Contacts of the helix formed by residues 5 - 20 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P THR* 1.3 69.7 - - - +
6P ARG* 1.3 69.0 + - - +
8P ALA* 2.9 4.3 + - - +
9P ILE* 2.8 34.7 + - + +
147P PRO* 5.9 1.6 - - + -
148P TRP 4.1 8.7 - - - +
149P ASN* 3.9 6.7 - - - +
150P SER* 3.6 25.6 - - - +
153P ALA* 3.5 24.7 - - + -
171P GLU* 6.3 0.9 - - + -
172P ASN 5.8 0.2 - - - +
175P MET* 3.4 29.2 - - + +
176P TYR* 3.3 10.6 + - + -
178P VAL 3.3 6.7 + - - +
180P PHE* 4.0 8.1 - - + -
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Residues in contact with ARG 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P THR* 3.9 5.7 + - - +
5P VAL* 1.3 76.9 - - - +
7P ASP* 1.3 70.1 + - - +
9P ILE* 3.4 3.6 + - - +
10P ASN* 3.1 20.8 + - + +
37P TYR* 2.9 25.1 + - - +
38P LYS* 3.4 34.0 - - - +
39P VAL* 4.1 16.4 - - + +
41P ARG* 4.1 11.2 - - - +
173P GLU 5.4 0.4 + - - -
176P TYR* 2.9 46.5 + - + +
177P GLY* 3.5 26.1 - - - +
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Residues in contact with ASP 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P VAL* 4.3 11.7 - - + +
4P THR* 3.1 32.9 + - - +
6P ARG* 1.3 85.4 - - - +
8P ALA* 1.3 69.9 + - - +
10P ASN* 3.3 7.2 + - - +
11P GLN* 3.0 30.5 + - - +
41P ARG* 5.0 5.9 + - - -
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Residues in contact with ALA 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P VAL* 3.9 6.2 - - - +
4P THR 2.8 15.9 + - - +
5P VAL* 3.4 7.4 - - - +
7P ASP* 1.3 75.7 - - - +
9P ILE* 1.3 64.3 + - - +
11P GLN* 3.3 7.3 - - - +
12P GLY 3.2 15.9 + - - -
150P SER* 3.4 39.5 - - - +
153P ALA* 4.3 0.9 - - + -
154P LYS* 3.7 19.5 - - + +
182P PHE* 4.1 7.6 - - + -
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Residues in contact with ILE 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P VAL* 2.8 30.1 + - + +
6P ARG 3.8 4.3 - - - +
8P ALA* 1.3 71.1 - - - +
10P ASN* 1.3 65.9 + - - +
12P GLY* 3.1 3.6 + - - -
13P MET* 3.0 36.0 + - + +
39P VAL* 3.9 20.0 - - + -
115P ARG* 4.4 2.2 - - - +
147P PRO* 5.9 1.6 - - + -
153P ALA* 3.8 20.9 - - + +
154P LYS* 4.7 0.2 - - - +
157P ILE* 4.4 19.7 - - + +
171P GLU* 3.4 37.0 - - + +
176P TYR* 3.9 19.3 - - + -
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Residues in contact with ASN 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P ARG* 3.1 13.0 + - + +
7P ASP* 3.3 9.6 + - - +
9P ILE* 1.3 80.0 - - - +
11P GLN* 1.3 67.2 + - - +
13P MET* 3.1 6.9 + - - +
14P ASP* 3.0 23.9 + - - +
38P LYS 5.0 0.8 + - - +
39P VAL 2.9 27.4 + - - +
40P SER* 3.3 9.3 + - - +
41P ARG* 2.8 32.2 + - - +
43P LEU* 4.0 12.9 - - - +
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Residues in contact with GLN 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P VAL* 4.8 11.9 - - - +
7P ASP* 3.0 18.5 + - - +
8P ALA* 3.3 10.5 - - - +
10P ASN* 1.3 78.2 + - - +
12P GLY* 1.3 50.0 + - - +
14P ASP* 3.3 8.3 + - - +
15P GLU* 2.7 50.1 + - + +
154P LYS* 2.7 35.8 + - + +
182P PHE* 4.0 14.3 - - - -
187P GLN* 4.4 4.2 - - - +
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Residues in contact with GLY 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ALA 3.2 3.8 + - - -
9P ILE 3.1 7.5 + - - -
11P GLN* 1.3 78.2 - - - +
13P MET* 1.3 56.3 + - - +
15P GLU* 3.1 3.1 + - - +
16P GLU* 2.9 36.6 + - - +
154P LYS* 4.1 8.1 - - - +
157P ILE* 4.2 6.1 - - - -
158P LYS* 3.7 27.8 - - - -
