 + - - +
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Residues in contact with LYS 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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47D LEU 3.0 12.6 + - - +
48D PHE* 3.0 9.2 + - - +
50D LEU* 1.3 75.4 - - - +
52D VAL* 1.3 60.1 + - - +
54D GLN* 3.0 31.2 + - - +
55D PHE* 2.7 30.0 + - - +
104D ILE* 3.4 32.4 - - + +
107D LEU* 4.1 15.9 - - + -
108D ASP* 2.8 41.1 + - - -
111D MET* 3.3 15.5 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 3.8 26.7 - - + -
33D TYR* 3.3 28.5 - - + +
48D PHE* 2.9 43.0 + - + +
49D LYS 3.2 2.0 + - - +
51D LYS* 1.3 75.3 - - - +
53D ASN* 1.3 66.2 + - - +
55D PHE* 3.0 10.5 + - + +
56D TYR* 2.9 35.0 + - + -
83D LEU* 5.1 3.6 - - + -
87D PHE* 4.4 11.7 - - + -
107D LEU* 4.4 10.8 - - + -
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Residues in contact with ASN 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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29D LEU* 5.5 3.6 - - - +
33D TYR* 4.6 5.5 + - - -
49D LYS* 3.0 17.0 + - - +
50D LEU* 3.5 17.1 - - + +
52D VAL* 1.3 82.8 - - - +
54D GLN* 1.3 62.7 + - - +
56D TYR* 3.2 9.8 + - - +
57D ARG* 3.0 42.4 + - - +
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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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50D LEU 2.9 15.3 + - - +
51D LYS* 3.0 37.3 + - + +
53D ASN* 1.3 75.2 - - - +
55D PHE* 1.3 56.7 + - - +
57D ARG* 3.3 29.2 + - + +
58D HIS* 2.9 31.2 + - + +
108D ASP* 3.9 2.4 + - - -
111D MET* 3.3 26.2 - - + +
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Residues in contact with PHE 55 (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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51D LYS 2.7 16.4 + - - +
52D VAL* 3.0 14.6 - - - +
54D GLN* 1.3 73.5 - - - +
56D TYR* 1.3 68.9 + + - +
58D HIS* 3.0 4.3 + - - +
59D ALA* 3.0 20.3 + - - +
79D MET* 3.4 43.3 - - + +
80D PHE* 4.5 11.9 - + - -
83D LEU* 3.7 35.4 - - + -
107D LEU* 4.0 17.5 - - + -
110D ILE* 3.4 37.5 - - + -
111D MET* 3.7 27.5 - - + -
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Residues in contact with TYR 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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23D VAL* 3.6 17.3 - - + -
24D PHE* 2.5 44.9 + - - +
26D ASN* 5.9 2.9 - - - -
29D LEU* 3.7 12.5 - - + +
52D VAL* 2.9 36.9 + - + +
53D ASN* 3.5 11.7 - - - +
55D PHE* 1.3 79.1 - + - +
57D ARG* 1.3 64.5 + - + +
59D ALA* 3.1 4.7 + - - +
60D PHE* 3.0 50.3 + + + -
80D PHE* 3.6 22.2 - + - -
83D LEU* 4.3 8.1 - - + -
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Residues in contact with ARG 57 (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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50D LEU* 4.3 5.1 + - - +
53D ASN* 3.0 39.4 + - - +
54D GLN* 3.5 31.4 + - - +
56D TYR* 1.3 76.2 - - + +
58D HIS* 1.3 57.4 + - - +
60D PHE* 3.8 4.4 + - - +
61D GLY* 2.9 25.6 + - - -
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Residues in contact with HIS 58 (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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4D ARG* 3.4 9.7 + - - -
54D GLN* 2.9 15.7 + - + +
55D PHE 3.0 9.2 + - - +
57D ARG* 1.3 76.2 - - - +
59D ALA* 1.3 64.5 + - - +
61D GLY* 3.1 2.8 + - - -
62D ILE* 3.1 32.7 + - + +
79D MET* 4.1 6.7 - - + -
111D MET* 3.6 41.4 + - + -
115D ASP* 2.8 40.7 + - - -
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Residues in contact with ALA 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 PHE* 3.0 12.0 + - + +
56D TYR 3.1 7.6 + - - +
58D HIS* 1.3 75.7 - - - +
60D PHE* 1.3 62.2 + - - +
62D ILE* 3.0 16.3 + - - +
63D VAL* 3.2 11.8 + - - +
76D PHE* 3.5 26.1 - - + -
79D MET* 3.3 27.1 - - + +
