Contacts of the helix formed by residues 5 - 20 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B THR* 1.3 71.2 - - - +
6B ARG* 1.3 66.0 + - - +
8B ALA* 2.9 14.2 + - - +
9B ILE* 3.2 20.2 + - + +
147B PRO* 6.0 2.2 - - + -
148B TRP 3.9 11.2 - - - +
149B ASN 3.9 4.7 - - - -
150B SER* 3.4 26.0 - - - +
153B ALA* 3.8 23.8 - - + -
172B ASN 5.7 0.2 - - - +
175B MET* 3.3 29.6 - - + +
176B TYR* 3.0 10.5 + - + -
178B VAL 2.9 17.0 + - - +
180B PHE* 3.9 9.9 - - + -
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 3.9 7.2 + - - +
5B VAL* 1.3 76.9 - - - +
7B ASP* 1.3 70.0 + - - +
9B ILE* 3.4 6.9 + - - +
10B ASN* 3.2 19.5 + - + +
37B TYR* 2.8 24.4 + - - +
38B LYS* 3.3 36.1 - - - +
39B VAL* 4.3 7.9 - - + +
41B ARG* 4.5 9.0 - - - +
173B GLU 5.5 0.2 + - - -
176B TYR* 2.8 52.5 + - + +
177B GLY* 3.7 22.8 - - - +
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Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.5 10.8 - - + +
4B THR* 3.1 33.6 + - - +
6B ARG* 1.3 84.5 - - - +
8B ALA* 1.3 61.0 + - - +
10B ASN* 3.2 8.1 + - - +
11B GLN* 2.8 38.7 + - - +
41B ARG* 5.6 2.6 + - - -
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.3 9.3 - - + +
4B THR 3.2 10.3 + - - +
5B VAL 2.9 9.9 + - - +
7B ASP* 1.3 76.5 - - - +
9B ILE* 1.3 63.5 + - - +
11B GLN* 3.4 7.0 + - - +
12B GLY 3.1 15.9 + - - -
150B SER* 3.3 38.4 - - - +
153B ALA* 4.4 1.1 - - + -
154B LYS* 3.3 23.6 - - + +
182B PHE* 4.3 3.6 - - + -
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Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.2 19.7 + - + +
6B ARG 3.8 4.3 - - - +
7B ASP 3.1 0.2 - - - -
8B ALA* 1.3 78.1 - - - +
10B ASN* 1.3 62.1 + - - +
12B GLY* 2.9 12.5 + - - -
13B MET* 3.1 22.3 + - + +
39B VAL* 4.2 16.6 - - + -
115B ARG* 4.4 4.3 - - - +
147B PRO* 5.9 0.4 - - + -
153B ALA* 3.7 22.9 - - + +
157B ILE* 4.3 23.3 - - + +
171B GLU* 3.4 42.6 - - + +
176B TYR* 3.7 22.4 - - + -
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Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 3.2 12.3 + - + +
7B ASP* 3.6 12.3 - - - +
9B ILE* 1.3 77.6 - - - +
11B GLN* 1.3 61.2 + - - +
13B MET* 3.6 5.3 + - - +
14B ASP* 3.2 24.8 + - - +
38B LYS 5.4 1.6 - - - +
39B VAL 3.0 29.5 + - - +
40B SER* 3.4 1.0 - - - +
41B ARG* 3.2 33.6 + - - +
43B LEU* 3.3 20.0 - - - +
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.9 10.3 - - - +
7B ASP* 2.8 21.4 + - - +
8B ALA* 3.5 9.4 - - - +
10B ASN* 1.3 74.0 + - - +
12B GLY* 1.3 70.7 + - - +
14B ASP* 2.9 7.6 + - - +
15B GLU* 2.9 37.0 + - + +
154B LYS* 2.9 30.1 + - + -
182B PHE* 3.8 18.2 - - - -
187B GLN* 4.2 8.7 - - - +
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Residues in contact with GLY 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 3.1 8.1 + - - -
9B ILE 2.9 8.0 + - - -
11B GLN* 1.3 80.8 - - - +
13B MET* 1.3 61.7 + - - +
15B GLU* 3.4 2.2 + - - +
16B GLU* 3.1 27.8 + - - +
154B LYS* 4.2 5.6 - - - +