161P ILE* 5.3 0.2 - - - -
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Residues in contact with MET 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P ILE* 3.0 17.2 + - + +
10P ASN* 3.7 4.0 - - - +
12P GLY* 1.3 75.4 - - - +
14P ASP* 1.3 54.3 + - - +
16P GLU* 3.2 6.6 + - - +
17P LEU* 2.7 45.0 + - + +
25P LEU* 4.2 15.7 - - + -
39P VAL* 3.8 37.7 - - + +
40P SER* 4.5 2.5 - - - -
43P LEU* 4.1 21.1 - - + -
77P ILE* 4.6 15.5 - - + -
115P ARG* 4.1 30.7 - - - +
157P ILE* 4.2 15.3 - - + -
161P ILE* 4.5 8.5 - - + +
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Residues in contact with ASP 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P ASN* 3.0 20.4 + - - +
11P GLN* 3.5 7.0 - - - +
13P MET* 1.3 79.5 - - - +
15P GLU* 1.3 65.6 + - - +
17P LEU* 4.0 10.0 - - - +
18P GLU* 3.0 21.9 + - - +
43P LEU* 3.8 15.7 - - + +
46P LYS* 2.9 23.2 + - - -
47P TYR* 2.6 40.9 + - - -
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Residues in contact with GLU 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLN* 2.7 38.6 + - + +
12P GLY 3.6 2.0 - - - +
14P ASP* 1.3 76.4 - - - +
16P GLU* 1.3 57.8 + - - +
18P GLU* 3.4 8.0 - - - +
19P ARG* 3.0 28.8 + - - +
154P LYS* 3.3 34.8 + - - -
158P LYS* 2.7 39.0 + - - +
187P GLN 3.8 5.2 - - - +
189P LYS* 3.4 29.2 - - + +
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Residues in contact with GLU 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P GLY 2.9 19.2 + - - +
13P MET 3.6 3.4 - - - +
15P GLU* 1.3 76.4 - - - +
17P LEU* 1.3 64.8 + - - +
19P ARG* 3.2 20.4 + - - +
20P ASP* 3.1 24.9 + - - +
23P VAL* 4.5 5.2 - - + +
158P LYS* 3.4 32.5 + - + +
161P ILE* 3.7 41.3 - - + +
162P ARG* 2.7 40.4 + - - -
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Residues in contact with LEU 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P MET* 2.7 37.5 + - + +
14P ASP* 3.7 6.7 - - - +
16P GLU* 1.3 74.2 - - - +
18P GLU* 1.3 60.0 + - - +
20P ASP 3.0 9.6 + - - +
21P GLU* 4.4 0.5 - - - +
23P VAL* 3.1 40.1 - - + +
24P PHE* 4.3 8.5 - - - -
25P LEU* 5.3 3.1 - - + -
43P LEU* 3.9 26.7 - - + -
47P TYR* 3.8 24.1 - - + -
51P ARG* 2.9 35.8 + - + +
52P ILE* 4.4 15.3 - - + -
77P ILE* 5.2 2.7 - - + -
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Residues in contact with GLU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ASP* 3.0 18.7 + - - +
15P GLU* 3.4 8.4 - - - +
17P LEU* 1.3 74.9 - - - +
19P ARG* 1.3 66.0 + - - +
20P ASP* 3.3 1.0 + - - -
46P LYS* 3.7 17.7 + - - -
47P TYR* 3.2 23.4 + - + +
189P LYS* 5.8 3.6 - - - +
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Residues in contact with ARG 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P GLU 3.0 13.8 + - - +
16P GLU* 3.3 23.0 + - - +
18P GLU* 1.3 81.2 - - - +
20P ASP* 1.3 69.4 + - + +
161P ILE* 6.1 0.4 - - - +
162P ARG* 3.3 56.9 - - - +
189P LYS 5.8 1.6 - - - -
190P ASP* 5.7 3.6 - - - -
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Residues in contact with ASP 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P GLU 3.1 11.7 + - - +
17P LEU 3.0 13.0 - - - +
18P GLU 3.2 2.3 + - - -
19P ARG* 1.3 94.8 + - + +
21P GLU* 1.3 63.4 + - - +
22P LYS* 2.6 43.5 + - - +
23P VAL* 3.5 12.0 + - + +
51P ARG* 3.0 6.8 + - - -
75P ARG* 3.2 28.8 + - - -
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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