Contacts of the helix formed by residues 9 - 22 (chain J) in PDB entry 2X86
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 GLY 9 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6J GLY 2.7 14.3 + - - -
8J ALA* 1.3 81.3 - - - +
10J PHE* 1.3 57.7 + - - -
11J ILE 3.7 0.7 - - - -
13J SER* 2.7 34.9 + - - -
31J ASP* 3.2 3.4 + - - -
38J LYS* 4.9 0.2 - - - -
41J ASN* 4.2 0.2 - - - -
177J HIS* 3.8 9.4 - - - -
400J NAP 3.6 24.7 - - - -
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Residues in contact with PHE 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J GLY* 1.3 69.6 - - - -
11J ILE* 1.3 69.1 + - + +
13J SER* 3.0 8.8 + - - -
14J ASN* 2.8 28.5 + - - -
170J VAL* 3.6 31.9 - - + -
171J TYR* 3.5 5.4 - - - -
172J GLY 3.2 34.5 - - - -
173J PRO 3.1 22.0 - - - -
174J ARG 3.1 25.6 - - - +
175J GLU* 3.6 15.9 - - + -
177J HIS* 3.5 2.2 - - + -
178J LYS* 4.0 8.1 - - + -
214J VAL* 3.6 12.1 - - + -
400J NAP 3.0 43.6 + - - +
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Residues in contact with ILE 11 (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 PHE* 1.3 86.4 - - + +
12J GLY* 1.3 63.5 + - - +
14J ASN* 3.1 6.1 + - + +
15J ILE* 3.0 27.1 + - + +
75J GLU* 3.5 21.1 - - - +
167J TYR* 3.5 38.1 - - + +
170J VAL* 4.1 24.0 - - + -
214J VAL* 4.5 7.9 - - + -
217J VAL* 4.0 15.0 - - + -
400J NAP 2.8 44.1 + - + +
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Residues in contact with GLY 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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4J VAL* 3.7 15.3 - - - +
6J GLY 3.5 18.8 + - - -
7J GLY* 3.8 6.5 - - - -
9J GLY 4.3 0.2 - - - -
10J PHE 3.3 0.6 - - - -
11J ILE* 1.3 78.6 - - - +
13J SER* 1.3 62.0 + - - +
15J ILE* 3.0 7.2 + - - +
16J VAL* 2.9 23.7 + - - +
75J GLU* 4.0 15.7 - - - +
400J NAP 4.4 0.8 + - - -
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Residues in contact with SER 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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7J GLY 3.3 17.3 + - - -
9J GLY 2.7 25.2 + - - -
10J PHE 3.0 7.8 + - - -
12J GLY* 1.3 75.2 - - - +
14J ASN* 1.3 56.7 + - - +
16J VAL* 3.2 7.9 + - - +
17J LYS* 2.9 24.4 + - - +
41J ASN* 3.6 29.7 - - - +
45J LEU* 3.4 7.7 - - - +
174J ARG* 3.3 22.3 - - - +
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Residues in contact with ASN 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 PHE* 2.8 22.8 + - - -
11J ILE* 3.1 9.2 + - + +
13J SER* 1.3 80.1 + - - +
15J ILE* 1.3 60.2 + - - +
17J LYS* 3.4 12.7 + - - +
18J ALA* 3.0 27.7 + - - +
173J PRO* 2.9 29.8 + - - +
174J ARG* 3.8 14.2 + - - +
214J VAL* 3.5 38.3 - - + +
215J GLY* 5.2 1.6 + - - -
218J ALA* 3.9 13.1 - - + +
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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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4J VAL* 4.4 5.8 - - + -
11J ILE* 3.0 20.3 + - + +
12J GLY* 3.0 8.3 + - - +
14J ASN* 1.3 74.1 - - - +
16J VAL* 1.3 65.3 + - - +
18J ALA* 3.2 7.1 + - - +
19J LEU* 2.9 36.3 + - + +
73J PHE* 4.0 26.0 - - + -
75J GLU* 3.6 31.6 - - + +
