Contacts of the strand formed by residues 684 - 693 (chain A) in PDB entry 4Z96
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 ASP 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A LYS 4.5 3.8 - - - +
679A PHE* 3.5 30.1 - - + -
680A ASP* 3.0 41.2 + - - +
681A LYS 4.2 7.1 - - - +
682A ASP 4.8 0.9 - - - -
683A HIS* 1.3 84.7 + - - +
685A VAL* 1.3 62.0 + - - +
706A TYR* 5.6 2.0 - - + -
707A THR 3.3 10.1 - - - +
708A PRO* 3.1 28.8 - - - +
709A ILE* 4.0 4.4 - - - +
762A ASP* 3.9 2.6 - - - +
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Residues in contact with VAL 685 (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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679A PHE* 3.6 4.9 - - - -
684A ASP* 1.3 75.0 - - - +
686A MET* 1.3 61.4 + - - +
687A LEU* 3.7 21.6 + - + -
706A TYR* 3.6 2.1 - - - -
707A THR* 2.8 53.3 + - + +
709A ILE* 3.9 17.5 - - + +
753A LEU* 4.4 2.7 - - + -
760A LEU* 4.4 11.2 - - + -
761A MET* 3.2 42.8 - - - +
762A ASP* 3.2 8.7 - - - +
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Residues in contact with MET 686 (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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623A TRP* 3.2 66.9 - - + -
635A PRO* 4.2 7.6 - - + -
661A PHE* 4.4 4.3 - - + -
663A GLU* 4.2 1.3 - - - +
679A PHE* 3.6 1.9 - - + -
685A VAL* 1.3 72.1 - - - +
687A LEU* 1.3 61.7 + - - +
688A PHE* 3.7 32.2 - - + -
704A HIS* 3.7 27.8 - - + -
705A ILE 3.4 11.4 - - - +
706A TYR* 3.9 9.6 - - + -
762A ASP* 3.0 12.4 + - + +
763A GLY* 2.9 29.6 + - - +
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Residues in contact with LEU 687 (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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685A VAL* 3.7 22.8 + - + -
686A MET* 1.3 73.5 - - - +
688A PHE* 1.3 65.7 + - - +
689A LEU* 5.5 2.9 - - + -
704A HIS* 3.2 6.1 - - - +
705A ILE* 2.9 46.3 + - + +
707A THR* 4.5 3.6 - - + -
716A LEU* 4.5 7.0 - - + -
753A LEU* 3.8 24.9 - - + -
757A LEU* 5.3 2.2 - - + -
760A LEU* 4.2 9.9 - - + -
761A MET 4.2 4.0 - - - +
764A ASP* 3.6 33.2 - - + +
766A ILE* 3.7 31.9 - - + +
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Residues in contact with PHE 688 (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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575A PHE* 4.0 17.3 - + - -
583A MET* 4.7 12.1 - - + -
635A PRO* 3.5 33.9 - - + -
661A PHE* 3.9 13.9 - + - -
686A MET* 3.7 30.7 - - + -
687A LEU* 1.3 77.5 - - - +
689A LEU* 1.3 64.2 + - - +
690A LYS* 6.1 1.8 - - + -
701A TYR* 3.1 35.9 - + + -
703A GLY 3.5 2.5 - - - +
704A HIS* 3.6 12.3 - + + -
763A GLY* 3.9 17.9 - - - -
764A ASP 2.9 11.1 + - - +
765A ILE* 3.4 15.9 - - + +
766A ILE* 3.0 25.5 + - - +
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Residues in contact with LEU 689 (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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687A LEU* 5.1 3.6 - - + +
688A PHE* 1.3 76.9 - - - +
690A LYS* 1.3 66.5 + - - +
701A TYR* 3.7 6.2 - - - -
702A CYS* 2.8 50.8 + - + +
703A GLY 3.0 9.0 + - - +
705A ILE* 3.9 40.2 - - + -
719A VAL* 4.6 4.5 - - + -
720A MET* 3.6 46.2 - - + -
723A ARG* 4.2 11.4 - - - -
766A ILE* 3.5 11.9 - - + -
768A PHE* 4.0 7.9 - - + -
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Residues in contact with LYS 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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578A HIS* 4.9 5.3 + - - +
580A GLY 3.3 16.8 + - - -
582A ASP 3.0 28.2 + - - -
583A MET* 5.3 3.8 - - - +
688A PHE* 4.1 2.0 + - + -
689A LEU* 1.3 79.1 - - - +
691A MET* 1.3 60.9 + - - +
692A TYR 4.1 0.2 - - - -
699A LEU* 4.2 26.0 - - + -
700A ASN 3.8 6.3 - - - +
701A TYR* 4.6 17.3 - - + -
702A CYS* 4.7 0.2 - - - -
737A GLU* 2.6 29.0 + - - +
765A ILE* 4.2 18.8 - - + -
766A ILE 3.0 7.3 + - - -
767A VAL* 3.3 15.3 - - + -
768A PHE* 2.8 32.5 + - - -
787A PHE* 4.5 1.2 - - - -
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Residues in contact with MET 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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690A LYS* 1.3 73.7 - - - +
692A TYR* 1.3 77.3 + - - +
693A ASP* 3.9 11.7 + - + -
699A LEU* 3.6 4.8 - - - -
700A ASN* 2.9 67.1 + - + +
702A CYS* 3.8 16.3 - - - -
724A ALA* 3.7 21.3 - - + +
726A PHE* 4.1 17.9 - - + -
768A PHE* 3.2 28.9 - - + +
769A GLN* 5.0 0.7 - - - -
770A LYS 6.0 0.2 - - - -
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Residues in contact with TYR 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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690A LYS 4.0 1.2 + - - -
691A MET* 1.3 79.6 - - - +
693A ASP* 1.3 70.9 + - - +
694A PRO* 3.2 24.2 + - + +
697A ARG* 4.1 6.1 - - - -
698A SER 3.4 17.5 - - - -
699A LEU* 4.1 9.2 - - + -
767A VAL* 4.0 9.0 - - + -
768A PHE 2.7 11.9 + - - +
769A GLN* 3.2 40.2 - - + +
770A LYS 4.6 0.9 + - - -
780A LEU* 2.4 42.9 + - - +
781A PRO 3.6 7.0 - - - -
782A THR 3.6 12.8 - - - -
783A ALA* 3.5 22.2 - - + -
786A TYR* 3.6 36.0 - + + +
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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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691A MET* 3.9 16.1 + - + -
692A TYR* 1.3 76.6 - - - +
694A PRO* 1.3 66.8 - - - +
695A LYS* 3.4 16.3 + - - +
696A THR* 2.5 34.5 + - - +
697A ARG* 3.0 18.5 + - - -
698A SER* 3.1 21.5 + - - +
700A ASN* 4.3 6.1 - - - +
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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