Contacts of the strand formed by residues 3 - 7 (chain P) in PDB entry 1G3I
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 ILE 3 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P THR* 3.8 7.0 - - + -
2P THR* 1.3 76.3 - - - +
4P VAL* 1.3 59.8 + - - +
14P VAL* 4.2 11.4 - - + -
15P GLY 3.3 11.9 - - - +
16P GLY* 3.4 21.8 - - - -
33P LYS* 3.7 19.3 - - + +
34P VAL* 4.6 0.2 - - + -
45P GLY* 4.0 22.7 - - - +
46P PHE 3.5 26.7 - - - +
47P ALA* 3.9 15.0 - - + -
96P ILE* 3.9 8.3 - - + +
122P ALA* 2.9 5.7 - - - -
123P ILE* 2.7 48.3 + - + +
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Residues in contact with VAL 4 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P THR 4.1 0.2 + - - -
3P ILE* 1.3 77.0 - - - +
5P SER* 1.3 66.0 + - - +
6P VAL* 4.6 3.6 - - + -
14P VAL* 3.6 0.6 - - - -
15P GLY 2.9 32.0 + - - -
96P ILE* 5.1 0.4 - - - -
120P ILE* 4.4 15.0 - - + -
121P LEU 2.9 11.4 - - - +
122P ALA* 4.0 9.2 - - + -
130P ALA* 3.9 22.9 - - + +
134P ALA* 4.5 11.0 - - + -
149P VAL* 3.6 18.0 - - + +
152P SER* 4.4 3.8 - - - -
153P LEU* 3.3 30.7 - - + -
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Residues in contact with SER 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P VAL* 1.3 74.5 - - - +
6P VAL* 1.3 64.3 + - - +
7P ARG* 5.8 0.5 - - - +
12P VAL* 4.6 5.7 - - - +
13P VAL 2.6 23.1 + - - -
14P VAL* 3.1 22.2 - - - +
96P ILE* 4.2 13.5 - - - -
98P ALA* 4.9 3.5 - - - +
103P SER* 5.2 5.0 - - - -
119P GLN 3.8 2.1 - - - +
120P ILE* 3.3 5.9 - - - +
121P LEU* 2.5 47.8 + - - +
149P VAL* 4.0 0.7 - - - -
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Residues in contact with VAL 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P VAL* 4.6 2.2 - - + -
5P SER* 1.3 80.3 + - - +
7P ARG* 1.3 70.5 + - - +
8P ARG* 4.8 2.7 - - + -
13P VAL* 3.2 25.0 + - - +
118P ASP 5.6 0.4 - - - +
119P GLN 4.0 2.2 - - - -
120P ILE* 4.0 21.1 - - + +
134P ALA* 4.0 5.4 - - + -
138P VAL* 3.5 26.9 - - + -
145P ALA* 3.5 24.1 - - - +
148P ILE* 3.5 22.0 - - + -
149P VAL* 3.2 26.9 - - + +
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Residues in contact with ARG 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P SER* 5.8 0.4 - - - +
6P VAL* 1.3 76.5 - - - +
8P ARG* 1.3 71.2 + - - +
10P GLY* 5.9 4.3 - - - +
11P GLN 3.2 12.1 - - - +
12P VAL* 2.8 34.7 - - + +
98P ALA* 4.1 1.0 - - - +
99P ASP 3.3 6.5 + - - -
100P GLU 3.8 13.3 + - - -
101P LYS 3.8 16.8 + - - -
102P GLU* 2.6 38.7 + - - +
103P SER* 3.3 21.6 + - - +
118P ASP 4.1 11.3 - - - +
119P GLN* 3.5 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
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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