Contacts of the helix formed by residues 28 - 59 (chain C) 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 28 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER* 1.3 75.8 - - - +
29C ILE* 1.3 64.3 + - - +
31C LYS* 3.4 18.5 - - - +
32C GLY* 3.3 18.9 + - - -
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER* 2.9 3.5 - - - +
28C SER* 1.3 84.8 - - - +
30C GLU* 1.3 54.2 + - + +
31C LYS 3.4 0.7 - - - -
32C GLY* 3.1 3.1 + - - +
33C GLN* 2.6 52.7 + - + +
128C CYS* 4.3 9.9 - - + +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER* 2.6 37.4 + - - +
29C ILE* 1.3 69.2 - - - +
31C LYS* 1.3 61.6 + - - +
33C GLN* 3.2 40.5 + - - +
34C ASN* 3.3 17.0 + - - -
134C ARG* 4.0 12.7 + - - -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER* 3.0 27.5 + - - +
28C SER* 3.4 24.9 - - - +
30C GLU* 1.3 75.9 - - - +
32C GLY* 1.3 55.3 + - - +
34C ASN* 3.0 33.2 + - - +
35C ARG* 3.4 15.3 + - - +
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER 3.3 16.2 + - - -
29C ILE* 3.1 8.7 + - - -
31C LYS* 1.3 72.0 - - - +
33C GLN* 1.3 64.1 + - - +
34C ASN 3.1 1.3 - - - -
35C ARG* 2.9 29.7 + - - +
36C VAL* 3.0 18.1 + - - +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 2.6 29.2 + - + +
30C GLU* 3.2 32.5 + - - +
32C GLY* 1.3 70.8 - - - +
34C ASN* 1.3 57.4 + - - +
36C VAL* 3.2 4.7 + - - +
37C ILE* 3.0 31.0 + - - +
128C CYS* 2.8 41.5 + - + +
129C GLY* 3.2 23.6 + - - -
130C VAL* 3.8 13.3 - - + -
134C ARG* 3.0 26.2 + - - +
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Residues in contact with ASN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLU* 3.3 20.0 + - - -
31C LYS* 3.0 18.5 + - - +
33C GLN* 1.3 74.8 - - - +
35C ARG* 1.3 53.5 + - + +
37C ILE* 3.7 7.8 - - - +
38C ASP* 2.7 47.1 + - - +
134C ARG* 2.8 31.3 + - - +
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 3.6 12.3 - - - +
32C GLY* 2.9 24.1 + - - +
34C ASN* 1.3 76.1 - - + +
36C VAL* 1.3 63.1 + - - +
38C ASP* 4.0 6.3 - - - +
39C ALA* 3.2 25.3 + - - +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLY 3.0 17.6 + - - +
33C GLN 3.2 7.8 + - - +
35C ARG* 1.3 77.5 - - + +
37C ILE* 1.3 50.0 + - + +
39C ALA* 3.7 3.9 - - - +
40C SER* 2.8 46.5 + - - +
124C GLU* 4.9 7.6 - - + -
125C ILE* 4.6 15.3 - - + +
128C CYS* 4.0 33.2 - - + -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN 3.0 19.7 + - - +
34C ASN* 3.7 7.6 - - - +
36C VAL* 1.3 72.9 - - + +
38C ASP* 1.3 64.2 + - - +
40C SER* 3.1 7.3 + - - -
41C LEU* 2.8 55.9 + - + +
125C ILE* 4.5 10.5 - - + -
130C VAL* 3.9 25.4 - - + -
134C ARG* 3.8 28.5 - - + +
138C VAL* 3.7 29.6 - - + -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 2.7 30.6 + - - +
35C ARG* 4.0 6.9 - - - +
37C ILE* 1.3 79.0 - - - +
39C ALA* 1.3 51.1 + - - +
41C LEU* 3.2 9.2 + - - +
42C THR* 2.3 42.1 + - - +
45C ARG* 5.4 0.3 + - - -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG 3.2 16.4 + - - +
36C VAL* 3.7 3.6 - - - +
38C ASP* 1.3 73.4 - - - +
40C SER* 1.3 68.6 + - - +
42C THR* 3.5 9.6 + - - -
