Contacts of the helix formed by residues 5 - 20 (chain J) in PDB entry 3EXG
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 VAL 5 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J THR* 1.3 70.5 - - - +
6J ARG* 1.3 63.7 + - - +
8J ALA* 3.0 11.8 + - - +
9J ILE* 3.1 21.1 + - + +
147J PRO* 6.3 0.9 - - + -
148J TRP 3.7 14.8 - - - +
149J ASN* 3.7 7.6 - - - -
150J SER* 3.5 28.4 + - - +
153J ALA* 3.5 22.9 - - + -
171J GLU* 6.4 0.4 - - + -
175J MET* 3.0 32.1 - - + +
176J TYR* 3.7 4.9 + - + -
178J VAL 3.1 13.0 + - - +
180J PHE* 4.1 6.1 - - + -
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Residues in contact with ARG 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J THR* 3.8 8.5 + - - +
5J VAL* 1.3 72.4 - - - +
7J ASP* 1.3 75.4 + - - +
9J ILE* 3.0 9.9 + - - +
10J ASN* 2.9 20.1 + - + +
37J TYR* 3.0 24.2 + - - +
38J LYS* 3.2 28.6 + - - +
39J VAL* 3.9 13.6 - - + +
41J ARG* 4.2 10.8 - - - +
176J TYR* 2.8 69.3 + - + +
177J GLY* 3.9 8.1 - - - +
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Residues in contact with ASP 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J GLN 5.6 0.2 - - - +
3J VAL* 4.9 5.4 - - + -
4J THR* 3.1 34.4 + - - +
6J ARG* 1.3 91.8 + - - +
8J ALA* 1.3 64.0 + - - +
10J ASN* 3.6 9.1 - - - +
11J GLN* 2.9 37.8 + - - +
41J ARG* 5.4 2.8 + - - -
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Residues in contact with ALA 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J VAL* 4.5 4.8 - - + +
4J THR 2.9 12.8 + - - +
5J VAL 3.0 10.3 + - - +
7J ASP* 1.3 77.9 - - - +
9J ILE* 1.3 62.6 + - - +
11J GLN* 3.4 3.4 + - - +
12J GLY 3.2 15.6 + - - -
150J SER* 3.3 39.7 - - - +
153J ALA* 4.3 0.4 - - + -
154J LYS* 3.4 26.8 - - + +
182J PHE* 4.5 6.3 - - + -
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Residues in contact with ILE 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J VAL* 3.1 12.4 + - + +
6J ARG 3.0 8.1 + - - +
8J ALA* 1.3 73.0 - - - +
10J ASN* 1.3 65.3 + - - +
12J GLY* 3.3 1.0 + - - -
13J MET* 3.1 41.5 + - + +
39J VAL* 3.5 20.9 - - + -
115J ARG* 4.3 4.7 - - - +
147J PRO* 5.7 1.6 - - + -
153J ALA* 3.5 37.0 - - + +
157J ILE* 4.4 12.2 - - + +
169J VAL* 6.0 0.7 - - + -
171J GLU* 3.3 41.3 - - + +
176J TYR* 4.1 16.6 - - + -
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Residues in contact with ASN 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ARG* 2.9 12.9 + - + +
7J ASP* 3.0 13.9 + - - +
9J ILE* 1.3 79.4 - - - +
11J GLN* 1.3 64.2 + - - +
13J MET* 3.8 5.8 + - - +
14J ASP* 3.3 20.8 + - - +
38J LYS 5.6 0.2 - - - +
39J VAL 3.0 27.4 + - - +
40J SER* 3.7 2.0 - - - +
41J ARG* 3.2 30.8 + - - +
43J LEU* 3.4 20.3 - - - +
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Residues in contact with GLN 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J VAL* 4.8 15.0 - - - +
7J ASP* 2.9 25.4 + - - +
8J ALA* 3.6 7.2 - - - +
10J ASN* 1.3 78.0 + - - +
12J GLY* 1.3 57.2 + - - +
13J MET 3.2 0.2 - - - -
14J ASP* 2.8 7.2 + - - +
15J GLU* 2.7 47.0 + - + +
154J LYS* 2.9 35.0 + - + +
182J PHE* 3.9 10.6 - - - -
187J GLN* 4.6 5.2 - - - +
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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
----------------------------------------------------------
8J ALA 3.2 7.8 + - - -
9J ILE 3.3 3.1 + - - -
11J GLN* 1.3 79.8 - - - +
13J MET* 1.3 62.6 + - - +
15J GLU* 3.3 3.8 + - - +
16J GLU* 3.1 28.0 + - - +
154J LYS* 4.1 8.7 - - - -
157J ILE* 4.1 7.4 - - - -
158J LYS* 3.7 28.4 - - - +
