Contacts of the helix formed by residues 33 - 54 (chain A) in PDB entry 6V3O
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 LYS 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU 5.8 1.0 + - - -
31A ASP* 3.9 15.8 + - - +
32A ASP* 1.3 76.7 - - - +
34A LEU* 1.3 58.7 + - - +
35A ILE 3.3 2.5 - - - -
36A GLU* 3.1 31.9 + - - +
37A TYR* 2.8 45.5 + - + +
116A GLN* 3.1 9.3 + - - +
201A ASN* 3.6 37.4 + - - +
203A LYS* 6.3 0.6 - - - +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 3.6 16.7 + - - +
33A LYS* 1.3 76.5 - - - +
35A ILE* 1.3 58.9 + - - +
37A TYR* 3.1 6.1 + - + +
38A ASP* 2.8 40.3 + - - +
109A ALA 5.0 0.2 - - - +
112A ALA* 3.7 10.1 - - + +
113A GLU* 3.7 48.2 - - + +
116A GLN* 3.7 17.7 + - + -
120A ARG* 5.9 1.8 - - - +
889A GLN* 4.2 18.6 - - + +
890A GLY* 4.6 7.9 - - - -
893A LEU* 4.0 24.9 - - + -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 4.0 22.7 - - - +
20A LEU* 4.0 22.3 - - + +
21A ARG* 3.9 24.0 - - + -
24A VAL* 3.9 24.9 - - + +
26A GLY 5.9 2.2 - - - +
32A ASP* 4.8 3.4 + - - +
33A LYS 3.3 0.4 - - - -
34A LEU* 1.3 75.9 - - - +
36A GLU* 1.3 63.2 + - - +
38A ASP* 3.4 7.4 + - - +
39A ALA* 3.0 23.2 + - - +
889A GLN* 4.7 8.1 - - - +
893A LEU* 4.2 25.1 - - + -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 4.9 5.8 - - - +
33A LYS* 3.1 41.0 + - + +
35A ILE* 1.3 81.5 - - - +
37A TYR* 1.3 61.7 + - + +
39A ALA* 3.7 3.7 - - - +
40A LEU* 2.9 51.0 + - + +
201A ASN* 5.4 2.3 - - - +
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 2.8 34.7 + - + +
34A LEU* 3.1 10.1 + - - +
36A GLU* 1.3 77.3 - - + +
38A ASP* 1.3 68.2 + - - +
40A LEU* 3.1 16.0 + - + +
41A LEU* 3.1 17.3 + - - +
112A ALA* 3.7 32.5 - - + -
115A VAL* 3.9 24.1 - - + +
116A GLN* 4.1 19.7 - - + -
119A HIS* 6.2 0.2 - - - +
197A LEU* 3.9 31.7 + - + -
198A THR* 5.3 2.1 - - - -
201A ASN* 3.2 38.1 + - + +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.5 1.1 - - + -
20A LEU* 4.6 13.2 - - + +
34A LEU* 2.8 28.8 + - - +
35A ILE* 3.7 7.2 - - - +
37A TYR* 1.3 71.2 - - - +
39A ALA* 1.3 63.9 + - - +
41A LEU* 3.3 2.0 + - - +
42A VAL* 2.9 31.8 + - + +
108A LEU 5.9 0.7 - - - -
109A ALA* 3.7 29.1 - - - +
112A ALA* 3.4 21.0 - - - +
893A LEU* 4.1 25.3 - - - +
897A TYR* 4.4 9.6 + - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 4.5 0.2 - - - +
16A ILE* 3.9 13.0 - - + +
17A ASP* 3.7 36.8 - - + +
20A LEU* 5.3 1.1 - - + +
35A ILE 3.0 18.6 + - - +
36A GLU* 3.7 4.0 - - - +
38A ASP* 1.3 76.2 - - - +
40A LEU* 1.3 66.3 + - + +
43A ASP* 2.9 40.1 + - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 6.1 0.2 - - - +
36A GLU* 2.9 41.1 + - + +
