Contacts of the helix formed by residues 2 - 16 (chain B) in PDB entry 2O02
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 ASP 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 76.7 - - - +
3B LYS* 1.3 68.2 + - - +
4B ASN* 3.4 18.9 + - - +
5B GLU* 3.2 35.8 + - + +
6B LEU* 3.1 18.7 + - - +
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Residues in contact with LYS 3 (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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1B MET 3.5 3.8 + - - -
2B ASP* 1.3 74.0 + - - +
4B ASN* 1.3 84.9 + - - +
6B LEU* 3.3 10.4 + - - +
7B VAL* 2.9 23.4 + - + +
29B VAL* 3.8 30.1 - - + +
32B GLN* 3.2 23.0 + - + +
34B ALA* 5.4 15.5 - - + -
35B GLU 6.1 0.7 - - - -
36B LEU* 5.9 0.4 - - + -
40B GLU* 2.8 29.6 + - - +
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Residues in contact with ASN 4 (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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2B ASP* 3.3 18.1 + - - +
3B LYS* 1.3 97.1 - - - +
5B GLU* 1.3 57.5 + - - +
7B VAL* 3.4 8.4 + - - +
8B GLN* 2.9 38.9 + - - +
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Residues in contact with GLU 5 (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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78A MET* 3.4 27.3 - - + +
81A GLU* 5.8 0.3 - - - +
1B MET* 2.9 40.9 - - + +
2B ASP* 3.2 25.6 + - + +
4B ASN* 1.3 79.5 - - - +
6B LEU* 1.3 51.0 + - - +
8B GLN* 3.2 8.0 + - - +
9B LYS* 2.9 45.0 + - - +
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Residues in contact with LEU 6 (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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1B MET* 3.8 36.3 - - + +
2B ASP 3.1 9.2 + - - +
3B LYS* 3.6 7.4 - - - +
5B GLU* 1.3 78.7 - - - +
7B VAL* 1.3 57.3 + - - +
9B LYS* 3.4 5.4 + - + +
10B ALA* 3.0 27.9 + - - +
25B CYS* 3.6 34.3 - - + +
28B SER* 3.7 24.5 - - - +
29B VAL* 3.6 18.6 - - + +
32B GLN* 3.7 26.2 - - - +
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Residues in contact with VAL 7 (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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3B LYS* 2.9 23.5 + - + +
4B ASN* 3.7 7.4 - - - +
6B LEU* 1.3 72.7 - - - +
8B GLN* 1.3 66.9 + - + +
10B ALA* 3.2 8.2 + - - +
11B LYS* 3.0 35.7 + - - +
26B MET* 4.4 5.4 - - + -
29B VAL* 4.1 14.1 - - + -
39B GLU* 4.4 10.8 - - - +
40B GLU* 3.9 31.9 - - + +
43B LEU* 3.8 19.5 - - + -
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 3.3 48.8 + - - +
78A MET* 3.6 28.7 - - - +
4B ASN* 2.9 23.6 + - - +
5B GLU* 3.2 10.0 + - - +
7B VAL* 1.3 76.0 - - + +
9B LYS* 1.3 62.2 + - - +
11B LYS* 3.2 13.0 + - + +
12B LEU* 3.0 24.6 + - - +
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Residues in contact with LYS 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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78A MET* 3.5 22.2 - - + -
82A TYR* 5.2 12.8 - - + -
85A LYS* 6.4 0.2 - - - +
1B MET* 2.8 40.4 - - + -
5B GLU* 2.9 24.9 + - - +
6B LEU* 3.6 11.0 - - + +
7B VAL 3.3 0.2 - - - -
8B GLN* 1.3 74.9 - - - +
10B ALA* 1.3 60.8 + - - +
12B LEU* 3.2 9.3 + - + +
13B ALA* 2.9 28.9 + - - +
25B CYS* 3.8 16.4 - - - -
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Residues in contact with ALA 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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6B LEU 3.0 16.8 + - - +
7B VAL 3.2 4.2 + - - +
9B LYS* 1.3 75.6 - - - +
11B LYS* 1.3 58.7 + - - +
13B ALA* 3.2 3.9 + - - -
14B GLU* 2.9 26.9 + - - +
22B MET* 3.4 20.9 - - + +
25B CYS* 3.9 12.3 - - + -
26B MET* 3.5 36.1 - - + -
43B LEU* 4.8 4.9 - - + -
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Residues in contact with LYS 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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7B VAL* 3.0 23.2 + - + +
8B GLN* 3.6 13.9 - - + +
9B LYS 3.2 0.2 - - - -
10B ALA* 1.3 77.9 - - - +
12B LEU* 1.3 62.1 + - - +
14B GLU* 3.4 11.4 + - - +
15B GLN* 3.2 27.2 + - + +
39B GLU* 2.4 40.4 + - - -
43B LEU* 4.0 25.4 - - + -
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Residues in contact with LEU 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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62A VAL* 4.5 18.6 - - + +
65A ILE* 3.9 37.7 - - + -
75A LYS 5.6 0.4 - - - +
78A MET* 3.6 33.9 - - + +
79A ALA* 3.8 18.8 - - + +
82A TYR* 4.1 19.0 - - + -
8B GLN 3.0 14.2 + - - +
9B LYS* 3.5 9.2 - - - +
11B LYS* 1.3 75.4 - - - +
13B ALA* 1.3 64.7 - - - +
15B GLN* 3.3 6.3 + - - +
16B ALA* 3.0 23.2 + - - +
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Residues in contact with ALA 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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82A TYR* 3.5 24.0 - - + +
9B LYS 2.9 16.9 + - - +
10B ALA 3.5 4.9 - - - +
12B LEU* 1.3 75.8 - - - +
14B GLU* 1.4 62.2 + - - +
16B ALA* 3.2 1.8 + - - -
17B GLU 3.1 4.5 + - - -
18B ARG 2.9 45.8 + - - +
21B ASP* 4.0 3.4 - - + -
22B MET* 3.7 16.8 - - + +
25B CYS* 5.8 0.7 - - - -
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Residues in contact with GLU 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 ALA 2.9 14.0 + - - +
11B LYS* 3.6 12.2 - - - +
13B ALA* 1.4 76.3 - - - +
15B GLN* 1.3 74.1 + - - +
17B GLU* 3.0 18.2 + - - +
19B TYR* 4.2 16.9 + - + +
22B MET* 3.6 28.6 - - + +
43B LEU* 3.7 19.0 - - - +
46B VAL* 3.6 19.5 - - - +
424Q ASP* 4.5 5.7 - - - +
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Residues in contact with GLN 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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61A VAL* 3.5 23.0 - - + +
65A ILE* 3.9 27.9 - - + +
11B LYS 3.2 15.6 + - - +
12B LEU* 3.3 7.6 + - - +
14B GLU* 1.3 87.8 + - - +
16B ALA* 1.3 58.2 + - - +
17B GLU* 3.2 10.3 + - - +
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Residues in contact with ALA 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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58A SER* 2.7 33.4 + - - +
61A VAL* 4.1 8.5 - - - +
62A VAL* 4.0 21.1 - - + -
82A TYR* 4.2 3.8 - - + -
12B LEU 3.0 17.0 + - - +
13B ALA 3.6 4.5 - - - +
14B GLU 3.2 0.4 - - - -
15B GLN* 1.3 74.7 - - - +
17B GLU* 1.3 68.1 + - - +
18B ARG* 3.3 20.3 + - - +
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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