Contacts of the helix formed by residues 2 - 19 (chain A) in PDB entry 3W7F
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 THR 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 80.0 - - - +
3A MET* 1.3 65.4 + - - +
4A MET* 3.9 6.1 + - - +
5A ASP* 2.9 40.8 + - - +
6A MET* 3.2 10.7 + - - +
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Residues in contact with MET 3 (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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2A THR* 1.3 69.7 - - - +
4A MET* 1.3 59.0 + - - +
6A MET* 2.8 55.0 + - + +
7A ASN* 3.0 14.1 + - - +
84A ARG* 5.3 12.3 - - - +
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Residues in contact with MET 4 (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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2A THR* 3.4 6.8 + - - +
3A MET* 1.3 76.4 - - - +
5A ASP* 1.3 65.2 + - - +
7A ASN* 2.8 35.0 + - - +
8A PHE* 3.0 45.3 + - + -
35A LYS* 5.8 1.6 - - - +
88A MET* 3.8 27.4 - - + +
89A ALA* 4.2 1.3 - - - -
92A HIS* 3.7 32.5 - - + +
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Residues in contact with ASP 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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1A MET* 3.2 33.5 - - + +
2A THR* 2.9 36.2 + - - +
3A MET 3.2 0.8 - - - -
4A MET* 1.3 78.9 - - - +
6A MET* 1.3 57.0 + - - +
8A PHE* 3.3 8.9 + - - +
9A LYS* 2.9 28.4 + - - +
35A LYS* 4.3 16.3 + - - +
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Residues in contact with MET 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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1A MET* 3.8 25.6 - - + +
2A THR 3.6 8.3 - - - +
3A MET* 2.8 57.7 + - + +
5A ASP* 1.3 78.3 - - - +
7A ASN* 1.3 61.0 + - - +
9A LYS* 3.4 5.4 + - - +
10A TYR* 3.0 27.4 + - - +
85A ARG* 4.8 4.5 + - - -
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Residues in contact with ASN 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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3A MET* 3.0 16.0 + - - +
4A MET* 2.8 33.5 + - - +
6A MET* 1.3 79.8 - - - +
8A PHE* 1.3 61.1 + - - +
10A TYR* 3.2 5.5 + - - +
11A CYS* 3.2 25.4 + - - -
84A ARG* 4.9 6.9 + - - +
85A ARG* 3.0 46.1 - - - +
88A MET* 3.4 26.9 - - - +
89A ALA* 4.5 3.4 - - + -
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Residues in contact with PHE 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 MET* 3.0 45.3 + - + -
5A ASP* 3.7 7.4 - - - +
7A ASN* 1.3 73.6 - - - +
9A LYS* 1.3 62.0 + - - +
11A CYS* 3.1 6.1 + - - +
12A HIS 2.9 23.9 + - - -
35A LYS* 3.2 73.1 - - + -
38A TRP* 3.3 14.5 - - + -
39A ALA* 4.1 4.0 - - + -
89A ALA* 3.6 28.7 - - + -
92A HIS* 3.5 33.9 - + - -
93A VAL* 4.0 13.7 - - + -
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Residues in contact with LYS 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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1A MET* 4.0 28.0 - - + +
5A ASP 2.9 16.4 + - - +
6A MET* 3.7 8.1 - - + +
7A ASN 3.3 0.2 - - - -
8A PHE* 1.3 75.0 - - - +
10A TYR* 1.3 65.9 + - - +
12A HIS* 3.5 10.2 - - + +
13A LYS* 3.1 22.5 + - + +
38A TRP* 4.8 3.8 - - - -
178B GLU* 3.9 21.8 + - - +
180B GLU* 3.3 26.5 + - - +
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Residues in contact with TYR 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 MET 3.0 13.7 + - - +
7A ASN 3.5 7.2 - - - +
8A PHE 3.2 0.4 - - - -
9A LYS* 1.3 77.6 - - - +
11A CYS* 1.3 64.3 + - - +
13A LYS* 3.2 31.5 + - + +
14A ILE* 3.1 40.9 + - + +
46A LYS* 3.7 14.6 + - - -
83A ASP* 2.5 39.3 + - - -
85A ARG* 3.4 57.2 + - + +
86A ILE* 3.6 9.6 - - + -
53B VAL* 4.3 8.7 + - - -
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Residues in contact with CYS 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 ASN 3.2 13.8 + - - -
