Contacts of the strand formed by residues 8 - 14 (chain C) in PDB entry 1P9Q
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 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LYS 4.0 2.0 - - - +
7C ALA* 1.3 78.4 - - - +
9C ILE* 1.3 63.3 + - - +
22C LEU* 3.3 5.3 - - - -
23C VAL* 2.8 41.5 + - + +
25C PRO* 3.7 28.9 - - + -
85C VAL* 3.8 24.5 - - + -
86C GLN 3.4 19.1 - - - +
87C ILE* 4.5 0.2 - - - -
88C THR* 5.1 5.2 - - + +
91C GLN* 3.7 28.0 - - - +
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Residues in contact with ILE 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 1.3 75.2 - - - +
10C ALA* 1.3 69.6 + - - +
11C ARG* 4.1 1.3 - - + +
20C GLU* 3.5 37.7 - - + +
21C VAL 3.4 3.6 - - - -
22C LEU* 3.7 19.7 - - + -
52C ALA* 3.9 11.4 - - + -
53C LYS* 3.9 36.1 - - + +
85C VAL* 3.9 0.3 - - - -
86C GLN* 2.8 63.2 + - - +
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL 3.9 0.6 + - - -
9C ILE* 1.3 73.5 - - - +
11C ARG* 1.3 60.5 + - - +
20C GLU* 3.3 4.5 - - - +
21C VAL* 3.0 44.8 + - + +
23C VAL* 4.3 11.0 - - + -
79C ILE* 3.4 10.4 - - + +
80C ILE* 3.9 22.9 - - + -
84C GLU 3.2 10.3 - - - +
85C VAL* 4.1 9.9 - - + +
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Residues in contact with ARG 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.1 1.1 - - + -
10C ALA* 1.3 74.7 - - - +
12C LEU* 1.3 65.8 + - - +
13C ARG* 5.0 1.0 - - - +
18C GLU* 2.7 50.7 + - - +
19C PHE 3.3 8.3 - - - +
20C GLU* 2.5 31.3 + - + +
50C LYS 5.3 0.6 + - - -
53C LYS* 6.0 0.6 - - - +
79C ILE* 3.9 4.0 - - - +
83C GLY* 3.3 2.9 - - - -
84C GLU* 2.9 56.7 + - + +
86C GLN* 2.9 29.4 + - - +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 1.3 75.1 - - - +
13C ARG* 1.3 80.1 + - - +
14C LYS* 3.8 9.8 + - + -
18C GLU* 4.4 3.6 - - - -
19C PHE* 2.9 33.6 + - + +
67C PHE* 4.2 13.0 - - + -
78C LYS* 4.0 30.3 - - + +
79C ILE* 3.9 31.2 - - + -
82C GLU* 4.1 17.0 - - + +
83C GLY* 4.0 17.3 - - - -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 5.0 1.7 - - - +
12C LEU* 1.3 84.6 - - - +
14C LYS* 1.3 60.4 + - - +
16C GLY* 3.2 36.1 + - - +
17C GLU 3.3 9.9 - - - +
18C GLU* 3.5 38.6 + - - +
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Residues in contact with LYS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.8 14.2 + - + -
13C ARG* 1.3 74.8 - - - +
15C GLY* 1.3 69.9 + - - +
16C GLY 3.2 2.2 - - - -
17C GLU* 2.8 27.9 + - - +
19C PHE* 3.8 12.6 - - + -
66C ILE* 3.5 44.0 - - + +
67C PHE* 3.6 25.6 - - + +
78C LYS* 4.2 19.6 - - + +
82C GLU* 5.6 1.8 + - - -
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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
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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