37A TYR* 3.1 9.4 + - + +
39A ALA* 1.3 82.0 - - + +
41A LEU* 1.3 62.4 + - + +
43A ASP* 4.0 2.1 - - - +
44A ARG* 3.0 76.7 + - - +
197A LEU* 4.6 13.5 - - + -
200A LEU* 5.3 7.6 - - + -
217A LEU* 5.6 3.4 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR 3.1 13.2 + - - +
38A ASP* 4.1 3.1 - - - +
40A LEU* 1.3 75.0 - - - +
42A VAL* 1.3 58.9 + - + +
44A ARG* 3.2 5.2 + - - +
45A PHE* 2.9 26.9 + - - +
108A LEU* 3.8 47.1 - - + +
111A LEU* 4.9 2.7 - - + -
112A ALA* 4.2 8.1 - - + +
193A ILE* 4.1 10.1 - - + -
197A LEU* 3.8 32.1 - - + -
217A LEU* 3.7 40.2 - - + -
221A ILE* 3.8 11.8 - - + +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.6 24.2 - - + -
38A ASP* 2.9 23.8 + - + +
41A LEU* 1.3 75.7 - - + +
43A ASP* 1.3 58.4 + - - +
45A PHE* 3.1 7.1 + - - +
46A LEU* 2.9 43.6 + - + +
65A TYR* 6.2 1.3 - - + -
105A MET* 4.2 40.8 - - + +
108A LEU* 4.7 8.3 - - + -
109A ALA 5.4 2.0 - - - +
897A TYR* 3.9 21.1 - - + +
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A HIS 5.0 0.9 - - - +
15A SER* 3.0 31.9 + - - -
16A ILE* 3.2 30.6 + - - +
39A ALA* 2.9 30.9 + - - +
40A LEU* 4.0 4.4 - - - +
42A VAL* 1.3 76.0 - - - +
44A ARG* 1.3 68.4 + - - +
46A LEU* 3.5 7.5 + - - +
47A ASN* 3.1 34.6 + - - +
58A ARG* 4.8 4.1 + - - +
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.0 63.5 + - - +
41A LEU* 3.2 8.0 + - - +
43A ASP* 1.3 82.6 - - - +
45A PHE* 1.3 61.9 + - - +
47A ASN* 3.4 11.6 + - - +
48A ILE* 3.1 30.0 + - + +
200A LEU* 4.6 7.7 - - - +
214A ASP* 2.8 39.6 + - - -
217A LEU* 4.6 10.9 - - + +
218A GLN* 3.7 30.1 - - + +
221A ILE* 3.9 16.6 - - + -
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU 2.9 13.8 + - - +
42A VAL* 3.1 7.4 + - - +
44A ARG* 1.3 74.1 - - - +
46A LEU* 1.3 64.9 + - + +
48A ILE* 3.1 9.8 + - + +
49A LEU* 2.8 41.4 + - + +
101A SER* 3.7 37.5 - - - -
104A HIS* 3.9 12.1 - - + -
105A MET* 3.6 32.8 - - + -
108A LEU* 3.8 19.5 - - + -
221A ILE* 4.1 21.1 - - + +
225A PHE* 3.6 36.8 - + + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.8 26.5 - - + -
42A VAL* 2.9 27.3 + - + +
43A ASP* 3.9 4.3 - - - +
44A ARG 3.4 0.2 - - - -
45A PHE* 1.3 75.8 - - + +
47A ASN* 1.3 58.4 + - - +
49A LEU* 3.1 26.6 + - + +
50A GLN* 2.8 25.6 + - - +
58A ARG* 3.4 40.8 - - + +
61A VAL* 4.7 0.9 - - + -
62A GLN* 3.8 31.4 - - + +
105A MET* 4.2 19.3 - - - -
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Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP* 3.1 23.0 + - - +
44A ARG* 3.7 11.5 - - - +
46A LEU* 1.3 76.4 - - - +
48A ILE* 1.3 58.0 + - + +
50A GLN* 3.3 4.4 + - - +
51A ASP* 2.9 30.1 + - - +