8A PHE* 3.1 9.7 + - - +
10A TYR* 1.3 76.1 - - - +
12A HIS* 1.3 64.3 + - - +
14A ILE* 3.2 6.6 + - - +
15A MET* 3.1 21.8 + - - +
38A TRP* 3.5 27.6 - - + +
39A ALA* 4.0 13.9 - - - +
42A ALA* 3.9 21.2 - - + +
86A ILE* 4.0 19.1 - - - -
89A ALA* 4.0 16.4 - - - -
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Residues in contact with HIS 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 PHE 2.9 6.9 + - - +
9A LYS* 3.5 13.2 - - + +
11A CYS* 1.3 77.3 - - - +
13A LYS* 1.3 58.0 + - - +
15A MET* 3.2 3.2 + - + +
16A LYS* 2.8 50.7 + - + +
23A SER* 4.8 2.0 - - - -
27A ASP* 2.7 28.2 + - - -
34A ARG* 4.7 5.2 - - - -
38A TRP* 3.2 64.5 - + + +
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Residues in contact with LYS 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 LYS* 3.1 12.8 + - + +
10A TYR* 3.2 36.9 + - + +
12A HIS* 1.3 75.3 - - - +
14A ILE* 1.3 63.2 + - - +
16A LYS* 3.1 11.1 + - - +
17A LYS* 2.8 34.3 + - + +
52B ASP 4.5 13.9 + - - -
179B ASN* 3.0 42.3 - - + +
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Residues in contact with ILE 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 TYR* 3.1 57.6 + - + +
11A CYS 3.2 5.1 + - - +
13A LYS* 1.3 83.2 - - - +
15A MET* 1.3 57.8 + - - +
17A LYS* 3.3 3.0 + - - -
18A HIS* 2.9 55.6 + - + +
41A TYR* 4.4 1.6 - - + -
42A ALA* 3.9 13.5 - - + +
45A ARG* 3.9 22.7 - - + -
46A LYS* 4.0 11.2 - - - +
86A ILE* 3.6 20.9 - - + -
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Residues in contact with MET 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 CYS 3.1 12.2 + - - +
12A HIS* 3.7 9.0 - - + +
14A ILE* 1.3 75.1 - - - +
16A LYS* 1.3 65.6 + - - +
19A SER* 2.9 31.0 + - - +
22A PHE* 4.3 11.9 - - + +
23A SER* 4.3 11.2 - - - +
26A PHE* 3.8 32.1 - - + -
27A ASP* 5.2 0.9 - - - +
37A VAL* 4.2 11.2 - - + -
38A TRP* 3.9 24.9 - - + -
41A TYR* 3.6 54.9 - - + -
301A FPS 4.0 9.0 - - + -
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Residues in contact with LYS 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 HIS* 2.8 50.2 + - + +
13A LYS* 3.6 10.8 - - + +
15A MET* 1.3 77.3 - - - +
17A LYS* 1.3 63.4 + - - +
19A SER 4.3 6.8 + - - +
20A LYS* 5.0 3.6 + - - +
23A SER* 3.7 17.9 + - - +
27A ASP* 5.5 1.1 - - - -
178B GLU* 3.0 41.5 + - + +
200B TYR* 4.5 2.4 + - - -
263B HIS* 6.0 0.8 - - - -
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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 LYS* 2.8 20.5 + - + +
14A ILE* 3.6 5.4 - - - +
16A LYS* 1.3 80.1 - - - +
18A HIS* 1.3 81.2 + - + +
20A LYS* 3.0 26.2 + - - +
20B LYS* 6.3 0.7 - - - +
175B GLU* 2.7 36.2 + - - +
265B ARG* 4.1 18.1 - - - +
301B FPS 4.7 15.0 + - - +
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Residues in contact with HIS 18 (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 ILE* 2.9 44.8 + - + +
17A LYS* 1.3 97.6 + - + +
19A SER* 1.3 60.0 + - - +
20A LYS* 3.6 20.2 + - - +
41A TYR* 3.4 15.5 - - + +
45A ARG* 3.5 25.1 + - + +
49A ASP* 3.9 15.8 + - - -
54A TYR* 6.0 0.2 + - - -
265A ARG* 5.7 0.2 + - - -
301A FPS 4.8 0.3 + - - -
302A FPS 3.2 16.5 + - - -
304A MG 4.1 2.8 - - - -
17B LYS* 5.5 8.2 + - - -
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Residues in contact with SER 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 MET* 2.9 18.8 + - - -
16A LYS 4.6 1.9 - - - +
17A LYS 3.7 0.6 - - - -
18A HIS* 1.3 75.2 - - - +
20A LYS* 1.3 66.1 + - - +
21A SER 3.1 0.2 - - - -
22A PHE* 3.1 32.8 + - - +
23A SER* 3.1 30.6 + - - -
41A TYR* 3.4 16.8 - - - -
302A FPS 2.9 21.0 + - - -
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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
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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