Contacts of the helix formed by residues 2 - 17 (chain J) in PDB entry 5A31
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 ASN 2 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3J LEU* 1.3 69.3 + - + +
4J GLU* 3.3 6.4 - - - +
5J ARG* 3.3 14.9 + - - +
6J LEU* 3.0 27.0 + - - +
196K GLU* 2.8 39.9 + - - +
197K GLU* 6.1 1.1 - - - -
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Residues in contact with LEU 3 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ASN* 1.3 80.9 - - + +
4J GLU* 1.3 57.6 + - - +
6J LEU* 3.4 9.3 + - - +
7J ARG* 2.9 58.6 + - - +
29J VAL* 5.5 1.8 - - + +
32J LEU* 6.1 3.6 - - + -
33J SER* 5.0 12.3 - - - +
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Residues in contact with GLU 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ASN 3.3 4.4 - - - +
3J LEU* 1.3 77.6 - - - +
5J ARG* 1.3 62.1 + - - +
7J ARG* 3.2 17.0 + - - +
8J LYS* 3.0 45.9 + - - +
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Residues in contact with ARG 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ASN* 3.3 16.2 + - - +
4J GLU* 1.3 78.2 - - - +
6J LEU* 1.3 58.6 + - - +
8J LYS* 3.5 17.4 + - - +
9J ARG* 3.1 32.0 + - + +
162K TYR* 6.1 0.4 - - - +
197K GLU* 4.8 13.0 - - - +
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Residues in contact with LEU 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ASN 3.0 17.2 + - - +
3J LEU* 3.7 7.9 - - - +
5J ARG* 1.3 74.7 - - - +
7J ARG* 1.3 60.1 + - - +
9J ARG* 3.1 9.7 + - + +
10J VAL* 2.9 29.3 + - - +
25J TRP* 3.4 41.7 - - + -
29J VAL* 4.0 21.2 - - + +
32J LEU* 3.7 29.8 - - + -
162K TYR* 4.1 23.3 - - + +
200K LEU* 4.7 7.0 - - + -
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Residues in contact with ARG 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J LEU* 2.9 40.3 + - - +
4J GLU* 3.2 16.0 + - - +
6J LEU* 1.3 72.5 - - - +
8J LYS* 1.3 67.2 + - + +
10J VAL* 3.2 11.6 - - + +
11J ARG* 3.0 32.3 + - + +
29J VAL* 4.3 14.1 - - + +
33J SER* 3.3 25.1 + - - -
36J GLU* 4.2 8.6 + - - -
39J ASP* 3.1 26.9 + - - +
42J TRP* 5.4 8.3 - - + +
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Residues in contact with LYS 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J GLU* 3.0 37.7 + - - +
5J ARG* 3.5 15.7 - - - +
7J ARG* 1.3 75.7 - - + +
9J ARG* 1.3 56.4 + - - +
11J ARG* 3.4 4.9 + - - +
12J GLN* 2.9 32.9 + - - +
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Residues in contact with ARG 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ARG* 3.1 26.7 + - + +
6J LEU* 3.1 18.1 + - + +
8J LYS* 1.3 77.2 - - - +
10J VAL* 1.3 62.3 + - - +
12J GLN* 3.3 36.6 + - - +
13J TYR* 3.0 50.5 + - + -
16J GLN* 5.3 0.8 - - - +
25J TRP* 6.1 1.3 - - + -
127K SER 5.6 4.4 - - - +
160K ASP* 3.5 24.2 + - - -
162K TYR* 3.6 48.6 - - + +
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Residues in contact with VAL 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU 2.9 18.6 + - - +
7J ARG* 3.2 25.4 - - + +
9J ARG* 1.3 73.2 - - - +
11J ARG* 1.3 66.9 + - + +
13J TYR* 3.2 10.1 + - - +
14J LEU* 3.1 23.4 + - + +
