Contacts of the strand formed by residues 8 - 12 (chain A) in PDB entry 3KCN
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 ARG 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASN* 2.9 28.8 + - - +
7A GLU* 1.3 78.1 - - - +
9A ILE* 1.3 58.4 - - - +
31A GLU* 3.6 34.4 + - + +
49A ASP* 3.5 34.4 + - - +
50A PRO* 2.9 30.8 + - - +
51A PHE* 3.5 19.2 - - + -
52A SER* 2.9 31.4 + - - -
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU 3.9 11.0 - - - +
8A ARG* 1.3 80.6 - - - +
10A LEU* 1.3 62.4 + - - +
11A LEU* 4.5 7.4 - - + -
26A LEU* 4.0 27.6 - - + -
30A PHE* 4.2 15.3 - - + -
31A GLU 2.9 13.6 + - - +
32A VAL* 4.3 13.9 - - + -
33A THR* 3.0 27.2 + - - +
51A PHE* 3.8 4.0 - - - -
52A SER* 4.3 3.1 - - - +
53A VAL* 3.2 29.2 - - + +
119A ILE* 4.1 29.8 - - + -
123A ILE* 4.6 2.9 - - + -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 1.3 74.8 - - - +
11A LEU* 1.3 72.6 + - - +
12A VAL* 4.1 12.1 - - + -
33A THR* 3.5 22.9 - - + +
35A CYS* 3.8 27.1 - - + -
41A ALA* 4.5 7.4 - - + +
44A CYS* 4.3 4.7 - - - -
45A ILE* 3.6 37.9 - - + -
51A PHE* 3.8 23.8 - - + -
53A VAL* 2.9 8.8 + - - +
54A ILE* 3.4 11.3 - - + +
55A MSE 2.8 28.1 + - - +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.5 9.4 - - + -
10A LEU* 1.3 77.1 - - - +
12A VAL* 1.3 63.3 + - - +
13A ASP 4.1 0.4 - - - -
19A LEU* 4.0 15.9 - - + +
22A LEU* 3.7 32.5 - - + -
23A LYS 4.4 2.9 - - - +
26A LEU* 4.1 16.4 - - + -
32A VAL* 3.8 26.9 - - + -
33A THR 3.0 10.0 + - - +
34A THR* 3.4 10.0 - - + -
35A CYS* 3.0 26.7 + - - +
55A MSE 3.4 39.0 - - + -
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.1 15.3 - - + -
11A LEU* 1.3 79.4 - - - +
13A ASP* 1.3 65.3 + - - +
35A CYS* 3.4 7.9 - - + +
37A SER 3.4 33.0 - - - +
38A GLY* 4.8 1.1 - - - -
41A ALA* 3.7 22.4 - - + -
54A ILE* 4.4 5.4 - - + -
55A MSE 2.8 19.9 + - - +
56A VAL* 3.5 23.2 - - + +
57A ASP 3.1 23.4 + - - -
60A MSE 4.0 11.8 - - + +
68A VAL* 5.1 0.7 - - + -
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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