Contacts of the helix formed by residues 4 - 20 (chain A) in PDB entry 2WV1
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 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 1.3 63.7 + - - +
6A GLU* 3.7 6.7 + - - +
7A GLN* 2.8 47.9 + - - +
8A THR* 2.8 31.6 + - - -
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Residues in contact with ARG 5 (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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4A SER* 1.3 74.7 - - - +
6A GLU* 1.3 74.5 + - + +
8A THR* 3.3 2.3 + - - -
9A MET* 3.0 47.0 + - - +
47A TYR* 3.7 59.2 + - + +
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Residues in contact with GLU 6 (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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4A SER* 3.4 6.0 + - - +
5A ARG* 1.3 90.0 + - + +
7A GLN* 1.3 57.1 + - + +
9A MET* 3.2 11.8 + - - +
10A GLU* 3.0 32.8 + - - +
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Residues in contact with GLN 7 (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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4A SER* 2.8 37.4 + - - +
6A GLU* 1.3 76.2 - - + +
8A THR* 1.3 67.3 + - - +
10A GLU* 3.4 16.6 + - - +
11A ASN* 3.0 33.6 + - - +
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Residues in contact with THR 8 (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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4A SER 2.8 23.5 + - - -
5A ARG 3.7 4.0 - - - -
7A GLN* 1.3 76.2 - - - +
9A MET* 1.3 58.3 + - - +
11A ASN* 3.4 8.1 + - - +
12A ILE* 3.0 42.0 + - + +
39A VAL* 3.8 20.4 - - + -
43A MET* 3.8 29.9 - - - +
47A TYR* 4.0 11.2 + - + -
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Residues in contact with MET 9 (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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5A ARG* 3.0 56.1 + - - +
6A GLU* 3.6 11.9 - - - +
7A GLN 3.1 0.2 - - - -
8A THR* 1.3 75.4 - - - +
10A GLU* 1.3 59.4 + - - +
12A ILE* 3.2 2.4 + - - +
13A LEU* 2.9 38.7 + - + +
47A TYR* 3.4 37.5 - - + +
48A PHE* 3.6 38.9 - - + -
57A GLU* 6.5 0.2 - - - -
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Residues in contact with GLU 10 (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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6A GLU* 3.0 12.8 + - - +
7A GLN* 3.5 25.5 + - - +
9A MET* 1.3 75.2 - - - +
11A ASN* 1.3 65.7 + - - +
13A LEU* 3.3 9.0 + - - +
14A LYS* 3.0 24.9 + - - +
61A LYS* 3.9 25.7 + - - +
62A TYR* 4.6 1.7 + - - -
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Residues in contact with ASN 11 (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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7A GLN* 3.0 27.5 + - - +
8A THR* 3.8 6.3 - - - +
9A MET 3.3 0.4 - - - -
10A GLU* 1.3 77.7 - - - +
12A ILE* 1.3 57.2 + - - +
14A LYS* 3.4 22.6 + - - +
15A ALA* 3.0 29.5 + - - +
37A ALA* 3.8 18.6 - - + +
39A VAL* 5.8 2.5 - - + -
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Residues in contact with ILE 12 (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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8A THR* 3.0 31.4 + - + +
9A MET* 3.2 7.4 + - - +
11A ASN* 1.3 73.9 - - - +
13A LEU* 1.3 59.1 + - - +
15A ALA* 3.3 3.2 + - - +
16A ALA* 2.8 27.2 + - - +
33A ILE* 3.7 6.8 - - + +
34A ALA* 6.0 0.4 - - - -
37A ALA* 4.0 8.5 - - + -
39A VAL* 3.9 20.9 - - + -
43A MET* 5.5 0.2 - - + -
44A ALA* 3.7 33.7 - - + -
