Contacts of the helix formed by residues 8 - 23 (chain B) in PDB entry 3V61
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 GLU 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B PHE* 3.6 17.5 - - - +
7B GLU* 1.3 89.9 - - + +
9B ALA* 1.3 62.2 + - - +
10B SER* 3.1 17.1 + - - +
11B LEU* 3.3 17.0 + - + +
12B PHE 4.0 0.2 + - - -
84B ASN* 3.3 12.4 - - - +
85B THR* 3.4 28.2 - - - +
86B ASP 3.3 5.2 - - - -
88B LEU 4.8 0.2 - - - -
263B BA 4.5 7.0 - - - -
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Residues in contact with ALA 9 (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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8B GLU* 1.3 70.6 - - - +
10B SER* 1.3 58.9 + - - +
11B LEU 3.3 0.4 - - - -
12B PHE* 3.3 5.0 + - - +
13B LYS* 2.8 29.1 + - - +
79B LEU* 5.3 3.7 - - + +
82B GLY 5.6 0.7 - - - -
83B ASN 3.8 17.0 - - - +
84B ASN* 3.5 2.5 + - - -
86B ASP 2.8 16.3 + - - +
88B LEU* 3.9 27.6 - - + +
103B PHE* 4.1 18.8 - - + -
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Residues in contact with SER 10 (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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8B GLU* 3.4 23.7 + - - +
9B ALA* 1.3 76.3 - - - +
11B LEU* 1.3 55.4 + - - +
13B LYS* 3.6 6.9 - - - +
14B ARG* 2.8 34.8 + - - +
84B ASN* 3.3 36.9 + - - +
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Residues in contact with LEU 11 (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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6B PHE* 3.7 21.5 - - + -
7B GLU 5.9 1.1 - - - +
8B GLU* 3.3 16.3 + - + +
10B SER* 1.3 76.4 + - - +
12B PHE* 1.3 63.1 + - - +
14B ARG* 3.4 10.6 + - + +
15B ILE* 3.3 29.6 + - + +
52B ILE* 6.2 0.2 - - + -
56B ALA* 3.5 32.3 - - + +
243B SER* 4.4 14.4 - - - +
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Residues in contact with PHE 12 (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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6B PHE* 3.6 40.1 - + + -
8B GLU 4.0 1.2 + - - -
9B ALA* 3.3 9.7 + - - +
11B LEU* 1.3 76.2 - - - +
13B LYS* 1.3 65.5 + - - +
15B ILE* 3.2 15.0 + - + +
16B ILE* 3.0 51.8 + - + +
28B PHE* 4.2 21.8 - + - -
35B ILE* 6.4 0.7 - - + -
52B ILE* 5.8 0.9 - - + -
70B MET* 5.4 2.0 - - - -
75B LEU* 4.2 16.8 - - + -
79B LEU* 3.8 20.6 - - + -
88B LEU* 3.5 26.2 - - + -
90B LEU* 4.4 22.2 - - + -
101B LEU* 4.7 0.2 - - + -
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Residues in contact with LYS 13 (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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9B ALA 2.8 17.6 + - - +
10B SER* 3.6 7.6 - - - +
12B PHE* 1.3 77.8 - - - +
14B ARG* 1.3 51.2 + - - +
16B ILE* 3.7 1.1 - - + +
17B ASP* 2.8 63.2 + - - +
79B LEU* 3.8 40.3 - - + +
80B ARG* 5.6 9.6 - - - +
84B ASN* 4.6 19.2 + - - +
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Residues in contact with ARG 14 (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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10B SER 2.8 18.0 + - - +
11B LEU* 3.7 13.5 - - + +
12B PHE 3.2 0.4 - - - -
13B LYS* 1.3 77.9 - - - +
15B ILE* 1.3 61.1 + - + +
17B ASP* 3.7 8.0 - - - +
18B GLY* 3.1 19.1 + - - -
220B SER* 3.3 35.6 + - - -
221B LEU* 3.5 28.5 - - + +
268B NEQ 5.5 0.7 - - - +
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Residues in contact with ILE 15 (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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6B PHE* 4.5 9.6 - - + -
11B LEU* 3.4 27.4 - - + +
12B PHE* 3.2 20.5 + - + +
14B ARG* 1.3 74.6 - - + +
16B ILE* 1.3 71.3 + - + +
18B GLY* 3.0 11.7 + - - -
19B PHE* 3.1 26.0 + - + -
28B PHE* 5.3 3.8 - - + -
50B LEU* 3.3 32.1 - - + -
52B ILE* 3.8 30.3 - - + -
243B SER* 5.4 5.6 - - - +
268B NEQ 4.3 4.4 - - - +
