Contacts of the strand formed by residues 13 - 18 (chain d) in PDB entry 5GJQ
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 13 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7d ILE 3.7 8.1 - - - +
8d GLN* 4.7 2.5 - - + -
12d TYR* 1.3 80.3 - - - +
14d LEU* 1.3 68.4 + - - +
15d VAL* 4.0 1.5 + - + +
105d ALA* 3.6 26.7 - - + -
106d GLY 3.3 28.9 - - - +
107d TYR* 5.4 0.4 - - + -
113d PRO* 3.6 11.9 - - + -
114d ALA 3.7 9.9 - - - +
115d LEU* 4.0 21.8 - - + -
181d ARG 4.0 0.2 - - - +
182d ILE* 3.3 6.2 - - - -
183d ILE* 2.9 40.5 + - + +
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Residues in contact with LEU 14 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6d GLY* 3.2 3.3 - - - -
7d ILE* 2.9 51.2 + - + +
12d TYR* 4.1 12.9 - - + -
13d VAL* 1.3 74.5 - - - +
15d VAL* 1.3 63.9 + - - +
153d ARG 5.6 0.2 - - - +
156d ALA* 3.7 36.3 - - + +
157d VAL* 4.1 7.4 - - + +
160d LEU* 3.8 22.4 - - + -
180d VAL* 3.7 26.7 - - + -
181d ARG 3.7 7.4 - - - +
182d ILE* 4.1 11.0 - - + -
191d LEU* 4.1 15.3 - - + -
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Residues in contact with VAL 15 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5d ILE 3.3 9.4 - - - +
6d GLY* 4.5 4.5 - - - -
13d VAL* 4.2 6.1 - - + +
14d LEU* 1.3 82.9 - - - +
16d ALA* 1.3 65.4 + - - +
35d MET* 3.7 24.6 - - + +
43d LEU* 3.8 17.3 - - + -
45d LEU* 4.1 18.8 - - + -
103d LEU* 5.3 1.6 - - + -
105d ALA* 3.7 27.6 - - + -
115d LEU* 4.6 4.5 - - + -
180d VAL* 3.3 3.3 - - - +
181d ARG* 2.9 42.0 + - + +
183d ILE* 5.6 0.9 - - + -
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Residues in contact with ALA 16 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4d LEU* 3.5 1.2 - - - -
5d ILE* 2.8 49.2 + - + +
15d VAL* 1.3 78.8 - - - +
17d SER* 1.3 65.0 + - - +
35d MET* 3.9 2.7 - - - -
45d LEU* 4.3 2.4 - - - +
160d LEU* 3.8 27.6 - - + -
164d LEU* 5.1 5.4 - - + -
178d PHE* 5.2 2.0 - - + -
179d SER 3.1 12.8 - - - +
180d VAL* 4.1 4.3 - - + -
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Residues in contact with SER 17 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3d TYR* 3.2 7.4 - - - -
4d LEU* 3.6 22.7 - - - -
16d ALA* 1.3 76.9 - - - +
18d ASP* 1.3 63.9 + - - +
32d HIS 5.6 0.2 + - - -
34d LYS* 3.9 14.6 + - - +
35d MET* 3.6 19.8 - - - +
45d LEU* 3.9 7.4 - - - -
178d PHE* 3.3 11.0 - - - -
179d SER* 2.9 36.7 + - - -
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Residues in contact with ASP 18 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1d MET 4.9 0.3 - - - +
2d GLU* 3.1 10.9 - - - +
3d TYR* 2.5 42.2 + - + +
17d SER* 1.3 80.7 + - - +
19d ARG* 1.3 59.6 + - - +
20d VAL* 2.8 23.5 + - + +
32d HIS 3.9 1.9 - - - +
34d LYS* 2.7 48.4 + - - +
175d LEU* 3.7 23.5 - - + +
177d THR 3.8 8.3 - - - +
178d PHE* 3.8 16.2 - - + -
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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
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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