157B ILE* 4.1 10.5 - - - -
158B LYS* 3.9 25.0 - - - +
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Residues in contact with MET 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.1 20.1 + - + +
10B ASN* 4.3 2.7 - - - +
12B GLY* 1.3 73.8 - - - +
14B ASP* 1.3 58.9 + - - +
16B GLU* 3.2 5.6 + - - +
17B LEU* 2.7 44.7 + - + +
25B LEU* 4.4 8.1 - - + -
39B VAL* 3.6 38.6 - - + +
40B SER* 4.2 8.5 - - - -
43B LEU* 4.0 22.4 - - + -
77B ILE* 4.2 28.0 - - + -
115B ARG* 4.2 28.3 - - - +
157B ILE* 4.6 7.9 - - + -
161B ILE* 4.5 3.6 - - - -
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.2 25.0 + - - +
11B GLN* 2.9 9.2 + - + +
13B MET* 1.3 80.5 - - - +
15B GLU* 1.3 58.5 + - + +
17B LEU* 4.6 5.2 - - - -
18B GLU* 3.2 10.4 + - - +
43B LEU* 4.7 13.2 - - + +
46B LYS* 2.7 36.0 + - - +
47B TYR* 2.9 31.3 + - - -
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 2.9 29.2 + - + +
12B GLY 4.0 0.4 - - - +
14B ASP* 1.3 70.6 - - + +
16B GLU* 1.3 66.8 + - - +
18B GLU* 3.8 7.1 - - - +
19B ARG* 3.1 26.7 + - - +
154B LYS* 2.8 35.5 + - - -
158B LYS* 2.8 43.7 + - - +
187B GLN 4.0 3.5 - - - +
189B LYS* 3.6 34.7 - - + +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 3.1 18.6 + - - +
13B MET* 3.7 3.4 - - - +
15B GLU* 1.3 80.7 - - - +
17B LEU* 1.3 56.5 + - - +
19B ARG* 2.8 33.3 + - - +
20B ASP* 3.1 30.8 + - - +
23B VAL* 4.2 6.6 - - + +
158B LYS* 2.8 28.5 + - + +
161B ILE* 3.6 43.1 - - + +
162B ARG* 2.5 36.6 + - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET* 2.7 33.4 + - + +
14B ASP 4.0 0.2 - - - +
16B GLU* 1.3 72.4 - - - +
18B GLU* 1.3 62.1 + - - +
20B ASP 3.5 4.7 - - - +
21B GLU* 4.6 0.2 - - - -
23B VAL* 3.3 41.1 - - + +
24B PHE* 3.9 11.7 - - - -
25B LEU* 4.5 4.0 - - + +
43B LEU* 4.5 10.8 - - + -
47B TYR* 3.7 29.7 - - + +
51B ARG* 2.5 38.4 + - - +
52B ILE* 3.6 25.8 - - + -
77B ILE* 5.2 3.6 - - + -
272W TYR* 5.1 0.2 + - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP 3.2 11.0 + - - +
15B GLU* 3.8 6.1 - - - +
17B LEU* 1.3 78.6 - - - +
19B ARG* 1.3 66.3 + - - +
20B ASP* 3.1 3.1 + - - -
21B GLU* 4.9 1.4 + - - +
46B LYS* 3.6 13.9 + - - -
47B TYR* 3.4 12.7 + - - +
189B LYS* 4.4 18.0 - - - +
272W TYR* 3.4 41.8 + - + +
276W GLU* 4.7 8.3 - - - +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU 3.1 16.6 + - - +
16B GLU* 2.8 28.1 + - - +
18B GLU* 1.3 79.4 - - - +
20B ASP* 1.3 68.5 + - + +
21B GLU* 5.3 0.3 - - - +
23B VAL* 5.9 0.4 - - - +
161B ILE* 5.8 0.8 - - - +
162B ARG* 3.4 49.6 - - - +
189B LYS* 6.1 5.6 - - - +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU 3.1 8.7 + - - +
17B LEU 3.5 4.0 - - - +
18B GLU 3.1 2.6 + - - -
19B ARG* 1.3 91.4 + - + +
21B GLU* 1.3 69.9 + - - +
22B LYS* 2.8 26.4 + - - +
23B VAL* 2.9 37.7 + - + +
51B ARG* 3.4 5.9 + - - -
75B ARG* 3.3 26.2 - - - -
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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