Contacts of the strand formed by residues 695 - 702 (chain A) in PDB entry 5IJ7
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 CYS 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A ILE* 3.5 30.5 - - - -
693A PRO* 3.4 22.5 - - - +
694A ASN* 1.4 86.1 - - - +
696A TYR* 1.3 64.2 + - - +
710A ILE* 3.9 16.6 - - + -
711A PHE 3.2 8.7 - - - +
713A LYS* 3.9 5.1 - - - +
716A ILE* 4.0 1.1 - - - -
722A LEU* 3.9 30.1 - - - -
723A PHE 3.1 11.5 + - - +
724A PHE* 3.4 11.8 - - + +
725A ASP 4.4 0.5 + - - -
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Residues in contact with TYR 696 (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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574A TYR* 5.6 1.4 + - - -
635A ASN* 2.8 30.2 + - - +
695A CYS* 1.3 75.9 - - - +
697A ALA* 1.3 69.0 + - - +
698A LYS* 4.4 21.5 + - + -
709A GLY 3.7 0.2 - - - +
710A ILE* 3.4 6.7 - - - -
711A PHE* 2.8 67.4 + + + +
712A ALA 3.2 20.6 - - - -
713A LYS* 3.7 27.8 - - + -
724A PHE* 4.3 5.2 - - - -
725A ASP 5.7 0.7 - - - +
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Residues in contact with ALA 697 (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 TYR* 1.3 78.4 - - - +
698A LYS* 1.3 60.8 + - - +
699A VAL* 6.0 0.4 - - + -
708A ILE* 3.9 11.0 - - + -
709A GLY 3.3 5.2 - - - -
710A ILE* 3.5 20.9 - - + -
724A PHE* 4.2 11.4 - - + -
725A ASP 6.0 0.2 - - - +
728A TYR* 6.2 0.5 - - - +
729A SER* 3.8 22.7 - - - +
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Residues in contact with LYS 698 (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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574A TYR* 3.7 35.1 + - - -
577A VAL* 4.2 22.7 - - + +
696A TYR* 4.2 22.5 + - + -
697A ALA* 1.3 76.2 - - - +
699A VAL* 1.3 64.6 + - - +
700A MET* 3.5 31.7 + - + +
708A ILE* 4.4 0.9 - - - -
709A GLY* 2.8 37.0 + - - -
711A PHE* 3.7 28.9 - - + -
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Residues in contact with VAL 699 (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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517A VAL* 6.0 1.6 - - + -
577A VAL* 3.4 19.9 - - - +
668A ASN 4.3 9.4 - - - +
669A LEU* 3.5 27.8 - - + +
697A ALA* 4.2 1.3 - - + -
698A LYS* 1.3 72.5 - - - +
700A MET* 1.3 59.5 + - - +
706A HIS* 3.8 28.9 - - + +
707A ARG 3.4 7.0 - - - +
708A ILE* 3.7 26.0 - - + -
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Residues in contact with MET 700 (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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574A TYR* 6.3 1.3 - - - -
577A VAL* 3.4 19.1 - - + +
578A ARG 4.7 1.8 - - - -
579A GLU* 3.6 24.5 - - + +
603A ASN* 4.5 11.2 - - - +
606A ILE* 3.5 21.5 - - + -
698A LYS* 3.6 36.6 - - + +
699A VAL* 1.3 79.1 - - - +
701A MET* 1.3 61.7 + - - +
702A VAL* 3.6 14.7 + - + +
706A HIS* 3.3 6.6 - - - -
707A ARG 2.8 32.4 + - - +
711A PHE* 3.6 22.4 - - + -
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Residues in contact with MET 701 (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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520A TYR* 4.1 15.7 - - + -
541A ASN* 4.4 12.8 - - - +
544A GLU* 4.1 9.0 - - - +
577A VAL 3.1 9.0 + - - +
578A ARG* 3.4 39.5 + - + +
579A GLU 3.1 23.4 + - - +
700A MET* 1.3 68.6 - - - +
702A VAL* 1.3 57.5 + - - +
703A ASN 4.1 1.9 + - - +
704A GLY* 3.6 38.1 - - - +
705A ASP 3.6 7.4 - - - +
706A HIS* 3.4 33.6 + - + +
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Residues in contact with VAL 702 (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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579A GLU* 3.6 38.8 - - + +
606A ILE* 4.0 6.7 - - + -
607A GLN* 3.6 26.9 - - + +
700A MET* 3.8 18.2 - - + +
701A MET* 1.3 75.4 - - - +
703A ASN* 1.3 70.2 + - + +
705A ASP* 2.7 28.2 + - - +
707A ARG* 3.9 37.1 + - + +
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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