58A ARG* 2.9 28.5 + - - +
218A GLN* 6.0 2.5 - - - +
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG 3.1 16.8 + - - +
45A PHE* 3.5 8.5 - - + +
47A ASN* 1.3 74.9 - - + +
49A LEU* 1.3 62.8 + - - +
51A ASP* 3.2 6.5 + - + +
52A LEU* 3.0 44.8 + - + +
218A GLN* 3.3 40.2 - - + +
221A ILE* 3.9 16.6 - - + -
222A GLN* 3.8 37.2 - - + +
225A PHE* 4.9 7.0 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 2.8 30.4 + - + +
46A LEU* 3.1 30.3 - - + +
48A ILE* 1.3 74.8 - - - +
50A GLN* 1.3 57.2 + - - +
52A LEU* 3.3 4.2 + - - +
53A HIS* 2.9 34.7 + - + +
54A GLY 3.9 0.5 + - - +
57A LEU* 4.0 10.3 - - + +
58A ARG* 4.0 11.4 - - - -
61A VAL* 3.8 28.7 - - + -
97A LEU* 3.9 17.7 - - + -
101A SER* 3.7 21.1 - - - +
225A PHE* 4.3 15.9 - - + -
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.3 33.9 + - - +
46A LEU 2.8 14.8 + - - +
47A ASN* 3.8 4.4 - - - +
49A LEU* 1.3 73.6 - - - +
51A ASP* 1.3 60.8 + - - +
54A GLY* 2.9 31.5 + - - -
55A PRO* 3.7 31.1 - - + +
58A ARG* 2.9 36.3 + - + +
927A LYS* 5.3 0.7 + - - -
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN 2.9 17.8 + - - +
48A ILE* 3.2 7.6 + - - +
50A GLN* 1.3 78.0 - - - +
52A LEU* 1.3 69.1 + - + +
54A GLY 4.8 0.2 - - - -
927A LYS* 4.8 7.4 - - - -
427B GLY 5.0 3.3 - - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.0 37.4 + - + +
49A LEU* 4.0 0.7 - - - +
51A ASP* 1.3 86.8 - - + +
53A HIS* 1.3 72.6 + - + +
54A GLY 3.9 0.2 - - - -
222A GLN* 4.3 7.4 - - - +
225A PHE* 3.9 13.2 - - + -
226A ARG* 3.7 47.1 - - + +
927A LYS* 4.2 7.6 - - - -
928A GLU* 2.6 31.6 - - - +
427B GLY* 3.2 30.5 - - - +
428B ASP* 4.1 1.3 - - - +
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 2.9 15.9 + - + +
52A LEU* 1.3 91.4 + - + +
54A GLY* 1.3 59.4 + - - +
57A LEU* 3.3 19.1 - - + +
97A LEU* 3.5 33.6 - - + +
225A PHE* 4.4 11.3 - + - -
226A ARG* 4.1 14.1 + - - -
925A LEU 4.0 2.9 - - - +
926A SER* 2.7 30.8 + - - +
927A LYS* 2.8 29.7 + - - +
928A GLU* 4.0 25.3 + - + +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 4.4 0.3 - - - +
50A GLN* 2.9 25.3 + - - -
52A LEU 3.9 0.4 - - - -
53A HIS* 1.3 80.0 - - - +
55A PRO* 1.3 77.9 - - - +
56A SER 3.4 2.6 + - - -
57A LEU* 3.5 2.8 + - - +
58A ARG 3.2 15.6 + - - -
925A LEU 5.4 0.9 - - - -
927A LYS* 4.0 14.6 - - - +
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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
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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) + - + + + + + -
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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