Contacts of the strand formed by residues 6 - 10 (chain C) in PDB entry 3KHU
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 LYS 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.8 0.7 - - - +
5C LYS* 1.3 88.5 - - + +
7C ILE* 1.3 65.0 + - - +
31C ARG* 3.4 25.5 - - + +
81C GLU* 3.6 55.4 + - + +
82C ALA* 4.1 3.8 - - - -
83C ASP* 2.9 32.8 + - - +
84C LEU 3.2 7.6 + - - -
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Residues in contact with ILE 7 (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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4C ILE* 3.7 19.5 - - + -
6C LYS* 1.3 78.6 - - - +
8C CYS* 1.3 65.2 + - - +
20C CYS* 4.6 1.6 - - - -
23C ILE* 4.0 23.8 - - + -
30C ILE* 3.8 19.1 - - + -
31C ARG 2.8 12.1 + - - +
32C VAL* 3.4 15.6 - - + -
33C THR* 2.8 29.1 + - - -
82C ALA* 4.4 1.3 - - - -
84C LEU* 3.3 21.5 - - + +
86C PHE* 3.7 31.9 - - + -
198C VAL* 4.6 10.1 - - + -
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Residues in contact with CYS 8 (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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7C ILE* 1.3 77.5 - - - +
9C CYS* 1.3 55.1 + - - +
10C ILE* 4.2 13.5 - - - -
33C THR* 3.3 6.1 - - - +
35C VAL* 4.0 18.2 - - - -
78C ALA* 3.5 47.1 - - + +
79C ILE* 3.9 9.4 - - - +
82C ALA* 3.7 10.0 - - + +
84C LEU 2.9 8.1 + - - +
85C VAL* 3.2 6.6 - - + -
86C PHE* 2.7 32.9 + - - +
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Residues in contact with CYS 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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7C ILE* 4.2 0.4 - - - +
8C CYS* 1.3 73.8 - - - +
10C ILE* 1.3 62.0 + - - +
11C GLY 3.3 19.7 + - - -
16C GLY* 3.9 9.9 - - - -
20C CYS* 3.3 36.3 - - + -
32C VAL* 5.9 0.2 - - - +
33C THR 2.9 12.2 + - - +
34C VAL* 3.5 6.2 - - - +
35C VAL* 3.0 26.7 + - - -
86C PHE* 3.5 12.3 - - + -
88C SER* 3.7 20.2 - - - -
129C LYS* 5.0 1.1 - - - -
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Residues in contact with ILE 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 CYS* 4.2 4.9 - - - -
9C CYS* 1.3 67.8 - - - +
11C GLY* 1.3 59.4 + - - +
35C VAL* 3.8 18.8 - - + -
75C ILE* 4.8 8.5 - - + -
79C ILE* 4.0 16.6 - - + -
85C VAL* 3.9 23.6 - - + -
86C PHE 2.9 17.1 + - - +
87C ILE* 4.7 2.0 - - + -
88C SER* 2.8 31.2 + - - -
89C VAL* 3.7 2.3 - - + +
112C CYS* 3.5 34.8 - - + +
115C ARG* 5.6 1.1 - - + -
116C ILE* 3.9 21.8 - - + -
502C UPG 4.0 20.2 - - + +
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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