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Residues in contact with ILE 16 (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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12B PHE* 3.0 48.9 + - + +
13B LYS* 3.8 3.6 - - + +
15B ILE* 1.3 77.5 - - + +
17B ASP* 1.3 62.9 + - - +
19B PHE* 3.8 5.1 + - + +
20B LYS* 3.1 22.1 + - + +
26B VAL* 4.9 0.2 - - + -
28B PHE* 3.8 17.3 - - + -
72B LEU* 3.9 26.7 - - + +
75B LEU* 3.4 28.5 - - + -
76B SER* 3.7 22.7 - - - +
79B LEU* 4.0 14.1 - - + -
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Residues in contact with ASP 17 (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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13B LYS* 2.8 57.0 + - - +
14B ARG* 3.7 9.0 + - - +
16B ILE* 1.3 77.1 - - - +
18B GLY* 1.3 63.2 + - - +
20B LYS* 3.3 21.3 - - - +
21B ASP* 3.6 9.0 + - - +
76B SER* 4.7 8.3 + - - -
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Residues in contact with GLY 18 (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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14B ARG 3.1 10.3 + - - -
15B ILE 3.0 8.4 + - - -
17B ASP* 1.3 73.6 - - - +
19B PHE* 1.3 64.6 + - - +
21B ASP* 3.1 27.5 + - - +
268B NEQ 3.5 31.4 - - - -
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Residues in contact with PHE 19 (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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15B ILE* 3.1 31.8 + - + +
16B ILE* 4.0 8.1 - - + +
18B GLY* 1.3 73.7 - - - +
20B LYS* 1.3 56.2 + - - +
21B ASP 2.9 4.5 + - - -
22B CYS 2.9 2.6 + - - -
23B VAL* 2.9 44.8 + - + +
26B VAL* 4.1 11.7 - - + -
28B PHE* 5.2 1.1 - + - -
37B ALA* 3.3 41.7 - - + -
39B ALA* 3.8 16.8 - - + -
48B VAL* 3.6 21.5 - - + -
50B LEU* 3.6 26.9 - - + -
72B LEU* 3.7 19.1 - - + -
268B NEQ 3.5 18.5 - - + +
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Residues in contact with LYS 20 (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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16B ILE* 3.1 13.3 + - + +
17B ASP* 3.3 19.3 - - - +
18B GLY 3.1 0.4 - - - -
19B PHE* 1.3 78.2 - - - +
21B ASP* 1.3 62.4 + - - +
23B VAL 3.3 19.5 + - - +
24B GLN* 3.6 25.5 + - - +
72B LEU* 3.7 27.3 - - + +
73B THR* 4.4 17.5 - - - +
76B SER* 4.7 9.4 - - - +
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Residues in contact with ASP 21 (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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17B ASP 3.6 7.3 + - - +
18B GLY* 3.1 18.2 + - - +
19B PHE 2.9 1.2 + - - -
20B LYS* 1.3 80.8 - - - +
22B CYS* 1.3 62.5 + - - +
24B GLN* 5.6 2.3 + - - -
214B ASP* 4.9 0.2 - - - -
217B LYS* 3.6 40.2 + - - +
259B BA 3.1 19.8 - - - -
268B NEQ 4.3 8.6 - - + -
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Residues in contact with CYS 22 (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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19B PHE 2.9 5.1 + - - -
21B ASP* 1.3 75.7 - - - +
23B VAL* 1.3 69.8 + - + +
24B GLN* 4.6 8.0 + - - +
41B ASP* 4.3 13.0 - - + +
42B ASP* 5.1 1.2 + - - +
46B LEU* 4.2 16.4 - - + -
48B VAL* 4.3 4.7 - - + -
214B ASP* 4.2 23.3 - - - +
248B PHE* 4.4 2.5 - - - -
268B NEQ 1.7 59.9 - - - +
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Residues in contact with VAL 23 (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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19B PHE* 2.9 55.2 + - + +
20B LYS* 3.3 18.9 + - - +
22B CYS* 1.3 84.9 - - + +
24B GLN* 1.3 65.1 + - - +
25B LEU 3.7 19.3 - - - +
26B VAL* 5.1 0.2 - - + -
39B ALA* 3.6 14.4 - - + -
40B VAL 3.4 32.5 - - - +
41B ASP* 3.7 6.3 - - + +
48B VAL* 4.4 6.5 - - + -
72B LEU* 3.5 7.5 - - + +
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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
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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