43C LEU* 2.9 26.9 + - - +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 2.8 34.8 + - - +
37C ILE* 3.1 8.9 + - - -
39C ALA* 1.3 75.4 - - - +
41C LEU* 1.3 63.3 + - - +
43C LEU* 3.3 7.2 + - - +
44C ILE* 3.3 24.6 + - - +
120C VAL* 5.9 0.2 - - - -
121C PRO* 3.3 35.4 - - - +
124C GLU* 5.7 0.5 - - - +
125C ILE* 3.9 18.9 - - - +
138C VAL* 5.2 1.8 - - - -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 2.8 43.3 + - + +
38C ASP* 3.6 10.1 - - - +
40C SER* 1.3 68.6 - - - +
42C THR* 1.3 66.8 + - - +
44C ILE* 3.1 8.4 + - + +
45C ARG* 2.9 26.4 + - - +
138C VAL* 3.7 22.4 - - + +
141C GLU* 3.8 23.6 - - + -
142C SER* 3.6 27.1 - - - +
145C LEU* 3.5 19.2 - - + +
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Residues in contact with THR 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 2.3 39.4 + - - +
39C ALA* 3.5 10.8 - - - -
41C LEU* 1.3 69.5 - - - +
43C LEU* 1.3 51.7 + - - +
45C ARG* 3.0 30.9 + - - +
46C GLU* 2.8 43.4 + - + +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA 2.9 17.6 + - - +
40C SER* 3.4 8.1 - - - +
42C THR* 1.3 72.7 - - - +
44C ILE* 1.3 67.1 + - + +
46C GLU* 3.4 6.9 + - + +
47C ARG* 3.0 63.1 + - + +
119C ASP 6.0 0.2 - - - +
121C PRO* 5.7 8.1 - - + -
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Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER 3.3 17.0 - - - +
41C LEU* 3.1 11.4 + - - +
43C LEU* 1.3 76.5 - - + +
45C ARG* 1.3 52.2 + - - +
47C ARG* 3.7 14.1 - - - +
48C ALA* 2.8 34.0 + - + +
68C LEU* 4.3 13.7 - - + -
117C VAL* 4.7 11.3 - - + +
119C ASP 3.7 24.5 - - - +
120C VAL* 3.8 24.7 - - + -
121C PRO* 4.6 3.1 - - + -
142C SER* 4.0 32.1 - - - +
145C LEU* 4.2 11.0 - - + -
146C VAL* 4.8 2.0 - - + -
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP 5.4 0.2 + - - -
41C LEU* 2.9 16.0 + - - +
42C THR* 3.5 40.6 + - - +
44C ILE* 1.3 74.4 - - - +
46C GLU* 1.3 65.3 + - - +
48C ALA* 3.1 6.9 + - - +
49C LYS* 2.9 31.0 + - + +
145C LEU* 4.1 27.5 - - + +
149C GLU* 4.1 15.7 - - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 2.8 27.5 + - + +
43C LEU* 3.4 9.2 + - + +
45C ARG* 1.3 79.4 - - + +
47C ARG* 1.3 60.9 + - - +
49C LYS* 3.5 23.7 + - - +
50C LEU* 3.3 32.9 + - - +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.0 60.4 + - + +
44C ILE* 3.7 8.1 - - - +
46C GLU* 1.3 72.6 - - + +
48C ALA* 1.3 65.7 + - - +
49C LYS 3.2 1.0 + - - -
50C LEU* 3.2 22.5 + - + +
51C LYS* 3.2 18.7 + - + +
117C VAL* 3.0 38.0 + - - +
118C GLY* 3.3 4.4 - - - -
119C ASP 3.0 44.8 + - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE 2.8 22.7 + - - +
45C ARG* 3.1 10.5 + - - +
47C ARG* 1.3 73.8 - - - +
49C LYS* 1.3 51.1 + - - +
51C LYS* 3.5 2.4 + - - +
52C GLY* 2.8 31.5 + - - -
117C VAL* 3.9 19.7 - - + +
145C LEU* 4.1 12.6 - - + +
146C VAL* 4.7 4.9 - - + -
149C GLU* 3.6 25.9 - - + +
152C LEU* 4.0 3.5 - - + +
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ARG* 2.9 16.6 + - + +
46C GLU* 3.7 25.3 + - - +
47C ARG 3.2 0.4 - - - -
48C ALA* 1.3 74.7 - - - +
50C LEU* 1.3 69.3 + - - +
52C GLY* 3.3 1.4 + - - -
