Contacts of the helix formed by residues 2 - 20 (chain J) in PDB entry 6XXD
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J PHE* 1.3 86.0 - - - +
3J LEU* 1.3 62.9 + - - +
4J ILE* 3.2 13.4 - - - +
5J GLU* 3.0 28.9 + - - +
6J LEU* 3.4 15.2 + - - +
1K PHE* 3.6 14.6 - - + -
5K GLU* 3.6 7.2 - - - +
9K VAL* 3.9 2.3 - - - +
20M LEU* 3.4 45.7 + - + +
21M ILE* 3.9 12.6 - - + -
22M PRO* 4.1 0.2 - - - +
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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
----------------------------------------------------------
2J THR* 1.3 72.5 - - - +
4J ILE* 1.3 54.6 + - - +
6J LEU* 3.2 13.4 + - + +
7J LEU* 2.7 44.5 + - + +
5K GLU* 2.9 27.1 + - + +
8K ILE* 4.2 15.5 - - + -
9K VAL* 3.6 20.4 - - + +
12K ILE* 5.7 2.5 - - + -
22N PRO* 4.3 25.6 - - + -
23N ASN 5.2 1.3 - - - +
27N ALA* 4.4 25.8 - - + -
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Residues in contact with ILE 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J THR* 3.2 17.2 - - - +
3J LEU* 1.3 78.6 - - - +
5J GLU* 1.3 58.3 + - - +
7J LEU* 4.0 22.9 - - + -
8J ILE* 3.0 32.1 + - + +
21M ILE* 4.0 20.2 - - + -
22M PRO* 3.9 15.7 - - + -
24M LEU* 4.0 31.4 - - + -
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Residues in contact with GLU 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I PHE 4.3 0.3 - - - +
2I THR* 3.6 6.8 - - - +
3I LEU* 2.9 41.5 + - + +
1J PHE* 3.2 42.5 - - - -
2J THR* 3.0 23.7 + - - +
4J ILE* 1.3 76.0 - - - +
6J LEU* 1.3 58.9 + - - +
8J ILE* 3.4 10.7 - - - +
9J VAL* 3.1 18.9 - - - +
20M LEU 5.1 1.3 - - - +
22M PRO* 3.9 22.9 - - + -
41P ASN* 5.9 1.0 + - - -
45P LYS* 4.5 9.2 - - - +
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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
----------------------------------------------------------
1I PHE* 4.1 14.6 - - + +
1J PHE* 3.9 18.6 - - + -
2J THR 3.4 11.5 + - - +
3J LEU* 3.2 14.7 + - + +
5J GLU* 1.3 79.4 - - - +
7J LEU* 1.3 58.1 + - - +
9J VAL* 3.3 6.6 + - + +
10J ILE* 3.0 36.0 + - + +
9K VAL* 3.8 29.4 - - + +
12K ILE* 3.5 37.0 - - + -
13K ILE* 4.3 10.1 - - + -
16K LEU* 4.3 19.1 - - + -
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Residues in contact with LEU 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J LEU* 2.7 29.4 + - + +
4J ILE* 3.4 23.5 + - + +
6J LEU* 1.3 71.1 - - - +
8J ILE* 1.3 60.0 + - - +
10J ILE* 3.4 12.5 + - + +
11J ALA* 3.0 25.6 + - + +
27N ALA* 5.6 9.0 - - + +
30N ARG* 4.3 27.4 - - + -
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Residues in contact with ILE 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 4.1 19.5 - - + -
4J ILE* 3.0 18.0 + - + +
5J GLU* 3.4 18.8 - - - +
7J LEU* 1.3 73.6 - - - +
9J VAL* 1.3 63.0 + - - +
11J ALA* 3.2 5.8 + - - +
12J ILE* 3.0 35.0 + - + +
22M PRO* 5.2 0.7 - - + -
24M LEU* 3.4 50.9 - - + +
27M ALA* 4.2 10.3 - - + -
28M ARG* 3.7 29.8 - - + +
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Residues in contact with VAL 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I PHE* 3.4 43.7 - - + +
2I THR 3.9 0.7 - - - +
3I LEU* 3.6 39.9 - - + +
6I LEU* 3.8 13.0 - - + +
5J GLU* 3.1 20.6 - - - +
6J LEU* 3.3 10.9 + - + +
7J LEU 3.3 0.6 - - - -
8J ILE* 1.3 75.2 - - - +
10J ILE* 1.3 65.5 + - - +
12J ILE 3.5 0.7 + - - -
13J ILE* 3.1 29.7 + - + +
16K LEU* 5.4 3.6 - - + -
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Residues in contact with ILE 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J LEU* 3.0 28.0 + - + +
7J LEU* 3.6 15.5 - - + +
9J VAL* 1.3 75.9 - - - +
11J ALA* 1.3 61.7 + - - +
13J ILE* 3.5 9.3 + - - +
14J ALA* 3.3 21.1 + - - +
12K ILE* 4.1 23.8 - - + -
16K LEU* 4.1 19.5 - - + -
27N ALA 5.3 3.4 - - - +
30N ARG* 3.5 26.0 - - + +
31N ALA* 4.6 12.8 - - + +
34N THR* 3.2 23.9 + - - +
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Residues in contact with ALA 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J LEU* 3.0 13.6 + - + +
8J ILE* 3.2 13.4 + - - +
10J ILE* 1.3 77.6 - - - +
12J ILE* 1.3 60.5 + - - +
14J ALA* 3.5 8.2 + - - +
