Contacts of the helix formed by residues 91 - 96 (chain B) in PDB entry 4O8M
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 ASP 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.9 5.3 + - - +
90B SER* 1.3 85.2 + - - +
92B TYR* 1.3 64.3 + - - +
93B GLY* 3.1 9.4 + - - -
94B ALA* 3.0 28.0 + - + +
95B LEU* 2.8 33.9 + - - +
106B ASN* 4.3 4.0 + - - +
172B GLN* 3.5 27.4 - - - +
174B SER* 3.7 9.9 + - - -
176B LEU* 6.1 0.6 - - - +
177B PHE* 4.4 4.8 - - - -
235B HIS* 3.2 29.9 + - - +
238B PRO* 4.0 4.5 - - - +
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 1.3 76.0 + - - +
93B GLY* 1.3 61.9 + - - +
95B LEU* 3.3 10.3 + - + +
96B MET* 3.1 22.5 + - - +
102B LEU* 3.4 27.3 - - + +
103B GLY* 3.7 9.1 + - - +
105B ILE* 3.6 38.6 - - + -
106B ASN* 4.1 7.6 - - + +
121B LEU* 4.0 2.2 - - + +
126B PHE* 3.5 21.5 - + - -
140B ILE* 4.0 10.7 - - + +
143B PRO* 2.7 47.6 + - - +
236B MET* 3.7 20.0 - - + -
238B PRO* 3.5 29.8 - - + +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 3.1 12.2 + - - -
92B TYR* 1.3 76.1 - - - +
94B ALA* 1.3 61.4 + - - +
96B MET* 2.9 30.0 - - - +
97B ASP* 4.5 0.9 + - - +
103B GLY* 4.4 2.8 - - - -
106B ASN* 5.5 0.8 - - - +
174B SER* 3.6 14.6 - - - -
175B ARG* 4.0 7.1 + - - +
176B LEU* 3.9 23.2 - - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 5.8 0.4 - - - +
74B THR* 5.5 4.9 - - - +
77B LEU* 6.2 2.7 - - + -
90B SER* 5.0 3.6 - - - +
91B ASP* 3.0 26.6 + - + +
93B GLY* 1.3 75.0 - - - +
95B LEU* 1.3 64.1 + - + +
96B MET 3.0 1.4 + - - -
97B ASP* 3.2 26.7 + - - +
98B ILE* 5.4 0.5 - - - +
172B GLN* 5.2 1.1 - - - +
173B HIS 3.6 24.2 - - - +
174B SER* 4.0 3.1 + - - +
175B ARG 5.2 0.2 - - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 4.0 21.3 - - + -
90B SER* 3.5 23.1 - - - +
91B ASP 2.8 24.8 + - - +
92B TYR* 3.3 15.7 + - + +
94B ALA* 1.3 74.8 - - + +
96B MET* 1.3 55.5 + - - +
97B ASP 3.1 2.0 - - - -
98B ILE* 2.8 37.5 + - + +
99B VAL 2.9 13.9 + - - +
102B LEU* 3.9 13.5 - - + +
133B LEU* 4.2 22.9 - - + -
138B ILE* 4.4 9.4 - - + -
140B ILE* 4.8 1.3 - - + -
238B PRO* 4.2 15.5 - - + -
240B VAL* 4.8 4.9 - - + -
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TYR 3.1 10.1 + - - +
93B GLY 2.9 21.3 - - - +
94B ALA 3.0 1.4 + - - -
95B LEU* 1.3 74.9 - - - +
97B ASP* 1.3 63.4 + - - +
98B ILE 3.1 0.6 + - - -
99B VAL 3.4 9.4 - - - -
100B PRO* 3.3 35.6 - - - +
103B GLY* 3.8 15.3 - - - +
175B ARG* 4.2 11.0 - - + -
176B LEU* 3.8 27.4 - - - -
310B PHE* 3.7 16.8 - - + -
312B GLU* 3.7 27.6 - - + +
313B TRP* 3.2 33.0 - - + +
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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