22J ALA* 3.4 30.7 - - + +
25J TRP* 4.6 7.3 - - + +
26J ALA* 3.8 22.7 - - + +
29J VAL* 4.5 11.2 - - + -
42J TRP* 5.0 15.0 - - + -
46J CYS* 4.7 3.6 - - - -
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Residues in contact with ARG 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J ARG* 3.0 22.9 + - - +
8J LYS* 4.1 4.3 - - - +
10J VAL* 1.3 76.4 - - + +
12J GLN* 1.3 56.2 + - - +
14J LEU* 3.3 12.5 + - + +
15J ASP* 3.0 29.0 + - - +
42J TRP* 3.3 61.5 - - + +
15K ASP* 4.5 15.8 + - - -
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Residues in contact with GLN 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LYS 2.9 20.1 + - - +
9J ARG* 3.3 30.3 + - - +
11J ARG* 1.3 76.6 - - - +
13J TYR* 1.3 62.0 + - - +
15J ASP* 3.4 12.2 + - - +
16J GLN* 2.9 62.7 + - - +
127K SER 4.3 12.9 - - - +
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Residues in contact with TYR 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 3.0 53.1 + - + -
10J VAL* 3.2 9.2 + - - +
12J GLN* 1.3 79.9 + - - +
14J LEU* 1.3 61.1 + - - +
16J GLN* 3.3 6.6 + - - -
17J GLN 2.9 23.4 + - - -
18J GLN* 2.9 38.4 + - + +
21J SER* 3.5 24.2 - - - -
22J ALA* 3.6 18.2 - - + -
25J TRP* 4.7 11.9 - + + -
160K ASP* 3.4 16.0 + - - -
162K TYR* 3.3 14.3 - + + +
163K CYS* 3.0 36.3 + - + -
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Residues in contact with LEU 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J VAL* 3.1 16.3 + - + +
11J ARG* 3.4 14.8 - - + +
13J TYR* 1.3 73.8 - - - +
15J ASP* 1.3 66.4 + - - +
17J GLN* 2.9 17.7 + - - +
19J TYR* 3.8 31.5 + - + -
22J ALA* 3.9 4.0 - - + -
42J TRP* 4.5 20.0 - - + +
45J GLN* 4.4 21.8 - - + -
46J CYS* 3.6 30.7 - - - -
49J LEU* 3.9 17.0 - - + -
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Residues in contact with ASP 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ARG 3.0 10.3 + - - +
12J GLN* 3.5 16.5 + - - +
14J LEU* 1.3 79.2 - - - +
16J GLN* 1.3 61.9 + - - +
17J GLN* 3.3 4.0 + - - +
11K ARG* 4.7 16.2 + - - -
42K TRP* 4.8 10.2 - - - -
45K GLN* 4.1 14.6 - - - +
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Residues in contact with GLN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 5.3 0.4 - - - +
12J GLN* 2.9 48.6 + - - +
13J TYR* 3.7 11.2 - - - +
15J ASP* 1.3 74.7 - - - +
17J GLN* 1.3 66.9 + - - +
18J GLN* 3.6 18.5 + - + +
45K GLN* 5.8 0.2 - - - -
74K TYR* 4.4 10.0 - - + -
78K ARG* 3.2 11.6 + - - -
127K SER 2.9 31.2 + - - +
128K ILE* 3.9 8.5 - - + +
131K SER* 3.6 19.1 + - - +
160K ASP* 5.3 2.8 + - - -
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Residues in contact with GLN 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J TYR 2.9 3.6 + - - -
14J LEU 2.9 13.5 + - - +
15J ASP 3.2 3.3 + - - +
16J GLN* 1.3 79.6 - - - +
18J GLN* 1.3 59.1 + - - +
19J TYR* 3.0 40.9 + - + +
45K GLN* 3.4 26.8 + - - +
48K TYR* 3.2 30.6 - - - -
49K LEU* 3.6 35.6 - - - +
75K LEU* 5.1 0.9 - - - +
78K ARG* 2.5 44.3 + - - +
165K GLU* 5.2 0.2 - - - +
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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