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Residues in contact with MET 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ILE* 3.1 22.7 + - + +
10J ASN* 3.9 4.5 - - - +
12J GLY* 1.3 75.5 - - - +
14J ASP* 1.3 54.0 + - - +
16J GLU* 3.3 1.9 + - - +
17J LEU* 2.7 41.3 + - + +
25J LEU* 3.9 24.7 - - + -
39J VAL* 4.3 19.3 - - + +
40J SER* 4.2 13.9 - - - -
43J LEU* 4.2 11.0 - - + -
77J ILE* 3.9 27.1 - - + -
115J ARG* 4.0 30.7 - - - +
157J ILE* 4.3 11.8 - - + +
161J ILE* 4.4 10.9 - - - +
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Residues in contact with ASP 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ASN* 3.3 15.0 + - - +
11J GLN* 2.8 14.4 + - + +
13J MET* 1.3 79.6 - - - +
15J GLU* 1.3 66.7 + - + +
17J LEU* 3.2 4.3 + - - -
18J GLU* 2.9 22.8 + - - +
43J LEU* 4.7 14.3 - - + +
46J LYS* 3.3 30.3 + - - +
47J TYR* 2.8 27.0 + - - -
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Residues in contact with GLU 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 GLN* 2.7 26.6 + - + +
12J GLY 3.8 0.7 - - - +
14J ASP* 1.3 79.8 - - + +
16J GLU* 1.3 56.8 + - - +
18J GLU* 3.3 7.7 + - - +
19J ARG* 2.8 30.6 + - - +
154J LYS* 3.4 29.3 + - - -
158J LYS* 3.0 36.1 + - - +
187J GLN 3.7 4.3 - - - +
189J LYS* 3.6 38.9 - - + +
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Residues in contact with GLU 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J GLY 3.1 16.8 + - - +
13J MET 3.7 1.8 - - - +
15J GLU* 1.3 73.9 - - - +
17J LEU* 1.3 64.2 - - - +
19J ARG* 3.0 32.1 + - - +
20J ASP* 3.1 26.5 + - - +
23J VAL* 4.0 6.6 - - + +
158J LYS* 2.9 23.9 + - + +
161J ILE* 3.7 42.5 - - + +
162J ARG* 2.3 46.0 + - - +
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Residues in contact with LEU 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 MET* 2.7 26.2 + - + +
14J ASP 3.5 5.2 - - - +
16J GLU* 1.3 73.5 - - - +
18J GLU* 1.3 58.9 + - - +
20J ASP 3.5 4.6 + - - +
21J GLU* 4.6 0.3 + - - +
23J VAL* 3.1 39.9 - - + +
24J PHE* 4.0 9.6 - - - -
25J LEU* 5.1 6.3 - - + -
43J LEU* 3.8 26.9 - - + -
47J TYR* 3.6 22.8 - - + +
51J ARG* 2.6 44.5 + - + +
52J ILE* 3.9 17.7 - - + -
77J ILE* 5.4 2.2 - - + -
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Residues in contact with GLU 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 ASP* 2.9 12.8 + - - +
15J GLU* 3.6 10.5 - - - +
17J LEU* 1.3 74.8 - - - +
19J ARG* 1.3 65.9 + - - +
20J ASP 3.3 0.6 - - - -
46J LYS* 3.2 36.1 + - - -
47J TYR* 3.2 11.5 + - + +
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Residues in contact with ARG 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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15J GLU 2.8 16.4 + - - +
16J GLU* 3.0 29.7 + - - +
18J GLU* 1.3 81.7 - - - +
20J ASP* 1.3 71.9 + - + +
21J GLU* 5.4 0.3 - - - +
158J LYS* 5.8 0.4 - - - +
162J ARG* 3.1 50.7 - - - +
189J LYS* 4.7 20.9 - - - +
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Residues in contact with ASP 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 GLU 3.1 7.8 + - - +
17J LEU 3.5 2.6 - - - +
18J GLU 3.3 1.6 - - - -
19J ARG* 1.3 95.6 + - - +
21J GLU* 1.3 63.2 + - - +
22J LYS* 2.6 34.2 + - - +
23J VAL* 3.0 27.3 + - + +
51J ARG* 3.1 10.1 + - - -
75J ARG* 3.4 22.5 + - - -
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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
------------------------------------------------------------
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