Contacts of the helix formed by residues 27 - 59 (chain B) in PDB entry 6VSU
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 SER 27 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 1.3 76.3 - - - +
28B SER* 1.3 58.7 + - - +
29B ILE 3.0 5.6 - - - +
30B GLU* 3.4 21.4 + - - +
31B LYS* 3.2 26.2 + - - +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.4 11.3 - - - +
27B SER* 1.3 76.7 - - - +
29B ILE* 1.3 63.7 + - - +
31B LYS* 4.2 5.7 - - - +
32B GLY* 3.3 17.3 + - - -
50E LEU* 5.4 2.3 - - - +
53E GLU* 4.9 9.4 + - - +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 4.2 20.6 - - - +
27B SER 3.0 1.2 - - - -
28B SER* 1.3 78.6 - - - +
30B GLU* 1.3 66.6 + - - +
32B GLY* 3.2 3.1 + - - -
33B GLN* 3.0 48.2 + - - +
128B CYS 5.4 0.9 - - - +
50E LEU* 5.6 1.3 - - - +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 5.2 0.2 + - - -
27B SER* 3.4 21.0 + - - +
29B ILE* 1.3 80.3 - - + +
31B LYS* 1.3 55.7 + - - +
33B GLN* 3.3 11.5 - - - +
34B ASN* 3.0 40.5 + - - +
134B ARG* 3.5 36.5 + - - +
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER 3.2 18.1 + - - +
28B SER* 4.4 6.1 - - - +
30B GLU* 1.3 75.5 - - - +
32B GLY* 1.3 62.6 + - - +
34B ASN* 3.3 15.2 + - + +
35B ARG* 3.2 33.3 + - + +
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER 3.3 10.7 + - - -
29B ILE 3.2 6.9 + - - -
31B LYS* 1.3 72.6 - - - +
33B GLN* 1.3 65.1 + - - +
35B ARG* 3.1 19.6 + - - +
36B VAL* 3.3 9.5 + - - +
46E GLU 5.5 0.2 - - - +
50E LEU* 3.7 35.9 - - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.0 36.6 + - + +
30B GLU* 3.3 7.9 - - - +
32B GLY* 1.3 73.5 - - - +
34B ASN* 1.3 58.5 + - - +
36B VAL* 3.1 5.4 + - - +
37B ILE* 2.9 33.4 + - - +
128B CYS* 3.0 38.7 + - - +
129B GLY* 3.3 18.0 + - - +
130B VAL* 3.8 16.1 - - + +
134B ARG* 2.6 45.8 + - - +
50E LEU* 4.2 2.2 - - + +
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.0 30.7 + - - +
31B LYS* 3.3 18.4 - - + +
32B GLY 3.1 0.4 - - - -
33B GLN* 1.3 78.9 - - - +
35B ARG* 1.3 52.7 + - + +
37B ILE* 3.4 10.1 + - - +
38B ASP* 2.8 48.7 + - - +
134B ARG* 3.1 21.5 + - - -
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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
----------------------------------------------------------
31B LYS* 3.2 23.4 - - + +
32B GLY* 3.1 12.0 + - - +
34B ASN* 1.3 76.3 - - + +
36B VAL* 1.3 57.1 + - - +
38B ASP* 3.5 6.7 + - - +
39B ALA* 3.0 30.5 + - - +
46E GLU* 3.8 38.1 + - + +
49E LYS* 6.0 4.9 - - - +
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY 3.3 10.5 + - - +
33B GLN 3.1 8.8 + - - +
35B ARG* 1.3 75.4 - - - +
37B ILE* 1.3 56.4 + - + +
39B ALA* 3.5 2.3 + - - -
40B SER* 2.8 43.9 + - - +
124B GLU* 4.6 1.6 - - + +
125B ILE* 4.5 12.3 - - + -
128B CYS* 4.2 18.6 - - + -
43E LEU* 3.7 5.4 - - + +
46E GLU* 4.0 28.0 - - + +
47E ARG* 4.1 25.4 - - + +
50E LEU* 3.8 19.7 - - + -
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN 2.9 19.7 + - - +
34B ASN* 3.7 11.2 - - - +
36B VAL* 1.3 75.1 - - + +
38B ASP* 1.3 65.2 + - - +
40B SER* 3.1 9.5 + - - -
41B LEU* 2.9 39.0 + - + +
125B ILE* 4.4 9.4 - - + -
130B VAL* 3.8 33.4 - - + -
134B ARG* 4.0 23.1 - - + +
138B VAL* 3.5 32.3 - - + -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASN* 2.8 32.4 + - - +
35B ARG* 3.9 6.3 - - - +
37B ILE* 1.3 80.3 - - - +
39B ALA* 1.3 51.6 + - - +
