Contacts of the helix formed by residues 5 - 14 (chain V) 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 THR 5 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4V MET* 1.3 76.6 - - - +
6V PRO* 1.3 79.6 - - - +
7V ARG* 4.0 7.2 + - + +
8V GLU* 3.0 44.5 - - + +
9V ILE* 2.9 30.3 + - - +
32V ARG* 3.3 10.0 + - - +
412W SER* 3.6 19.1 + - - -
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Residues in contact with PRO 6 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V THR* 1.3 87.2 - - - +
7V ARG* 1.3 59.2 + - + +
8V GLU 2.6 17.6 + - - -
9V ILE* 2.7 24.5 + - + +
10V VAL* 3.0 17.9 + - - +
28V ALA* 3.8 25.1 - - + -
29V ILE* 4.6 2.5 - - + +
32V ARG* 3.4 31.9 - - + +
408W SER 5.3 3.4 - - - +
409W PHE* 4.1 31.0 - - + +
412W SER* 4.8 3.8 - - - +
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Residues in contact with ARG 7 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V THR* 3.5 11.4 - - + +
6V PRO* 1.3 81.0 - - + +
8V GLU* 1.3 62.4 + - + +
10V VAL* 4.1 11.6 - - - +
11V SER* 3.9 12.8 + - - -
409W PHE* 3.5 41.3 - - - -
410W SER* 3.7 26.0 - - - +
412W SER* 5.9 1.8 - - - -
413W ASP* 3.2 38.5 + - - +
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Residues in contact with GLU 8 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 5.7 5.9 - - + +
5V THR* 3.0 33.4 + - + +
6V PRO 2.6 5.3 + - - -
7V ARG* 1.3 78.5 - - + +
9V ILE* 1.3 65.6 + - - +
10V VAL 2.9 3.1 + - - -
11V SER* 3.0 9.9 + - - +
12V GLU* 3.0 20.9 + - - +
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Residues in contact with ILE 9 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 4.8 14.1 - - + -
5V THR* 2.9 37.1 + - - +
6V PRO* 2.7 20.9 + - + +
8V GLU* 1.3 71.1 - - - +
10V VAL* 1.3 66.7 + - - +
12V GLU* 3.2 8.8 + - + +
13V LEU* 3.1 42.8 + - + +
28V ALA* 4.4 17.7 - - + +
31V LEU* 3.6 35.4 - - + -
32V ARG* 5.2 2.7 - - + +
70V LEU* 4.5 15.5 - - + -
73V LEU* 5.4 6.5 - - + +
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Residues in contact with VAL 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6V PRO 3.0 18.6 + - - +
7V ARG* 4.1 10.5 - - - +
9V ILE* 1.3 76.0 - - - +
11V SER* 1.3 57.1 + - - +
13V LEU* 2.6 35.2 + - - +
14V ASP* 3.0 29.7 + - - +
24V LYS* 4.6 13.2 - - + -
25V ARG* 5.0 14.1 - - + +
28V ALA* 4.8 9.6 - - + +
409W PHE* 4.6 16.4 - - + -
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Residues in contact with SER 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ARG 3.9 10.4 + - - -
8V GLU* 3.0 11.1 + - - -
10V VAL* 1.3 81.6 - - - +
12V GLU* 1.3 59.0 + - - +
14V ASP* 3.7 23.9 + - - +
15V GLN* 4.0 12.8 - - - +
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Residues in contact with GLU 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V MET* 4.2 22.4 - - - +
8V GLU 3.0 10.6 + - - +
9V ILE* 3.6 12.6 - - + +
10V VAL 2.8 1.4 + - - -
11V SER* 1.3 75.6 - - - +
13V LEU* 1.3 63.8 + - - +
15V GLN* 4.0 16.3 + - - +
16V HIS* 3.9 15.5 + - + -
73V LEU* 3.0 46.7 - - + +
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Residues in contact with LEU 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V ILE* 3.1 32.5 - - + +
10V VAL 2.6 8.1 + - - +
12V GLU* 1.3 77.0 - - - +
14V ASP* 1.3 53.0 + - - +
15V GLN 2.7 17.4 + - - -
16V HIS* 3.1 5.9 + - - +
17V ILE* 3.1 32.8 + - + +
24V LYS* 4.3 35.2 - - + +
27V VAL* 5.1 2.2 - - + -
28V ALA* 6.0 1.1 - - + +
66V ILE* 4.7 15.3 - - + +
69V ARG* 3.0 42.8 - - + +
70V LEU* 5.0 6.3 - - + -
73V LEU* 4.5 7.0 - - + -
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Residues in contact with ASP 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V VAL* 3.0 26.7 + - - +
11V SER* 3.8 17.2 + - - +
12V GLU 3.4 0.6 - - - -
13V LEU* 1.3 73.7 - - - +
15V GLN* 1.3 62.1 + - + +
16V HIS 3.6 0.9 - - - -
17V ILE 4.5 5.4 - - - -
18V ILE* 4.6 21.7 - - + +
24V LYS* 2.8 34.8 + - - +
347V GLU* 5.5 4.3 - - - +
348V PRO* 5.3 2.4 - - - +
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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