Contacts of the helix formed by residues 5 - 20 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z THR* 1.3 72.8 - - - +
6Z ARG* 1.3 63.3 + - - +
8Z ALA* 2.9 13.5 + - - +
9Z ILE* 3.1 19.0 + - + +
147Z PRO* 6.0 0.9 - - + -
148Z TRP 3.9 10.5 - - - +
149Z ASN 3.7 7.9 - - - +
150Z SER* 3.4 30.5 - - - +
153Z ALA* 3.6 26.0 - - + -
175Z MET* 3.0 32.8 - - + +
176Z TYR* 3.4 3.7 + - + -
178Z VAL 3.2 11.2 + - - +
180Z PHE* 3.8 9.9 - - + -
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Residues in contact with ARG 6 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Z THR* 3.8 7.7 + - - +
5Z VAL* 1.3 79.4 - - - +
7Z ASP* 1.3 67.7 + - - +
9Z ILE* 3.3 7.8 + - - +
10Z ASN* 3.1 18.5 + - + +
37Z TYR* 2.8 23.4 + - - +
38Z LYS* 3.5 28.1 - - - +
39Z VAL* 3.8 12.7 - - + +
41Z ARG* 4.3 12.6 - - - +
173Z GLU 5.2 0.8 + - - -
176Z TYR* 3.1 73.6 + - + +
177Z GLY* 3.8 9.7 - - - +
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Residues in contact with ASP 7 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Z VAL* 4.5 9.0 - - + -
4Z THR* 3.1 33.8 + - - +
6Z ARG* 1.3 80.5 - - - +
8Z ALA* 1.3 66.1 + - - +
9Z ILE 3.0 2.0 - - - -
10Z ASN* 3.0 10.0 + - - +
11Z GLN* 2.9 32.0 + - - +
41Z ARG* 4.7 9.4 + - - -
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Residues in contact with ALA 8 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Z VAL* 4.1 5.8 - - + +
4Z THR 3.1 5.6 + - - +
5Z VAL 2.9 10.3 + - - +
7Z ASP* 1.3 76.9 - - - +
9Z ILE* 1.3 61.6 + - - +
11Z GLN* 3.5 6.3 + - - +
12Z GLY 3.0 17.5 + - - -
150Z SER* 3.2 44.2 - - - +
153Z ALA* 4.8 0.9 - - + -
154Z LYS* 3.4 16.5 - - + +
182Z PHE* 3.9 14.8 - - + -
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Residues in contact with ILE 9 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Z VAL* 3.5 13.9 - - + +
6Z ARG 3.6 4.9 - - - +
7Z ASP 3.0 0.6 - - - -
8Z ALA* 1.3 73.2 - - - +
10Z ASN* 1.3 69.1 + - - +
12Z GLY* 2.9 12.4 + - - +
13Z MET* 2.9 22.9 + - + +
39Z VAL* 3.7 17.3 - - + -
115Z ARG* 4.5 0.2 - - - +
153Z ALA* 3.5 30.7 - - + +
154Z LYS* 4.9 0.7 - - - +
157Z ILE* 4.2 24.5 - - + -
171Z GLU* 3.7 32.1 - - + +
176Z TYR* 3.8 27.1 - - + -
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Residues in contact with ASN 10 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Z ARG* 3.1 11.8 + - + +
7Z ASP* 3.0 16.0 + - - +
9Z ILE* 1.3 77.3 - - - +
11Z GLN* 1.3 61.9 + - - +
13Z MET* 3.2 6.5 + - - +
14Z ASP* 3.1 22.9 + - - +
38Z LYS 4.8 0.8 + - - +
39Z VAL* 2.5 28.8 + - - +
41Z ARG* 3.1 33.7 + - - +
43Z LEU* 3.3 20.7 - - - +
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Residues in contact with GLN 11 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z VAL* 4.4 15.8 - - - +
7Z ASP* 2.9 21.8 + - - +
8Z ALA* 3.5 7.4 - - - +
10Z ASN* 1.3 69.5 + - - +
12Z GLY* 1.3 67.9 + - - +
14Z ASP* 3.1 7.8 + - - +
15Z GLU* 2.9 34.9 + - + +
154Z LYS* 2.8 32.4 + - - +
182Z PHE* 3.6 23.3 - - - -
187Z GLN* 4.1 10.0 - - - +
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Residues in contact with GLY 12 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Z ALA 3.0 7.9 + - - -
9Z ILE 2.9 11.6 + - - -
11Z GLN* 1.3 78.1 - - - +
13Z MET* 1.3 64.3 + - - +
15Z GLU* 3.5 9.1 + - - -
16Z GLU* 3.1 27.0 + - - +
154Z LYS* 4.3 2.2 - - - +
157Z ILE* 4.0 10.8 - - - -
158Z LYS* 3.8 18.6 + - - -
161Z ILE* 5.4 0.2 - - - -
