Contacts of the strand formed by residues 88 - 93 (chain C) in PDB entry 4WNP
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LYS 3.8 0.7 - - - +
47C CYS* 3.6 4.0 - - - -
48C ILE* 3.5 33.3 + - + +
57C GLN* 3.7 35.2 - - + +
60C LEU* 3.7 28.2 - - + +
61C GLY 4.5 0.7 - - - +
64C ILE* 3.9 17.0 - - + -
82C GLN 3.5 6.7 - - - +
83C GLU* 4.1 19.1 - - + +
84C MET 4.6 0.7 - - - +
87C SER* 1.3 81.5 - - - +
89C TYR* 1.3 72.1 + - - +
90C LEU* 3.9 10.5 - - + -
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Residues in contact with TYR 89 (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 GLU* 3.8 9.9 + - - -
11C VAL* 4.1 30.5 - - + -
16C PHE* 4.0 9.0 - + - -
18C ARG* 3.1 25.6 + - - -
45C VAL* 4.1 10.5 - - + -
46C LYS 3.3 2.7 - - - +
47C CYS* 3.5 36.3 - - + -
48C ILE 6.0 0.2 - - - -
81C PHE* 3.3 5.8 - - - +
82C GLN* 2.9 54.5 + - - +
87C SER* 3.9 28.1 - - - -
88C VAL* 1.3 79.0 - - - +
90C LEU* 1.3 66.1 + - - +
91C VAL 4.3 0.2 - - - -
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Residues in contact with LEU 90 (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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44C ALA 3.5 1.6 - - - +
45C VAL* 3.3 6.1 - - - -
46C LYS* 2.9 40.6 + - + +
60C LEU* 3.9 20.4 - - + -
63C GLU* 3.7 38.6 - - + +
64C ILE* 3.6 33.9 - - + +
67C LEU* 4.8 0.7 - - + -
78C LEU* 3.9 18.8 - - + -
80C ASP 3.9 3.1 - - - -
81C PHE* 4.3 0.4 - - + +
88C VAL* 3.9 15.3 - - + -
89C TYR* 1.3 81.9 - - - +
91C VAL* 1.3 63.0 + - - +
92C MET* 3.7 12.7 + - + +
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Residues in contact with VAL 91 (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 VAL* 3.9 31.0 - - + -
14C PHE* 3.6 50.7 - - + -
43C VAL* 3.9 17.3 - - + -
44C ALA 4.0 2.0 - - - -
45C VAL* 4.6 10.1 - - + +
78C LEU* 3.7 0.9 - - - +
79C TYR* 2.8 29.1 + - + -
80C ASP* 2.8 29.7 + - + +
90C LEU* 1.3 72.1 - - - +
92C MET* 1.3 63.2 + - - +
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Residues in contact with MET 92 (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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43C VAL* 3.3 9.7 - - - +
44C ALA 2.9 37.2 + - - +
46C LYS* 4.7 6.1 - - + -
63C GLU* 4.3 11.0 - - - +
67C LEU* 3.6 32.1 - - + -
76C VAL* 3.6 34.8 - - + +
77C ALA 3.3 7.2 - - - +
78C LEU* 4.0 11.9 - - + -
79C TYR* 4.1 4.9 - - - -
90C LEU* 4.1 20.0 - - + +
91C VAL* 1.3 79.7 - - - +
93C GLU* 1.3 66.8 + - - +
164C ALA* 5.8 0.4 - - - -
165C ASP 5.6 3.6 - - - +
166C PHE* 6.3 0.2 - - + -
401C 3RJ 4.3 24.0 - - + -
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Residues in contact with GLU 93 (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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44C ALA* 4.3 0.2 - - - +
75C ILE 4.0 1.6 - - - +
76C VAL* 3.6 11.9 - - + +
77C ALA* 2.8 45.0 + - + +
79C TYR* 3.7 30.3 - - + +
92C MET* 1.3 75.7 - - - +
94C TYR* 1.3 63.8 + - - +
95C CYS* 4.5 6.3 - - - -
147C SER* 5.4 1.6 + - - -
162C LYS* 2.5 42.6 + - - +
401C 3RJ 2.6 28.4 + - - -
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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