Contacts of the strand formed by residues 766 - 771 (chain A) in PDB entry 3OPY
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 766 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765A ARG* 1.4 77.2 - - - +
767A PHE* 1.3 68.6 + - - +
768A VAL* 5.4 0.7 - - + -
811A LEU* 3.6 29.2 - - + +
815A TYR* 3.7 9.1 + - - -
826A LYS 3.4 8.5 - - - +
828A PHE* 3.7 35.0 - - + -
847A ILE* 4.0 21.5 - - + -
855A PHE* 4.2 8.8 - - - +
856A GLU 3.2 6.6 + - - +
857A SER* 3.4 2.3 - - - -
858A ARG* 2.9 25.3 + - - +
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Residues in contact with PHE 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A VAL* 3.4 38.8 - - + -
758A SER* 4.2 13.5 - - - -
759A ALA* 3.7 28.5 - - + -
763A ARG* 6.3 0.2 - - + -
764A ARG* 3.5 32.5 - - + -
765A ARG 4.4 0.2 - - - -
766A THR* 1.3 78.8 - - - +
768A VAL* 1.3 63.4 + - - +
769A VAL* 3.6 4.2 + - + -
826A LYS 3.0 8.0 + - - -
827A ILE* 3.4 7.7 - - + +
828A PHE* 2.8 29.6 + - - +
858A ARG* 3.2 28.3 - - + -
859A THR 4.5 4.7 - - - -
860A ALA* 4.3 14.8 - - + -
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Residues in contact with VAL 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A THR* 5.4 0.9 - - + -
767A PHE* 1.3 75.6 - - - +
769A VAL* 1.3 58.7 + - - +
828A PHE* 3.6 14.8 - - + +
830A HIS* 3.8 21.1 - - + -
840A THR* 3.6 32.4 - - + +
843A ILE* 4.3 9.6 - - + -
844A ALA* 3.8 30.3 - - + +
847A ILE* 3.8 20.9 - - + -
857A SER* 5.5 0.9 - - - -
858A ARG 2.7 14.7 + - - +
859A THR* 3.4 2.8 - - - -
860A ALA* 3.0 25.5 + - - +
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Residues in contact with VAL 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A LEU* 5.3 1.3 - - + -
751A TYR* 4.8 1.3 - - + -
752A CYS* 3.9 26.5 - - - -
755A VAL* 4.2 27.8 - - + -
767A PHE* 4.5 4.7 - - + -
768A VAL* 1.3 70.8 - - - +
770A GLU* 1.3 63.3 - - - +
771A VAL* 3.7 11.5 + - + -
827A ILE* 4.6 6.5 - - + -
828A PHE 3.0 12.6 + - - +
829A ILE* 3.5 9.0 - - + +
830A HIS* 2.9 24.6 + - - -
860A ALA* 3.5 19.7 - - + -
862A PRO* 4.1 23.6 - - + -
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Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A VAL 3.6 0.8 + - - -
769A VAL* 1.3 71.5 - - - +
771A VAL* 1.3 61.6 + - - +
772A GLN* 3.6 12.8 + - - +
830A HIS 3.1 11.9 - - - +
832A GLU* 3.3 32.2 - - + +
840A THR* 3.2 35.1 + - + +
860A ALA 2.9 16.1 + - - +
861A VAL* 3.5 29.1 - - + +
862A PRO* 3.4 21.2 - - - +
863A GLY 4.7 0.7 + - - -
866A GLN* 3.9 5.0 - - - +
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Residues in contact with VAL 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A LEU* 3.8 27.4 - - + -
769A VAL* 3.7 9.8 + - + -
770A GLU* 1.3 74.3 - - - +
772A GLN* 1.3 60.9 + - - +
773A GLY 4.2 2.2 - - - +
779A LEU* 3.7 22.9 - - + -
780A ALA* 3.7 31.0 - - + +
783A ALA* 4.4 6.7 - - + -
829A ILE* 3.8 27.6 - - + -
830A HIS 2.8 9.3 + - - +
831A ASN* 3.2 9.2 - - - +
832A GLU 2.8 26.1 + - - -
866A GLN* 3.9 2.0 - - - -
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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