Contacts of the strand formed by residues 672 - 677 (chain A) in PDB entry 3ZHT
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 ILE 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A VAL* 4.2 20.4 - - + -
638A VAL* 4.1 20.6 - - + -
639A PRO 2.9 9.1 + - - +
640A LEU* 3.4 24.2 - - + +
641A MET 2.8 30.8 + - - -
671A THR* 1.3 75.5 - - - +
673A HIS* 1.3 55.5 + - - +
674A ILE* 4.6 0.7 - - + -
724A ALA* 3.5 38.4 - - + +
725A VAL* 3.9 13.5 - - + +
728A ARG* 3.7 20.0 - - + -
735A VAL* 3.8 7.2 - - + +
737A ILE* 4.3 19.3 - - + -
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Residues in contact with HIS 673 (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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614A GLU* 5.1 0.4 - - - -
641A MET* 3.4 29.5 - - + +
643A HIS* 2.8 28.7 + + + +
648A PHE* 4.2 5.6 - + + -
654A VAL* 6.2 0.4 - - + -
657A THR* 6.1 1.8 - - + -
658A LEU* 3.8 16.7 - - + +
671A THR* 3.6 20.6 - - + +
672A ILE* 1.3 72.3 - - - +
674A ILE* 1.3 60.6 + - - +
675A VAL 4.1 0.2 - - - -
734A ASP* 2.8 30.6 + - + -
735A VAL 2.9 16.6 + - - +
736A VAL* 4.0 27.6 - - + -
737A ILE* 2.8 33.9 + - - +
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Residues in contact with ILE 674 (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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514A VAL* 3.8 23.3 - - + -
517A MET* 3.9 31.0 - - + -
518A MET* 4.0 21.5 - - + -
521A VAL* 4.2 14.6 - - + -
640A LEU* 3.8 24.9 - - + -
641A MET 2.9 9.7 + - - +
642A LEU* 3.2 14.8 - - + +
643A HIS* 3.0 23.7 + - - +
672A ILE* 4.1 1.1 + - + -
673A HIS* 1.3 77.5 - - - +
675A VAL* 1.3 72.7 + - - +
676A VAL* 3.8 1.0 + - + -
737A ILE* 3.4 14.8 - - + +
739A MET* 4.9 2.9 - - + -
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Residues in contact with VAL 675 (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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643A HIS* 3.5 12.8 - - + +
644A GLY 3.8 6.3 - - - +
645A ASP* 3.7 22.4 - - - +
648A PHE* 3.9 22.0 - - + -
674A ILE* 1.3 74.0 - - - +
676A VAL* 1.3 61.0 + - - +
677A ASN* 3.1 8.2 + - + +
695A CYS* 3.6 23.6 - - - -
696A THR* 3.7 23.3 - - + -
736A VAL* 4.4 4.9 - - + -
737A ILE 2.8 15.3 + - - +
738A ASP* 4.3 7.9 - - - +
739A MET* 2.9 31.2 + - - +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU* 4.9 9.9 - - + -
511A ALA* 3.8 29.6 - - + +
514A VAL* 4.0 27.8 - - + -
540A ARG* 5.2 9.2 - - + +
642A LEU* 4.4 14.8 - - + -
643A HIS 2.8 18.9 + - - +
644A GLY* 4.0 4.9 - - - -
645A ASP* 3.7 13.9 + - - +
674A ILE* 4.6 3.4 - - + +
675A VAL* 1.3 69.5 - - - +
677A ASN* 1.3 58.4 + - - +
678A ASN* 3.2 18.8 + - - +
739A MET* 4.2 7.6 - - + -
741A CYS* 3.8 7.0 - - - -
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Residues in contact with ASN 677 (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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645A ASP* 3.3 26.4 - - + +
675A VAL* 3.1 4.0 + - + +
676A VAL* 1.3 70.7 - - - +
678A ASN* 1.3 54.6 + - - +
679A GLN* 3.2 22.4 + - - +
690A ARG* 5.1 8.5 + - - +
694A TYR* 6.1 0.6 - - - -
695A CYS* 3.9 8.5 - - - +
738A ASP* 2.8 37.3 + - - +
739A MET 3.0 15.4 + - - +
740A LEU* 3.5 17.3 - - - +
741A CYS* 2.9 24.6 + - - +
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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