15J ILE* 3.3 26.8 + - - +
28M ARG* 4.1 20.2 - - - +
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Residues in contact with ILE 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 5.7 3.4 - - + -
6I LEU* 3.5 28.3 - - + -
10I ILE* 4.1 7.2 - - + -
8J ILE* 3.0 23.9 + - + +
10J ILE 3.4 0.2 - - - -
11J ALA* 1.3 73.7 - - - +
13J ILE* 1.3 60.2 + - - +
15J ILE* 3.1 17.5 + - + +
16J LEU* 2.8 53.5 + - + +
27M ALA* 4.8 4.7 - - + +
28M ARG* 4.2 25.1 - - + +
31M ALA* 3.2 30.5 - - + -
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Residues in contact with ILE 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE 3.9 22.8 + - - +
1I PHE* 4.0 15.5 - - + -
6I LEU* 4.2 16.4 - - + -
9J VAL* 3.1 37.1 + - + +
10J ILE* 3.8 9.0 - - - +
11J ALA 3.4 0.2 - - - -
12J ILE* 1.3 75.2 - - - +
14J ALA* 1.3 57.1 + - - +
16J LEU* 4.1 5.5 - - - +
17J ALA* 2.9 33.9 + - + +
16K LEU* 4.9 5.2 - - + -
20K LEU* 4.1 21.3 - - + -
34N THR* 4.3 20.6 - - + -
37N THR* 6.1 3.4 - - + -
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Residues in contact with ALA 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ILE* 3.3 10.8 + - + +
11J ALA* 3.6 12.1 - - - +
12J ILE 3.2 0.4 - - - -
13J ILE* 1.3 80.3 - - - +
15J ILE* 1.3 60.3 + - + +
17J ALA* 3.8 5.4 + - - +
18J ALA* 3.5 20.3 + - - +
37N THR* 5.6 7.2 - - + +
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Residues in contact with ILE 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 ALA 3.3 15.2 + - - +
12J ILE* 3.1 20.8 + - + +
14J ALA* 1.3 75.6 - - + +
16J LEU* 1.3 72.3 + - + +
18J ALA* 3.3 5.1 + - - +
19J VAL* 3.2 26.1 + - + +
28M ARG* 3.4 29.2 - - - +
31M ALA* 4.8 5.6 - - + +
32M ASN* 5.7 4.9 - - - +
35M VAL* 3.3 32.5 - - + -
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Residues in contact with LEU 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 4.4 22.3 - - + -
6I LEU* 4.3 13.7 - - + -
9I VAL* 5.4 1.8 - - + -
10I ILE* 4.1 19.3 - - + -
13I ILE* 4.9 5.2 - - + -
12J ILE* 2.8 43.3 + - + +
13J ILE* 4.1 2.9 - - - +
15J ILE* 1.3 83.6 - - + +
17J ALA* 1.3 61.6 + - - +
19J VAL* 4.1 7.0 - - + -
20J LEU* 3.2 49.8 + - + +
21J ILE* 4.4 0.7 - - - +
31M ALA* 4.7 7.2 - - + +
34M THR* 4.4 22.0 - - + +
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Residues in contact with ALA 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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1A PHE* 5.9 3.1 - - - +
13J ILE* 2.9 23.5 + - + +
14J ALA 4.1 4.3 - - - +
15J ILE 3.3 0.2 - - - -
16J LEU* 1.3 76.2 - - - +
18J ALA* 1.3 58.0 + - - +
21J ILE* 3.3 32.0 - - + +
37N THR* 4.0 26.5 - - + -
41N ASN* 5.8 7.6 - - + +
109N VAL* 4.7 10.1 + - + +
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Residues in contact with ALA 18 (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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14J ALA 3.5 11.6 + - - +
15J ILE* 3.3 9.7 + - - +
16J LEU 3.2 0.6 - - - -
17J ALA* 1.3 80.1 - - - +
19J VAL* 1.3 67.8 + - + +
20J LEU 3.7 0.2 + - - -
21J ILE* 3.8 14.2 + - - +
70M LYS* 4.6 13.1 + - - -
109N VAL 4.6 12.6 - - - +
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Residues in contact with VAL 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ILE* 3.2 19.0 + - + +
16J LEU* 4.0 4.0 - - + +
18J ALA* 1.3 79.9 - - + +
20J LEU* 1.3 79.0 + - + +
21J ILE 3.5 4.7 + - - +
34M THR* 4.4 3.1 - - + +
35M VAL* 4.0 41.5 - - + +
38M ALA* 3.9 26.0 - - + +
39M TYR 5.7 0.4 - - - +
42M ASP* 3.7 19.9 - - - +
70M LYS* 5.5 2.6 + - - +
73M PRO* 5.7 4.5 - - + -
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Residues in contact with LEU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 3.4 34.1 - - + -
1H PHE 4.8 6.5 + - - +
2H THR* 3.4 27.2 + - + +
5H GLU* 5.1 1.6 - - - +
13I ILE* 4.0 22.2 - - + -
16J LEU* 3.2 34.9 + - + +
19J VAL* 1.3 78.2 - - + +
21J ILE* 1.3 62.7 + - + +
22J PRO* 3.3 8.3 - - - +
34M THR* 3.8 21.3 - - + -
38M ALA* 4.0 17.5 - - + -
42M ASP* 6.1 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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