Contacts of the strand formed by residues 721 - 725 (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 MET 721 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A PHE* 4.1 10.3 - - + -
692A LEU* 3.4 29.2 - - + +
704A LEU* 3.5 17.7 - - + -
707A LEU* 3.7 44.4 - - + -
711A ARG* 4.9 0.2 - - - -
717A PHE* 3.8 31.0 - - + +
719A ILE* 3.3 15.6 + - + +
720A PRO* 1.3 76.9 - - - +
722A CYS* 1.3 63.1 + - - +
889A PHE* 4.3 1.0 - - - -
890A ILE* 4.0 3.5 - - - +
934A THR 3.0 9.5 + - - +
935A SER* 3.3 16.2 - - - +
936A VAL 3.0 23.4 + - - -
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Residues in contact with CYS 722 (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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692A LEU 3.0 9.0 + - - +
693A ILE* 3.6 9.6 - - - -
694A ILE* 2.8 35.0 + - - +
704A LEU* 4.1 6.3 - - - -
721A MET* 1.3 75.6 - - - +
723A CYS* 1.4 55.0 + - - +
886A CYS* 3.5 38.6 - - - -
889A PHE* 4.6 1.6 - - + -
890A ILE* 4.0 19.1 - - + -
936A VAL* 3.1 16.8 - - + +
938A ILE* 3.7 19.5 - - + -
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Residues in contact with CYS 723 (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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694A ILE* 3.3 4.9 - - + +
696A GLY 4.5 3.4 - - - -
697A GLY 4.5 1.1 - - - -
700A ALA* 3.8 17.9 - - - +
701A PHE* 3.8 30.3 - - - -
704A LEU* 4.0 21.2 - - + +
722A CYS* 1.4 73.9 - - - +
724A LEU* 1.3 69.6 + - - +
725A PRO* 3.3 14.6 - - - +
732A VAL* 4.6 3.4 - - - -
886A CYS* 5.2 0.4 - - - -
936A VAL 3.1 6.1 + - - -
937A VAL* 3.8 10.6 - - + -
938A ILE* 3.1 24.4 + - - +
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Residues in contact with LEU 724 (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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616A ALA* 4.5 12.1 - - + +
693A ILE* 4.3 4.5 - - + -
694A ILE 3.0 7.1 + - - +
695A ILE* 3.4 24.0 - - + +
696A GLY 3.0 25.1 + - - +
722A CYS 4.1 1.2 + - - -
723A CYS* 1.3 71.2 - - - +
725A PRO* 1.3 75.0 - - + +
726A ALA 3.2 0.2 + - - -
739A LEU* 4.0 22.7 - - + -
882A LEU* 3.5 33.2 - - + -
883A ALA* 4.0 23.1 - - + +
886A CYS* 3.8 26.9 - - - -
938A ILE 4.2 3.6 - - - +
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Residues in contact with PRO 725 (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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696A GLY 3.3 6.5 - - - +
723A CYS* 3.3 6.9 - - - +
724A LEU* 1.3 81.3 - - + +
726A ALA* 1.3 60.3 + - - +
732A VAL* 4.0 20.6 - - + -
735A THR* 3.7 32.3 - - + -
737A TYR 4.5 2.4 - - - +
738A SER* 3.5 6.0 - - - -
739A LEU* 3.0 26.6 + - - +
882A LEU* 5.6 1.8 - - + +
937A VAL* 4.0 18.6 - - + -
938A ILE 3.0 29.2 - - - +
939A GLY* 4.9 0.4 - - - -
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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