47A TYR* 4.6 7.2 - - + -
48A PHE* 3.4 29.8 - - + -
54A LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 13 (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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9A MET* 2.9 24.8 + - + +
10A GLU* 3.8 6.1 - - - +
12A ILE* 1.3 73.6 - - - +
14A LYS* 1.3 67.4 + - - +
16A ALA* 3.8 3.3 - - - +
17A LYS* 3.0 25.5 + - - +
48A PHE* 3.7 21.5 - - + -
54A LEU* 4.2 4.3 - - + -
57A GLU* 3.6 43.7 - - + +
58A VAL* 3.7 14.2 - - + +
61A LYS* 4.3 25.8 - - + +
62A TYR* 3.6 16.1 - - + +
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Residues in contact with LYS 14 (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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10A GLU 3.0 17.2 + - - +
11A ASN* 3.6 19.8 + - - +
13A LEU* 1.3 75.7 - - - +
15A ALA* 1.3 62.8 - - - +
17A LYS* 3.5 5.9 + - + +
18A LYS* 3.1 22.7 + - - +
62A TYR* 3.5 17.2 + - + +
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Residues in contact with ALA 15 (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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11A ASN 3.0 17.6 + - - +
12A ILE 3.4 5.6 - - - +
14A LYS* 1.3 74.8 - - - +
16A ALA* 1.3 54.5 + - - +
18A LYS* 3.1 6.6 + - - +
19A LYS* 2.8 37.9 + - - +
33A ILE* 3.5 27.8 - - + +
36A GLU* 3.7 19.5 - - + -
37A ALA* 3.7 11.0 - - + +
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Residues in contact with ALA 16 (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 ILE 2.8 20.2 + - - +
13A LEU 3.8 1.3 - - - +
15A ALA* 1.3 69.8 - - - +
17A LYS* 1.3 60.6 + - - +
20A PHE* 2.6 49.6 + - + +
33A ILE* 3.5 24.1 - - + +
54A LEU* 3.9 13.2 - - + -
58A VAL* 3.5 21.8 - - + -
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Residues in contact with LYS 17 (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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13A LEU 3.0 17.5 + - - +
14A LYS* 3.5 7.0 - - + +
16A ALA* 1.3 75.3 - - - +
18A LYS* 1.3 64.2 + - - +
20A PHE* 4.1 1.0 - - - +
21A GLY 3.0 18.2 + - - -
58A VAL* 4.0 16.5 - - + +
62A TYR* 3.5 44.0 - - + -
96A GLU 4.0 7.9 + - - -
97A ASN* 2.7 37.7 + - - +
99A GLU* 3.4 42.3 + - + +
100A ILE* 5.4 1.3 - - + -
103A LEU* 5.1 0.4 - - - +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS 3.1 11.0 + - - +
15A ALA* 3.4 9.2 - - - +
17A LYS* 1.3 83.7 - - - +
19A LYS* 1.3 64.5 - - + +
21A GLY* 3.3 1.7 + - - -
22A GLU* 3.2 43.2 + - - +
36A GLU* 3.6 32.5 + - - +
99A GLU* 4.3 12.0 - - - +
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Residues in contact with LYS 19 (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 ALA 2.8 21.3 + - - +
18A LYS* 1.3 73.1 - - + +
20A PHE* 1.3 65.5 + - - +
22A GLU* 3.2 31.7 + - - +
23A ARG* 3.3 9.3 + - - +
28A THR* 3.1 29.0 + - + -
32A GLU* 3.8 47.5 + - - +
33A ILE* 4.0 7.9 - - + -
36A GLU* 4.1 31.3 + - + +
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Residues in contact with PHE 20 (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 ALA* 2.6 40.0 + - + +
17A LYS* 4.1 1.1 - - - +
19A LYS* 1.3 73.8 - - - +
21A GLY* 1.3 57.8 + - - +
24A GLY* 2.7 45.8 + - - -
25A TYR* 3.9 25.6 - + - -
28A THR* 3.7 21.5 - - + -
33A ILE* 3.7 20.6 - - + -
51A LYS* 4.0 23.3 - - + -
54A LEU* 4.4 2.5 - - + -
55A TYR* 3.6 41.3 - + + -
58A VAL* 4.3 5.8 - - + -
103A LEU* 3.6 21.2 - - + +
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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