Contacts of the helix formed by residues 757 - 763 (chain B) in PDB entry 2O8F
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 THR 757 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744B GLU* 3.3 13.2 - - - +
745B ILE 3.5 8.1 - - - -
746B PHE 4.1 0.4 - - - +
747B LEU* 3.6 6.6 + - - +
748B ASN* 3.5 39.7 - - - +
749B GLY* 3.7 9.6 - - - +
754B THR 3.8 1.8 - - - +
755B GLU* 3.0 25.8 + - - +
756B GLY 1.3 85.6 - - - +
758B LEU* 1.3 64.1 + - - +
759B LEU* 4.1 1.2 + - - +
760B GLU* 3.6 18.2 + - - +
761B ARG* 3.3 15.9 + - - +
1098B CYS* 3.4 7.1 - - - -
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Residues in contact with LEU 758 (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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744B GLU 3.0 9.3 + - - +
745B ILE* 3.9 21.3 - - + -
757B THR* 1.3 69.7 - - - +
759B LEU* 1.3 68.1 + - - +
761B ARG* 3.1 2.7 + - + +
762B VAL* 3.0 47.0 + - + +
778B LEU* 3.8 25.8 - - + -
1097B PRO* 3.7 31.4 - - + -
1098B CYS* 3.7 10.2 - - - -
1149B LEU* 3.7 25.8 - - + +
1152B VAL* 4.8 6.3 - - + -
1153B MET* 3.9 17.0 - - - -
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Residues in contact with LEU 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B TYR* 3.6 39.5 - - + +
745B ILE* 3.2 15.8 + - + +
746B PHE* 4.5 15.9 - - + -
747B LEU* 4.9 10.1 - - + +
757B THR* 3.4 2.9 - - - +
758B LEU* 1.3 78.2 - - - +
760B GLU* 1.3 56.7 + - - +
762B VAL* 4.3 0.4 - - - +
763B ASP* 2.9 35.4 + - + +
774B LEU* 3.8 24.0 - - + -
775B LYS* 4.4 22.9 - - + +
778B LEU* 3.8 27.3 - - + +
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Residues in contact with GLU 760 (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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55A ARG* 4.1 8.7 + - - -
755B GLU* 3.0 47.5 - - + +
756B GLY* 5.0 0.5 - - - -
757B THR* 3.6 18.9 + - - +
758B LEU 3.3 0.4 - - - -
759B LEU* 1.3 77.0 - - - +
761B ARG* 1.3 64.7 + - - +
762B VAL 3.5 0.2 + - - -
763B ASP* 3.8 17.0 + - - +
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Residues in contact with ARG 761 (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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757B THR 3.3 17.2 + - - +
758B LEU* 3.1 6.9 + - + +
760B GLU* 1.3 81.4 + - - +
762B VAL* 1.3 64.4 + - + +
763B ASP 5.1 0.3 - - - +
764B THR* 5.7 1.9 - - - +
1066B TYR* 3.6 30.6 + - + -
1071B ASP 6.0 0.2 + - - -
1074B MET* 5.3 7.9 - - - +
1095B ARG* 5.8 3.6 - - - +
1097B PRO* 3.0 34.3 + - + +
1098B CYS* 3.8 15.4 - - + +
1099B ILE 5.3 0.8 - - - +
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Residues in contact with VAL 762 (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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758B LEU* 3.0 37.4 + - + +
759B LEU* 4.3 2.2 - - - +
761B ARG* 1.3 82.7 - - + +
763B ASP* 1.3 64.0 + - - +
764B THR* 3.3 10.8 + - - +
774B LEU* 4.8 7.4 - - + -
778B LEU* 5.1 9.6 - - + -
1062B CYS* 3.3 16.7 - - - +
1063B LEU* 4.3 24.7 - - + -
1066B TYR* 4.4 29.9 - - + +
1153B MET* 4.4 17.0 - - + -
1156B MET* 5.8 0.7 - - + -
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Residues in contact with ASP 763 (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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535B TYR* 3.1 23.2 + - - -
759B LEU* 2.9 22.7 + - + +
760B GLU* 3.8 13.4 + - - +
761B ARG 3.7 0.9 - - - +
762B VAL* 1.3 75.6 - - - +
764B THR* 1.3 84.1 + - - +
765B CYS* 2.8 21.5 + - - +
771B LYS* 3.4 27.2 + - - +
774B LEU* 3.7 22.3 - - + +
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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