53C GLU* 2.8 70.3 + - + +
56C ARG* 3.8 3.0 + - - +
149C GLU* 3.8 18.6 - - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 3.3 23.1 - - - +
47C ARG* 3.2 13.9 + - + +
49C LYS* 1.3 96.6 - - - +
51C LYS* 1.4 66.5 + - + +
53C GLU* 3.5 9.6 + - + +
54C LEU* 3.1 27.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ARG* 3.2 12.4 + - + +
48C ALA 3.7 7.0 - - - +
50C LEU* 1.4 82.2 - - - +
52C GLY* 1.3 66.3 + - - +
53C GLU 3.1 0.5 + - - -
54C LEU* 3.1 19.0 + - + +
55C VAL* 3.1 29.6 + - - +
115C THR* 3.9 32.7 - - + +
116C ASP* 3.6 31.6 - - - +
117C VAL* 4.3 6.1 - - + -
152C LEU* 4.3 8.1 - - + -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ALA 2.8 19.1 + - - -
49C LYS 3.5 4.9 - - - -
51C LYS* 1.3 72.5 - - - +
53C GLU* 1.3 55.8 - - - +
55C VAL* 3.5 2.9 + - - +
56C ARG* 3.0 56.2 + - - +
149C GLU* 4.6 2.5 - - - -
150C GLU 4.3 3.2 - - - +
152C LEU* 3.9 14.6 - - - +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 2.8 57.2 + - + +
50C LEU* 3.7 11.0 - - + +
51C LYS 3.1 0.4 - - - -
52C GLY* 1.3 69.9 - - - +
54C LEU* 1.3 54.9 + - - +
56C ARG* 3.3 21.7 + - - +
57C LEU* 2.7 36.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU 3.1 17.1 + - - +
51C LYS* 3.1 21.3 + - + +
53C GLU* 1.3 72.0 - - - +
55C VAL* 1.3 63.7 + - - +
57C LEU* 3.4 15.8 + - + +
58C LEU* 3.0 46.1 + - + +
111C PRO* 3.8 29.8 - - + -
115C THR* 5.6 0.7 - - + -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS 3.1 18.8 + - - +
52C GLY 3.7 3.6 - - - +
54C LEU* 1.3 73.7 - - - +
56C ARG* 1.3 60.9 + - - +
58C LEU* 3.0 19.2 + - - +
59C GLY* 3.2 11.3 + - - +
61C ALA* 4.0 10.9 - - + +
64C SER* 3.3 22.7 - - - +
111C PRO* 3.5 29.4 - - + +
112C ARG* 4.4 5.6 - - - +
115C THR* 3.9 8.5 - - + -
151C PRO* 3.6 22.0 - - + -
152C LEU* 3.8 18.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 3.8 4.0 + - - +
52C GLY* 3.0 47.4 + - - +
53C GLU* 3.6 26.3 + - - +
55C VAL* 1.3 68.3 - - - +
57C LEU* 1.3 66.4 + - - +
58C LEU 3.2 0.7 + - - -
59C GLY* 3.5 11.8 + - - +
149C GLU* 3.8 15.8 + - - +
150C GLU* 2.5 52.8 + - - +
151C PRO* 4.8 4.3 - - + -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLU 2.7 20.2 + - - +
54C LEU* 3.4 19.5 - - + +
55C VAL 3.3 0.2 - - - -
56C ARG* 1.3 72.8 - - - +
58C LEU* 1.3 72.7 + - + +
59C GLY* 4.8 0.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.0 33.4 - - + +
55C VAL* 3.0 8.3 + - - +
57C LEU* 1.3 92.2 - - + +
59C GLY* 1.3 58.8 + - - +
110C ASP* 3.8 11.7 - - - +
111C PRO* 3.6 32.3 - - + -
112C ARG* 3.5 36.3 + - + +
----------------------------------------------------------
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Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL 3.2 8.0 + - - -
56C ARG* 3.5 10.9 + - - -
57C LEU 4.8 0.2 - - - -
58C LEU* 1.3 77.8 - - - +
60C GLY* 1.3 57.3 + - - -
61C ALA 3.1 6.7 + - - -
112C ARG* 3.1 30.0 + - - +
----------------------------------------------------------
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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