Contacts of the helix formed by residues 5 - 20 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N THR* 1.3 69.6 - - - +
6N ARG* 1.3 66.9 + - - +
8N ALA* 3.0 13.0 + - - +
9N ILE* 3.0 21.9 + - + +
147N PRO* 5.9 0.9 - - + -
148N TRP 3.9 13.7 - - - +
149N ASN 3.7 6.1 - - - +
150N SER* 3.2 27.3 + - - +
153N ALA* 3.4 27.1 - - + -
175N MET* 3.1 27.6 - - + +
176N TYR* 3.1 9.7 + - + -
178N VAL 3.3 9.2 + - - +
180N PHE* 4.0 5.8 - - + -
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Residues in contact with ARG 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N THR* 3.8 8.1 + - - +
5N VAL* 1.3 78.1 - - - +
7N ASP* 1.3 66.6 + - - +
9N ILE* 3.3 6.4 + - - +
10N ASN* 3.0 23.4 + - + +
37N TYR* 2.7 24.2 + - - +
38N LYS* 3.4 28.8 - - - +
39N VAL* 3.9 10.9 - - + +
41N ARG* 3.9 15.0 - - - +
176N TYR* 2.7 54.0 + - + +
177N GLY* 3.6 22.6 - - - +
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Residues in contact with ASP 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N VAL* 4.9 6.1 - - + -
4N THR* 3.0 25.5 + - - +
6N ARG* 1.3 87.9 - - - +
8N ALA* 1.3 61.1 + - - +
10N ASN* 3.5 13.3 - - + +
11N GLN* 2.8 38.4 + - + +
38N LYS 4.9 0.3 - - - +
41N ARG* 3.9 15.7 + - - +
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Residues in contact with ALA 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N VAL* 3.9 10.4 - - + +
4N THR 2.9 12.0 + - - +
5N VAL* 3.2 9.6 - - - +
7N ASP* 1.3 78.0 - - - +
9N ILE* 1.3 56.5 + - - +
11N GLN* 3.4 6.3 + - - +
12N GLY 3.1 20.1 + - - -
150N SER* 3.3 39.7 - - - +
153N ALA* 4.5 2.2 - - + -
154N LYS* 3.3 16.2 - - + +
182N PHE* 4.1 9.6 - - + -
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Residues in contact with ILE 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N VAL* 3.0 19.8 + - + +
6N ARG 3.6 4.0 - - - +
8N ALA* 1.3 73.0 - - - +
10N ASN* 1.3 67.9 + - - +
12N GLY* 3.0 10.8 + - - +
13N MET* 3.0 22.0 + - + +
39N VAL* 3.8 17.0 - - + -
115N ARG* 4.7 0.2 - - - +
153N ALA* 3.5 22.4 - - + +
154N LYS* 4.9 0.2 - - - +
157N ILE* 4.4 27.5 - - + +
171N GLU* 3.5 34.1 - - + +
176N TYR* 3.6 29.8 - - + -
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Residues in contact with ASN 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N ARG 3.0 13.1 + - - +
7N ASP* 3.6 18.6 - - + +
9N ILE* 1.3 79.2 - - - +
11N GLN* 1.3 63.3 + - - +
13N MET* 3.3 5.6 + - - +
14N ASP* 3.2 21.1 + - - +
38N LYS 5.4 0.2 - - - +
39N VAL* 2.5 30.4 + - - +
41N ARG* 3.2 19.9 + - - +
43N LEU* 3.1 31.9 - - - +
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Residues in contact with GLN 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N VAL* 3.9 19.0 - - - +
7N ASP* 2.8 22.9 + - + +
8N ALA 3.4 7.2 - - - +
10N ASN* 1.3 73.6 + - - +
12N GLY* 1.3 65.5 + - - +
14N ASP* 3.2 7.6 + - - +
15N GLU* 3.1 33.1 + - + +
154N LYS* 2.8 33.8 + - - +
182N PHE* 3.8 23.6 - - - -
187N GLN* 4.2 11.3 - - - +
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Residues in contact with GLY 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ALA 3.1 8.3 + - - -
9N ILE 3.0 8.4 + - - -
11N GLN* 1.3 80.9 - - - +
13N MET* 1.3 62.8 + - - +
15N GLU* 3.6 8.9 + - - -
16N GLU* 3.3 27.7 + - - +
154N LYS* 4.1 1.3 - - - -
157N ILE* 4.0 10.8 - - - -
158N LYS* 3.8 19.9 + - - +
161N ILE* 5.3 0.4 - - - -
