Contacts of the strand formed by residues 689 - 693 (chain A) in PDB entry 1OH7
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 LEU 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A ILE* 4.3 18.8 - - + -
603A LEU* 4.2 22.2 - - + -
627A THR* 4.6 3.1 - - + -
628A ALA* 4.1 27.8 - - + +
631A ALA* 4.6 6.7 - - + -
650A ILE* 4.2 13.5 - - + +
652A ARG 3.2 5.4 + - - +
653A ILE* 3.4 26.5 - - + +
654A PHE* 3.1 22.0 + - - -
687A TYR 4.1 0.8 + - - -
688A SER* 1.3 73.6 - - - +
690A VAL* 1.3 59.3 + - - +
691A LEU* 3.8 25.4 - - + -
722A LEU* 3.3 16.8 - - + +
724A LEU* 4.7 7.0 - - + -
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Residues in contact with VAL 690 (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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654A PHE* 3.6 26.5 - - + +
680A ILE* 4.0 10.5 - - + -
684A ALA* 4.1 10.5 - - + -
688A SER* 4.6 1.1 - - - -
689A LEU* 1.3 73.9 - - - +
691A LEU* 1.3 62.8 + - - +
692A MET* 3.6 34.3 - - + -
715A LEU* 4.0 20.6 - - + -
721A ALA* 4.4 9.6 - - + -
722A LEU 2.8 12.4 + - - +
723A THR* 3.2 15.5 - - + +
724A LEU 2.9 28.6 + - - +
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Residues in contact with LEU 691 (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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273A THR* 5.9 0.2 - - + -
276A ASN* 5.1 7.0 - - - +
277A LEU* 5.2 1.6 - - + -
624A MET* 3.6 40.6 - - + +
625A ARG* 4.7 2.7 - - - +
627A THR* 5.4 0.2 - - - -
628A ALA* 3.7 19.7 - - + -
653A ILE* 4.6 4.9 - - + -
654A PHE 2.7 16.1 + - - +
655A THR* 3.4 20.6 - - + +
656A ARG 3.1 24.3 + - - +
689A LEU* 3.8 28.7 - - + -
690A VAL* 1.3 79.2 - - - +
692A MET* 1.3 61.8 + - - +
693A ASP* 3.7 0.7 + - - +
724A LEU* 3.5 21.1 - - + +
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Residues in contact with MET 692 (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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624A MET* 3.9 1.7 - - - +
656A ARG* 3.8 12.8 - - + -
677A THR* 3.8 28.7 - - + -
680A ILE* 3.5 40.8 - - + -
681A LEU* 5.9 0.7 - - + -
690A VAL* 3.6 18.8 - - + -
691A LEU* 1.3 71.2 - - - +
693A ASP* 1.3 60.2 + - - +
694A GLU 3.9 0.7 - - - -
695A ILE* 3.8 21.8 - - + -
711A CYS* 5.5 2.0 - - + -
715A LEU* 4.3 12.8 - - + -
723A THR* 4.6 0.7 - - + -
724A LEU 3.0 7.9 + - - +
725A PHE* 3.5 33.4 - - + -
726A ALA 3.1 27.4 + - - +
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Residues in contact with ASP 693 (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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620A LYS* 5.4 0.2 - - - +
621A SER* 2.3 35.0 + - - -
624A MET* 3.3 18.8 - - + +
625A ARG* 5.5 1.4 + - - -
655A THR* 5.9 0.2 - - + -
656A ARG 2.8 16.2 + - - +
657A VAL* 3.8 24.2 - - + +
658A GLY 3.4 18.9 + - - +
691A LEU 3.7 1.7 + - - +
692A MET* 1.3 71.2 - - - +
694A GLU* 1.3 80.7 + - - +
695A ILE* 3.6 2.0 - - - +
726A ALA* 3.4 16.7 - - - +
1802A MG 3.6 3.5 - - - -
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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