Contacts of the strand formed by residues 3 - 9 (chain C) in PDB entry 6WVM
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 GLU 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 2.8 35.9 + - - -
2C ARG* 1.3 77.6 - - - +
4C CYS* 1.3 58.5 + - - +
50C ASN* 2.8 19.4 + - - +
51C THR* 3.6 4.9 - - - +
64C ARG* 3.5 37.8 + - - +
128C GLN 4.9 0.5 - - - +
129C CYS* 3.4 25.1 - - + +
130C THR* 3.0 25.3 + - - +
131C GLY 3.5 5.8 + - - +
132C LEU* 3.7 5.8 - - + +
133C GLN* 2.8 34.5 + - - +
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Residues in contact with CYS 4 (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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3C GLU* 1.3 77.9 - - - +
5C ILE* 1.3 65.2 + - - +
6C SER* 3.4 9.5 + - - -
51C THR* 2.9 20.4 + - - +
52C PHE* 4.3 8.2 - - + -
64C ARG* 3.6 9.7 - - - +
133C GLN* 4.1 8.1 - - - -
134C GLY 3.5 10.1 - - - +
136C LEU* 4.0 26.5 - - + -
239C THR* 5.2 2.2 - - - -
242C LEU* 3.5 29.6 - - - -
252C LEU* 4.2 17.5 - - - -
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Residues in contact with ILE 5 (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 CYS* 1.3 71.0 - - - +
6C SER* 1.3 61.2 + - - +
7C ILE* 4.1 14.2 + - + -
64C ARG* 3.5 9.4 - - + +
66C VAL* 5.2 0.7 - - + -
122C ILE* 4.1 14.4 - - + +
125C LEU* 4.1 27.6 - - + -
126C ALA* 3.8 27.4 - - + +
129C CYS* 4.7 5.8 - - - -
132C LEU* 3.8 33.1 - - + +
134C GLY 3.4 5.3 + - - -
135C PHE* 3.4 34.6 - - + +
136C LEU 2.9 23.6 + - - +
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Residues in contact with SER 6 (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 CYS 3.5 11.3 + - - -
5C ILE* 1.3 71.7 - - - +
7C ILE* 1.3 60.6 + - - +
8C HIS* 3.7 18.9 - - - -
21C TRP* 3.7 24.1 - - - -
24C TYR* 5.2 0.7 - - - -
52C PHE* 3.9 13.2 - - - -
64C ARG 3.0 8.8 + - - -
65C ALA* 3.1 3.6 - - - +
66C VAL 2.9 26.0 + - - +
136C LEU* 3.4 15.4 - - - +
138C PHE* 4.4 5.5 - - - -
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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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5C ILE* 4.1 11.7 - - + +
6C SER* 1.3 77.0 - - - +
8C HIS* 1.3 63.2 + - - +
9C VAL* 3.9 13.4 + - + -
66C VAL* 3.5 16.2 - - + +
68C VAL* 4.9 5.6 - - + -
122C ILE* 3.5 30.3 - - + -
135C PHE* 3.8 17.5 - - + -
136C LEU 2.9 8.1 + - - +
137C VAL* 3.5 18.0 - - + +
138C PHE* 2.8 28.6 + - - +
153C LEU* 3.8 21.8 - - + -
157C LEU* 3.8 21.8 - - + -
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Residues in contact with HIS 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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6C SER* 3.7 24.5 - - - -
7C ILE* 1.3 70.9 - - - +
9C VAL* 1.3 59.9 + - - +
13C GLY 3.0 30.4 + - - +
14C VAL* 3.6 8.1 - - + +
17C GLY* 3.3 20.0 + - - -
20C CYS* 4.7 2.2 - - + -
21C TRP* 3.1 20.8 + + - -
24C TYR* 6.4 0.2 - + - -
65C ALA* 4.5 0.2 - - + -
66C VAL 2.9 10.7 + - - +
67C PHE* 3.5 33.6 - + + -
68C VAL 2.9 27.5 + - - +
138C PHE* 3.2 41.3 - + - -
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Residues in contact with VAL 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* 3.9 24.0 - - + +
8C HIS* 1.3 74.4 - - - +
10C GLY* 1.3 70.2 + - - +
12C ALA* 5.4 0.2 - - - +
13C GLY* 3.5 12.5 + - - -
68C VAL* 3.5 8.1 - - + +
137C VAL* 5.1 4.9 - - + -
138C PHE 3.0 14.8 + - - +
139C HIS* 3.9 7.9 - - + +
140C SER* 4.6 0.9 + - - -
145C THR* 3.7 28.7 - - + +
146C GLY* 4.5 3.7 - - - +
149C PHE* 3.8 21.8 - - + -
150C THR* 3.5 26.5 - - - +
153C LEU* 4.5 7.2 - - + -
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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