41B LEU* 3.3 11.4 + - - +
42B THR* 2.8 39.4 + - - +
45B ARG* 5.2 0.5 + - - -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG 3.0 18.4 + - - +
36B VAL 3.8 4.0 - - - +
38B ASP* 1.3 73.2 - - - +
40B SER* 1.3 59.6 + - - +
42B THR* 3.5 7.6 + - - +
43B LEU* 3.0 30.3 + - - +
39E ALA* 4.5 5.2 - - - +
42E THR* 4.3 15.7 - - + -
43E LEU* 3.9 32.2 - - + +
46E GLU* 4.5 5.6 - - + -
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 2.8 21.0 + - - +
37B ILE 3.1 8.0 + - - -
39B ALA* 1.3 75.7 - - - +
41B LEU* 1.3 62.7 + - - +
43B LEU* 3.2 12.8 + - - +
44B ILE* 3.3 17.8 + - - +
121B PRO* 3.5 28.9 - - - +
125B ILE* 3.8 24.9 - - - +
138B VAL* 5.0 3.8 - - - -
43E LEU* 3.6 17.0 - - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 2.9 34.8 + - + +
38B ASP* 3.7 10.5 - - - +
40B SER* 1.3 73.4 - - - +
42B THR* 1.3 66.4 + - - +
44B ILE* 3.1 5.0 + - - -
45B ARG* 3.0 26.3 + - - +
138B VAL* 3.7 23.6 - - + +
141B GLU* 3.9 25.4 - - + -
142B SER* 3.5 27.6 - - - +
145B LEU* 3.5 22.9 - - + +
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 2.8 24.9 + - - +
39B ALA* 3.8 8.7 - - - -
40B SER 3.4 0.2 - - - -
41B LEU* 1.3 71.6 - - - +
43B LEU* 1.3 64.7 + - - +
45B ARG* 3.1 33.5 + - - +
46B GLU* 2.9 36.7 + - - +
39E ALA* 4.3 15.3 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA 3.0 18.0 + - - +
40B SER 3.5 5.6 - - - +
41B LEU 3.2 0.4 - - - -
42B THR* 1.3 77.0 - - - +
44B ILE* 1.3 63.2 + - + +
46B GLU* 3.4 1.1 + - - +
47B ARG* 3.2 59.2 + - - +
121B PRO* 5.4 5.8 - - + -
36E VAL* 3.9 15.9 - - + +
39E ALA* 3.9 15.7 - - + +
40E SER* 3.6 31.4 - - - +
43E LEU* 3.8 23.8 - - + -
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER 3.3 13.9 + - - +
41B LEU* 3.1 7.0 + - - +
43B LEU* 1.3 73.2 - - + +
45B ARG* 1.3 59.7 + - - +
47B ARG* 3.3 35.3 + - - +
48B ALA* 2.9 29.2 + - + +
68B LEU* 4.3 19.3 - - + -
117B VAL* 4.3 10.8 - - + +
119B ASP 3.8 15.0 - - - +
120B VAL* 4.4 7.2 - - + +
121B PRO* 4.8 3.8 - - + -
142B SER* 4.1 37.9 - - - +
145B LEU* 4.3 11.9 - - + -
146B VAL* 4.8 3.1 - - + -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP 5.2 0.4 + - - -
41B LEU* 3.0 16.5 + - - +
42B THR* 3.1 54.5 + - - +
44B ILE* 1.3 77.8 - - - +
46B GLU* 1.3 66.8 + - + +
48B ALA* 3.4 4.4 + - - +
49B LYS* 3.0 30.9 + - + +
145B LEU* 4.2 30.0 - - + +
149B GLU* 5.0 3.1 - - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 2.9 31.2 + - + +
43B LEU 4.0 3.8 - - - +
44B ILE 3.3 0.2 - - - -
45B ARG* 1.3 85.0 + - - +
47B ARG* 1.3 61.1 + - - +
49B LYS* 3.4 16.3 + - - +
50B LEU* 3.3 26.0 + - - +
35E ARG* 2.8 70.1 + - + +
36E VAL* 4.1 19.0 - - + +
39E ALA* 4.2 8.3 - - + -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.2 50.2 + - - +
44B ILE* 3.3 19.1 - - - +
46B GLU* 1.3 75.2 - - - +
48B ALA* 1.3 63.5 + - - +
50B LEU* 3.2 14.8 + - + +
51B LYS* 3.2 23.6 + - + +
117B VAL* 2.8 39.0 + - + +
118B GLY* 4.4 2.4 - - - -
119B ASP 2.9 39.6 + - - +
36E VAL* 4.1 25.4 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 2.9 22.0 + - + +
45B ARG* 3.6 6.1 - - - +
47B ARG* 1.3 71.2 - - - +
49B LYS* 1.3 56.3 + - - +
51B LYS* 3.3 2.6 + - - +
52B GLY 2.8 31.7 + - - -
117B VAL* 3.7 22.4 - - + +
145B LEU 4.2 13.7 - - - +
146B VAL* 4.5 8.1 - - - -
149B GLU* 3.5 20.7 - - + +
152B LEU* 3.9 3.0 - - + +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 3.0 16.0 + - + +
