Contacts of the helix formed by residues 5 - 20 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R THR* 1.3 68.6 - - - +
6R ARG* 1.3 65.7 + - - +
8R ALA* 2.9 14.0 + - - +
9R ILE* 3.1 20.8 + - + +
147R PRO* 6.2 0.4 - - + -
148R TRP 3.8 13.0 - - - +
149R ASN 3.8 6.3 - - - +
150R SER* 3.3 28.7 - - - +
153R ALA* 3.7 25.4 - - + -
175R MET* 3.2 29.8 - - + +
176R TYR* 3.0 7.4 + - + -
178R VAL 3.0 14.4 + - - +
180R PHE* 4.1 7.4 - - + -
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Residues in contact with ARG 6 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R THR* 3.8 6.7 + - - +
5R VAL* 1.3 74.7 - - - +
7R ASP* 1.3 70.9 + - - +
9R ILE* 3.5 6.2 + - - +
10R ASN* 3.0 22.0 + - + +
37R TYR* 2.9 24.5 + - - +
38R LYS* 3.4 26.9 - - - +
39R VAL* 4.2 9.3 - - + +
41R ARG* 4.2 12.8 - - - +
176R TYR* 2.8 52.7 + - + +
177R GLY* 3.6 22.8 - - - +
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Residues in contact with ASP 7 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R GLN 5.4 0.2 - - - +
3R VAL* 4.4 11.0 - - + -
4R THR* 3.0 40.9 + - - +
6R ARG* 1.3 81.3 - - - +
8R ALA* 1.3 60.1 + - - +
10R ASN* 3.0 8.1 + - - +
11R GLN* 2.8 39.0 + - - +
41R ARG* 5.5 3.1 + - - -
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Residues in contact with ALA 8 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R VAL* 4.4 2.9 - - + +
4R THR 3.0 9.8 + - - +
5R VAL 2.9 9.7 + - - +
7R ASP* 1.3 75.8 - - - +
9R ILE* 1.3 62.4 + - - +
11R GLN* 3.4 8.2 + - - +
12R GLY 3.2 15.9 + - - -
150R SER* 3.3 37.7 - - - +
153R ALA* 4.7 1.1 - - + -
154R LYS* 3.4 25.6 - - + +
182R PHE* 4.3 8.7 - - + -
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Residues in contact with ILE 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R VAL* 3.1 30.1 + - + +
6R ARG* 3.9 3.4 - - - +
8R ALA* 1.3 73.8 - - - +
10R ASN* 1.3 65.5 + - - +
12R GLY* 3.0 12.4 + - - +
13R MET* 3.1 24.8 + - + +
39R VAL* 3.8 18.6 - - + -
115R ARG* 4.2 15.7 - - - +
153R ALA* 3.7 28.0 - - + +
157R ILE* 4.5 13.6 - - + +
171R GLU* 3.7 28.7 - - + +
176R TYR* 3.8 17.7 - - + -
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Residues in contact with ASN 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R ARG* 3.0 11.0 + - + +
7R ASP* 3.0 13.0 + - - +
9R ILE* 1.3 78.4 - - - +
11R GLN* 1.3 60.8 + - - +
13R MET* 3.7 4.8 + - - +
14R ASP* 3.3 23.0 + - - +
38R LYS 5.4 1.6 - - - +
39R VAL 3.3 25.1 + - - +
40R SER* 3.4 5.5 - - - +
41R ARG* 2.8 31.9 + - - +
43R LEU* 3.1 20.2 - - - +
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Residues in contact with GLN 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R VAL* 4.8 15.8 - - - +
7R ASP* 2.8 27.1 + - - +
8R ALA* 3.5 10.0 - - - +
10R ASN* 1.3 74.4 + - - +
12R GLY* 1.3 57.1 + - - +
14R ASP* 3.0 6.5 + - - +
15R GLU* 2.8 44.8 + - + +
154R LYS* 2.8 34.0 + - + +
182R PHE* 4.0 12.1 - - - -
187R GLN* 4.4 8.5 - - - +
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Residues in contact with GLY 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ALA 3.2 7.7 + - - -
9R ILE 3.0 7.9 + - - -
11R GLN* 1.3 78.6 - - - +
13R MET* 1.3 57.0 + - - +
15R GLU* 3.3 8.0 + - - +
16R GLU* 2.9 34.1 + - - +
154R LYS* 4.4 3.8 - - - +
157R ILE* 4.2 11.7 - - - -
158R LYS* 4.0 20.7 + - - -