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Residues in contact with MET 13 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Z ILE* 2.9 19.7 + - + +
10Z ASN* 3.9 4.3 - - - +
12Z GLY* 1.3 77.0 - - - +
14Z ASP* 1.3 53.8 + - - +
16Z GLU* 2.9 8.1 + - - +
17Z LEU* 2.7 43.6 + - + +
25Z LEU* 4.3 20.2 - - - -
39Z VAL* 3.7 41.7 - - + +
40Z SER* 4.5 4.5 - - - -
43Z LEU* 4.3 18.4 - - + -
77Z ILE* 4.4 17.4 - - + +
115Z ARG* 4.0 29.8 - - - +
157Z ILE* 4.6 15.0 - - + -
161Z ILE* 4.8 2.7 - - + -
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Residues in contact with ASP 14 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z ASN* 3.1 19.9 + - - +
11Z GLN* 3.3 12.4 - - - +
13Z MET* 1.3 73.6 - - - +
15Z GLU* 1.3 69.4 + - + +
17Z LEU* 3.3 5.3 + - - +
18Z GLU* 2.9 23.4 + - - +
43Z LEU* 4.9 8.1 - - + +
46Z LYS* 2.8 26.3 + - - +
47Z TYR* 2.8 35.3 + - - -
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Residues in contact with GLU 15 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Z GLN* 2.9 22.0 + - + +
14Z ASP* 1.3 77.3 - - + +
16Z GLU* 1.3 57.7 + - - +
18Z GLU* 3.4 8.8 + - - +
19Z ARG* 2.8 31.1 + - - +
154Z LYS* 2.7 38.9 + - - -
158Z LYS* 2.7 35.1 + - - +
187Z GLN 3.5 9.7 - - - +
189Z LYS* 3.5 35.0 - - + +
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Residues in contact with GLU 16 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLY 3.1 18.1 + - - +
13Z MET 2.9 4.8 + - - +
15Z GLU* 1.3 78.0 - - - +
17Z LEU* 1.3 64.2 + - - +
19Z ARG* 3.1 36.1 + - - +
20Z ASP* 3.2 14.4 + - - +
23Z VAL* 4.1 10.3 - - + +
158Z LYS* 2.7 29.4 + - + +
161Z ILE* 3.8 40.3 - - + +
162Z ARG* 2.4 36.7 + - - -
189Z LYS 4.8 0.2 - - - +
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Residues in contact with LEU 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Z MET* 2.7 29.1 + - + +
14Z ASP 3.7 0.2 - - - +
16Z GLU* 1.3 72.6 - - - +
18Z GLU* 1.3 59.0 + - - +
20Z ASP 3.5 9.3 + - - +
21Z GLU* 4.4 0.7 + - - -
23Z VAL* 3.2 38.6 - - + +
24Z PHE* 4.1 9.0 - - - -
25Z LEU* 5.3 4.5 - - + -
43Z LEU* 4.0 26.7 - - + -
47Z TYR* 3.5 33.3 - - + -
51Z ARG* 2.8 31.8 + - + +
52Z ILE* 4.0 18.4 - - + -
77Z ILE* 5.4 1.8 - - + -
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Residues in contact with GLU 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Z ASP* 2.9 18.0 + - - +
15Z GLU* 3.8 7.3 - - - +
17Z LEU* 1.3 73.5 - - - +
19Z ARG* 1.3 65.4 + - - +
20Z ASP* 3.4 0.7 + - - -
21Z GLU 5.3 0.3 + - - -
46Z LYS* 4.4 18.5 + - - -
47Z TYR* 3.5 15.3 + - + +
189Z LYS* 5.8 5.2 - - - +
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Residues in contact with ARG 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Z GLU 2.8 18.8 + - - +
16Z GLU* 3.1 27.6 + - - +
18Z GLU* 1.3 79.4 - - - +
20Z ASP* 1.3 68.0 + - - +
161Z ILE* 6.1 0.4 - - - +
162Z ARG* 3.6 50.6 - - - +
189Z LYS 5.8 2.2 - - - -
190Z ASP* 6.2 0.2 - - - -
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Residues in contact with ASP 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z GLU 3.2 4.5 + - - +
17Z LEU 3.5 9.4 - - - +
18Z GLU 3.3 1.6 + - - -
19Z ARG* 1.3 93.0 + - + +
21Z GLU* 1.3 69.0 + - - +
22Z LYS* 2.6 44.2 + - - +
23Z VAL* 3.2 27.0 + - + +
51Z ARG* 3.6 0.5 + - - -
75Z ARG* 3.4 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
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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