46B GLU* 3.6 26.2 - - - +
47B ARG 3.2 0.4 - - - -
48B ALA* 1.3 77.6 - - - +
50B LEU* 1.3 63.3 + - + +
52B GLY* 3.2 1.7 + - - -
53B GLU* 2.9 59.1 + - + +
56B ARG* 4.3 1.4 + - - +
149B GLU* 3.5 23.5 - - - +
32E GLY* 6.2 0.8 - - - -
35E ARG* 4.0 25.2 - - - +
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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
----------------------------------------------------------
46B GLU 3.3 12.5 + - - +
47B ARG* 3.2 7.8 + - - +
49B LYS* 1.3 84.2 - - + +
51B LYS* 1.3 69.1 + - + +
53B GLU* 4.0 17.5 - - - +
54B LEU* 3.1 24.3 + - - +
32E GLY* 3.7 36.3 - - - +
33E GLN* 4.2 9.9 - - + +
35E ARG* 6.2 0.9 - - + -
36E VAL* 3.8 23.8 - - + -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 3.2 14.7 + - - +
48B ALA 3.7 6.3 - - - +
49B LYS 3.2 0.6 - - - -
50B LEU* 1.3 81.0 - - + +
52B GLY* 1.3 63.6 - - - +
54B LEU* 3.3 18.2 + - + +
55B VAL* 3.1 29.1 + - - +
115B THR* 4.0 32.7 - - + +
116B ASP* 3.3 30.1 + - - +
117B VAL* 4.2 8.1 - - + +
152B LEU* 4.4 8.5 - - + -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA 2.8 20.6 + - - -
49B LYS 3.6 1.6 - - - -
51B LYS* 1.3 72.6 - - - +
53B GLU* 1.3 55.4 - - - +
55B VAL* 3.3 4.4 + - - +
56B ARG* 3.0 53.2 + - - +
149B GLU* 4.0 8.7 - - - -
150B GLU 4.7 1.3 - - - +
152B LEU* 4.1 11.1 - - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 2.9 55.5 + - - +
50B LEU* 4.0 17.0 - - + +
52B GLY* 1.3 68.3 - - - +
54B LEU* 1.3 65.2 + - - +
56B ARG* 3.4 20.8 + - - +
57B LEU* 3.0 29.3 + - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU 3.1 15.2 + - - +
51B LYS* 3.3 28.2 + - + +
53B GLU* 1.3 75.7 - - - +
55B VAL* 1.3 62.5 + - - +
57B LEU* 3.3 11.1 + - + +
58B LEU* 3.2 33.7 + - + +
111B PRO* 3.9 33.2 - - + -
115B THR* 4.9 2.0 - - + -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS 3.1 16.9 + - - +
52B GLY 3.8 6.1 - - - +
54B LEU* 1.3 76.4 - - - +
56B ARG* 1.3 62.7 + - - +
58B LEU* 3.5 4.8 + - - +
59B GLY* 3.2 17.2 + - - -
61B ALA* 4.0 9.1 - - + +
64B SER* 3.4 28.3 - - - +
111B PRO* 3.5 31.6 - - + +
112B ARG* 4.1 10.4 - - + +
115B THR* 4.1 9.6 - - + -
151B PRO* 3.7 25.6 - - + -
152B LEU* 4.1 7.4 - - + -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 4.3 0.8 + - - +
52B GLY* 3.0 21.0 + - - +
53B GLU* 3.4 38.5 + - - +
55B VAL* 1.3 75.8 - - - +
57B LEU* 1.3 57.2 + - - +
59B GLY* 3.0 23.0 + - - -
149B GLU* 2.9 30.7 + - - -
150B GLU* 2.8 45.9 + - - +
151B PRO* 4.3 7.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.0 19.5 + - + +
54B LEU* 3.7 12.1 - - + +
55B VAL 3.3 0.2 - - - -
56B ARG* 1.3 77.6 - - - +
58B LEU* 1.3 70.8 + - + +
59B GLY* 3.7 0.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.2 17.0 + - + +
55B VAL 3.7 7.9 - - - +
57B LEU* 1.3 86.9 - - + +
59B GLY* 1.3 62.1 + - - +
110B ASP* 3.9 11.4 - - - +
111B PRO* 3.6 37.5 - - + -
112B ARG* 3.5 26.7 + - + +
----------------------------------------------------------
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL 3.2 7.7 + - - -
56B ARG* 3.0 18.6 + - - -
57B LEU 4.7 0.4 - - - -
58B LEU* 1.3 73.3 - - - +
60B GLY* 1.3 57.4 + - - -
61B ALA 3.4 3.4 - - - -
112B ARG* 2.9 34.1 + - - -
----------------------------------------------------------
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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