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Residues in contact with MET 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N ILE* 3.0 20.7 + - + +
10N ASN* 3.3 3.6 + - - +
11N GLN 3.2 0.2 - - - -
12N GLY* 1.3 76.4 - - - +
14N ASP* 1.3 54.5 + - - +
16N GLU* 2.9 7.0 + - - +
17N LEU* 2.7 42.9 + - + +
25N LEU* 4.3 10.3 - - + -
39N VAL* 4.0 31.9 - - + +
40N SER* 4.2 9.4 - - - -
43N LEU* 4.2 24.0 - - + -
77N ILE* 4.4 25.4 - - + -
115N ARG* 3.8 39.7 - - - +
157N ILE* 4.6 9.2 - - + -
161N ILE* 4.8 3.1 - - + -
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Residues in contact with ASP 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N ASN* 3.2 17.0 + - - +
11N GLN* 3.2 13.0 + - - +
13N MET* 1.3 76.1 - - - +
15N GLU* 1.3 65.5 + - + +
17N LEU* 3.3 3.5 + - - +
18N GLU* 3.0 16.2 + - - +
43N LEU* 5.0 9.3 - - + +
46N LYS* 2.9 34.8 + - - +
47N TYR* 3.0 38.2 + - - -
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Residues in contact with GLU 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N GLN* 3.1 20.1 + - + +
14N ASP* 1.3 78.0 - - + +
16N GLU* 1.3 58.8 + - - +
18N GLU* 3.7 10.5 - - - +
19N ARG* 3.0 28.9 + - - +
154N LYS* 2.9 39.7 + - - -
158N LYS* 2.8 31.8 + - - +
187N GLN 3.7 4.2 - - - +
189N LYS* 3.4 34.4 - - + +
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Residues in contact with GLU 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N GLY 3.3 18.3 + - - +
13N MET 2.9 4.1 + - - +
15N GLU* 1.3 78.2 - - - +
17N LEU* 1.3 64.7 + - - +
18N GLU 3.2 0.2 - - - -
19N ARG* 3.3 14.6 + - - +
20N ASP* 3.2 22.5 + - - +
23N VAL* 4.1 12.1 - - + +
158N LYS* 2.8 32.2 + - + +
161N ILE* 3.7 39.0 - - + +
162N ARG* 2.3 48.9 + - - -
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Residues in contact with LEU 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N MET* 2.7 25.2 + - + +
14N ASP 3.6 4.7 - - - +
16N GLU* 1.3 70.4 - - - +
18N GLU* 1.3 62.4 + - - +
20N ASP 3.2 9.4 - - - +
21N GLU* 4.3 0.5 + - - -
23N VAL* 3.3 39.9 - - + +
24N PHE* 4.0 10.3 - - - -
25N LEU* 4.8 3.6 - - + +
43N LEU* 4.1 15.7 - - + -
47N TYR* 3.6 30.5 - - + -
51N ARG* 3.0 31.6 + - + +
52N ILE* 3.6 28.5 - - + -
77N ILE* 5.3 2.7 - - + -
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Residues in contact with GLU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N ASP* 3.0 20.6 + - - +
15N GLU* 3.7 9.1 - - - +
17N LEU* 1.3 77.5 - - - +
19N ARG* 1.3 63.9 + - - +
20N ASP* 3.2 2.1 + - - -
21N GLU 4.9 0.7 + - - -
46N LYS* 4.1 18.3 + - - -
47N TYR* 3.5 15.0 + - + +
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Residues in contact with ARG 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N GLU 3.0 20.6 + - - +
16N GLU* 3.3 20.5 + - - +
18N GLU* 1.3 78.0 - - - +
20N ASP* 1.3 73.1 + - - +
162N ARG* 3.4 53.8 - - - +
189N LYS* 5.9 5.4 - - - +
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Residues in contact with ASP 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N GLU 3.2 4.8 + - - +
17N LEU 3.2 12.7 - - - +
18N GLU 3.2 1.3 + - - -
19N ARG* 1.3 96.9 + - - +
21N GLU* 1.3 69.5 + - - +
22N LYS* 2.7 39.3 + - - +
23N VAL* 3.2 23.0 + - + +
51N ARG* 3.4 1.7 + - - -
75N ARG* 3.3 30.0 + - - -
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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