80D PHE* 3.6 20.0 - - + -
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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
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23D VAL* 4.7 16.6 - - + -
56D TYR* 3.0 54.0 + + + +
57D ARG* 4.4 3.8 - - - +
59D ALA* 1.3 72.5 - - - +
61D GLY* 1.3 61.5 + - - +
63D VAL* 3.2 20.6 - - + +
64D ASN* 2.8 31.4 + - - +
76D PHE* 4.0 23.6 - + - -
80D PHE* 4.6 4.0 - + - -
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Residues in contact with GLY 61 (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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4D ARG* 4.2 9.5 + - - -
57D ARG 2.9 19.5 + - - -
58D HIS* 3.1 4.0 + - - -
59D ALA 3.1 0.8 - - - -
60D PHE* 1.3 76.9 - - - +
62D ILE* 1.3 62.0 + - - +
64D ASN* 3.1 16.0 + - - +
65D ASP* 3.2 18.2 + - - +
204D SER* 6.0 0.3 - - - -
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Residues in contact with ILE 62 (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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4D ARG* 3.5 30.5 - - - +
58D HIS* 3.1 16.7 + - + +
59D ALA 3.0 9.1 + - - +
61D GLY* 1.3 78.8 - - - +
63D VAL* 1.3 58.4 + - + +
66D TYR* 3.0 31.0 + - + +
72D TYR* 4.8 13.6 - - + +
75D ILE* 3.9 15.7 - - + -
76D PHE* 5.5 2.2 - - + +
79D MET* 3.2 28.5 - - + -
114D ALA* 3.9 15.3 - - + -
115D ASP* 4.2 2.7 - - - +
118D LEU* 4.0 29.2 - - + -
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Residues in contact with VAL 63 (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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59D ALA 3.2 4.9 + - - +
60D PHE* 3.2 39.7 - - + +
62D ILE* 1.3 77.0 - - - +
64D ASN* 1.3 59.4 + - - +
65D ASP 3.4 0.2 - - - -
67D ASN* 3.0 31.0 + - + +
72D TYR* 3.5 41.3 - - + +
76D PHE* 4.1 16.4 - - + -
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D PHE 2.8 17.0 + - - +
61D GLY* 3.1 8.9 + - - +
63D VAL* 1.3 80.9 - - - +
65D ASP* 1.3 58.7 + - + +
67D ASN* 3.4 14.1 + - - +
182D LEU* 4.9 2.3 - - - +
185D LYS* 2.8 53.7 + - - +
203D THR* 5.5 1.0 - - - +
204D SER* 4.6 13.4 - - - -
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Residues in contact with ASP 65 (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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4D ARG* 4.0 5.5 + - - -
61D GLY 3.2 11.3 + - - +
64D ASN* 1.3 80.5 - - - +
66D TYR* 1.3 81.7 + - + +
67D ASN* 3.7 2.5 + - - +
68D GLY 5.2 0.2 + - - -
128D PHE* 4.8 0.3 - - - -
132D TRP* 3.3 25.4 + - + -
178D TRP* 5.9 1.2 - - - -
182D LEU* 4.7 8.6 - - - +
185D LYS* 4.5 3.0 + - - +
204D SER* 3.3 17.0 + - - -
205D ASP* 2.8 37.3 + - - +
206D PHE* 3.3 28.8 - - - +
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Residues in contact with TYR 66 (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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1D MET* 5.3 3.6 - - - -
2D LYS 5.0 7.4 + - - -
3D LEU* 6.1 0.2 - - - -
4D ARG* 4.0 8.9 + - - +
62D ILE 3.0 20.6 + - - +
65D ASP* 1.3 97.5 - - + +
67D ASN* 1.3 55.8 + - - +
68D GLY 2.9 12.8 + - - +
69D LEU* 2.9 22.9 + - + +
72D TYR* 3.3 17.0 - - + +
118D LEU* 3.5 41.3 - - + -
122D ILE* 4.0 17.5 - - + +
128D PHE* 4.0 22.0 - + - -
132D TRP* 4.0 24.7 - + - -
205D ASP* 2.6 39.4 + - + +
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Residues in contact with ASN 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D VAL* 3.0 31.2 + - + +
64D ASN* 3.4 19.4 + - - +
65D ASP 3.7 1.5 - - - -
66D TYR* 1.3 74.1 - - - +
68D GLY* 1.3 60.7 + - - +
69D LEU 3.3 1.0 - - - -
72D TYR* 3.5 32.1 - - + +
177D TRP* 5.3 9.4 - - - -
178D TRP* 3.2 29.3 - - - +
181D SER* 6.0 0.9 - - - -
182D LEU* 5.7 5.8 - - - +
185D LYS* 5.4 0.6 - - - +
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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