218J ALA* 4.6 8.7 - - - -
221J ASN* 3.5 39.7 - - + +
222J LEU* 4.4 9.0 - - + -
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Residues in contact with VAL 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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4J VAL* 4.2 16.4 - - + -
7J GLY 4.2 8.5 - - - +
12J GLY 2.9 18.5 + - - +
13J SER 3.2 8.0 + - - +
15J ILE* 1.3 76.4 - - - +
17J LYS* 1.3 57.5 + - - +
19J LEU* 3.1 11.7 + - - +
20J ASN* 2.8 29.7 + - - +
27J ILE* 4.0 10.8 - - + -
29J VAL* 4.1 22.2 - - + -
42J LEU* 4.7 1.6 - - + -
45J LEU* 3.7 21.8 - - + -
47J ILE* 3.8 25.6 - - + -
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Residues in contact with LYS 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 SER 2.9 13.3 + - - +
14J ASN* 3.7 16.2 - - - +
15J ILE 3.3 0.2 - - - -
16J VAL* 1.3 76.6 - - - +
18J ALA* 1.3 58.2 + - - +
20J ASN* 3.1 7.6 + - + +
21J ASP* 2.8 61.7 + - - +
45J LEU* 3.9 28.4 - - + +
174J ARG* 4.1 19.9 - - - +
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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 ASN 3.0 17.1 + - - +
15J ILE* 3.5 5.8 - - - +
16J VAL 3.2 0.2 - - - -
17J LYS* 1.3 77.7 - - - +
19J LEU* 1.3 61.2 + - - +
21J ASP* 3.2 12.7 + - - +
22J LYS* 3.1 18.5 + - - +
218J ALA* 4.0 20.0 - - + +
219J ASP* 5.3 4.9 - - - +
222J LEU* 3.8 26.8 - - + +
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Residues in contact with LEU 19 (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 ILE* 3.8 45.8 - - + -
4J VAL* 4.2 6.5 - - + -
15J ILE* 2.9 32.8 + - + +
16J VAL* 3.4 6.1 - - - +
18J ALA* 1.3 72.3 - - - +
20J ASN* 1.3 67.7 + - - +
22J LYS* 3.0 10.5 + - + +
23J GLY 3.3 0.2 + - - -
24J ILE* 2.9 40.7 + - + +
27J ILE* 3.9 22.4 - - + -
73J PHE* 4.4 3.8 - - + -
222J LEU* 3.9 26.2 - - + -
225J LEU* 5.0 3.6 - - + -
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Residues in contact with ASN 20 (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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16J VAL* 2.8 18.5 + - - +
17J LYS* 3.3 11.9 - - + +
19J LEU* 1.3 76.0 - - - +
21J ASP* 1.3 56.8 + - - +
23J GLY* 2.7 26.3 + - - -
24J ILE 2.9 19.2 + - - -
25J THR* 3.8 8.9 - - + +
27J ILE* 3.8 4.2 - - - +
44J ASP 5.0 0.2 - - - +
45J LEU* 3.6 15.7 - - + +
46J ASN* 2.8 53.4 + - - +
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Residues in contact with ASP 21 (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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17J LYS* 2.8 50.9 + - - +
18J ALA* 3.2 12.3 + - - +
20J ASN* 1.3 78.9 - - - +
22J LYS* 1.3 62.3 + - + +
23J GLY 3.2 1.1 + - - -
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Residues in contact with LYS 22 (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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18J ALA 3.1 11.0 + - - +
19J LEU* 3.0 10.7 + - - +
21J ASP* 1.3 78.7 - - + +
23J GLY* 1.3 60.3 + - - +
24J ILE* 3.3 16.6 + - + +
222J LEU* 3.8 23.3 - - + -
226J GLU* 3.1 31.2 + - - +
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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