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Residues in contact with MET 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ILE* 3.1 20.5 + - + +
10R ASN* 4.2 1.3 - - - +
12R GLY* 1.3 77.7 - - - +
14R ASP* 1.3 53.6 + - - +
16R GLU* 3.2 5.6 + - - +
17R LEU* 2.7 44.0 + - + +
25R LEU* 3.8 29.4 - - + -
39R VAL* 3.8 26.0 - - + +
40R SER* 4.2 7.0 - - - -
43R LEU* 4.2 13.7 - - + -
77R ILE* 4.1 30.7 - - + -
115R ARG* 3.9 29.2 - - - +
157R ILE* 4.6 8.5 - - + -
161R ILE* 4.5 3.8 - - - -
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Residues in contact with ASP 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R ASN* 3.3 20.0 + - - +
11R GLN* 3.0 6.8 + - - +
13R MET* 1.3 77.7 - - - +
15R GLU* 1.3 65.7 + - + +
17R LEU* 4.5 3.8 - - - -
18R GLU* 3.1 21.1 + - - +
43R LEU* 4.7 13.7 - - + +
46R LYS* 2.8 28.2 + - - +
47R TYR* 2.7 36.0 + - - -
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Residues in contact with GLU 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R GLN* 2.8 30.1 + - + +
12R GLY* 3.8 0.8 - - - +
14R ASP* 1.3 74.7 - - + +
16R GLU* 1.3 60.7 + - - +
18R GLU* 3.6 5.0 + - - +
19R ARG* 2.9 28.9 + - - +
154R LYS* 2.8 40.8 + - - -
158R LYS* 2.8 36.8 + - - +
187R GLN 3.7 4.7 - - - +
189R LYS* 3.6 33.5 - - + +
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Residues in contact with GLU 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R GLY 2.9 19.3 + - - +
13R MET 3.6 2.7 - - - +
15R GLU* 1.3 78.4 - - - +
17R LEU* 1.3 64.7 + - - +
19R ARG* 2.9 33.0 + - - +
20R ASP* 3.1 24.4 + - - +
23R VAL* 4.1 9.0 - - + +
158R LYS* 2.8 24.9 + - + +
161R ILE* 3.5 47.0 - - + +
162R ARG* 2.4 38.2 + - - -
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Residues in contact with LEU 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G TYR* 5.4 0.2 + - - -
13R MET* 2.7 28.3 + - + +
16R GLU* 1.3 72.8 - - - +
18R GLU* 1.3 61.3 + - - +
20R ASP 3.6 6.6 + - - +
21R GLU* 4.6 0.5 - - - +
23R VAL* 3.2 43.1 - - + +
24R PHE* 3.9 6.3 - - - -
25R LEU* 5.0 6.7 - - + -
43R LEU* 4.6 10.5 - - + -
47R TYR* 3.5 30.6 - - + +
51R ARG* 2.6 36.6 + - + +
52R ILE* 3.7 27.6 - - + -
77R ILE* 5.3 2.0 - - + -
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Residues in contact with GLU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G TYR* 3.6 32.2 - - + +
276G GLU* 4.5 13.9 - - - +
14R ASP* 3.1 18.6 + - - +
15R GLU* 3.9 5.1 - - - +
17R LEU* 1.3 77.3 - - - +
19R ARG* 1.3 63.5 + - - +
20R ASP 3.5 0.2 + - - -
46R LYS* 3.4 21.1 + - - -
47R TYR* 3.3 7.7 + - - +
189R LYS* 5.9 2.9 - - - +
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Residues in contact with ARG 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R GLU 2.9 20.0 + - - +
16R GLU* 2.9 26.6 + - - +
18R GLU* 1.3 79.3 - - - +
20R ASP* 1.3 73.0 + - - +
23R VAL* 5.9 0.6 - - - +
161R ILE* 5.7 1.4 - - - +
162R ARG* 3.4 51.9 - - - +
189R LYS* 6.0 7.6 - - - +
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Residues in contact with ASP 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R GLU 3.1 6.1 + - - +
17R LEU 3.6 4.6 - - - +
18R GLU 3.3 2.2 + - - -
19R ARG* 1.3 94.2 + - + +
21R GLU* 1.3 68.7 + - - +
22R LYS* 2.8 27.2 + - - +
23R VAL* 3.0 34.7 + - + +
51R ARG* 3.5 5.2 + - - -
75R ARG* 3.3 25.6 + - - -
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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