Contacts of the strand formed by residues 677 - 684 (chain A) in PDB entry 5ZR1
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 VAL 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649A TYR* 4.0 25.6 - - + -
650A VAL 3.4 19.3 - - - +
651A ASP* 3.8 20.4 - - + +
676A ASP* 1.3 88.2 + - + +
678A ARG* 1.3 73.2 + - - +
679A LYS 4.2 0.3 + - - -
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Residues in contact with ARG 678 (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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648A PHE 3.9 0.7 - - - +
649A TYR* 5.3 0.4 - - - -
650A VAL* 3.0 34.2 + - + +
652A THR* 3.4 31.6 - - + +
676A ASP 4.3 0.6 + - - -
677A VAL* 1.3 80.0 - - - +
679A LYS* 1.3 59.7 + - - +
680A VAL* 3.3 12.2 + - + +
725A HIS* 5.8 5.9 - - - -
769A GLY* 6.0 7.0 - - - +
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Residues in contact with LYS 679 (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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647A PHE* 3.7 47.1 - - + -
648A PHE 3.7 11.0 - - - +
649A TYR* 4.7 27.3 + - + +
660A ILE* 5.1 4.7 - - - -
677A VAL 4.2 0.4 + - - -
678A ARG* 1.3 70.6 - - - +
680A VAL* 1.3 59.9 + - - +
681A ARG* 4.1 0.9 + - - +
769A GLY 4.8 2.1 - - - +
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Residues in contact with VAL 680 (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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422A ILE* 3.7 14.1 - - + -
647A PHE* 3.6 3.3 - - - -
648A PHE* 2.9 36.0 + - + +
650A VAL* 3.7 31.4 - - + -
678A ARG* 3.3 9.9 + - + +
679A LYS* 1.3 77.9 - - - +
681A ARG* 1.3 75.2 + - - +
769A GLY* 3.4 31.0 - - - +
770A VAL* 4.0 3.1 - - - +
771A GLN* 4.3 14.1 - - + +
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Residues in contact with ARG 681 (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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422A ILE* 5.6 0.4 - - - +
645A ASP* 3.6 35.4 + - - +
646A SER 3.3 15.0 + - - +
647A PHE* 3.6 38.0 - - + +
648A PHE* 4.6 1.6 - - - +
679A LYS 5.6 0.7 - - - +
680A VAL* 1.3 83.5 - - - +
682A LEU* 1.3 63.2 + - - +
683A ARG* 3.0 47.6 - - - +
769A GLY 4.1 3.0 + - - +
770A VAL* 3.5 23.1 - - + +
771A GLN* 3.2 25.1 + - - +
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Residues in contact with LEU 682 (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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422A ILE* 3.7 31.2 - - + -
423A PHE* 4.4 12.8 - - + -
426A VAL* 3.7 30.1 - - + -
643A LEU* 3.7 15.8 - - + +
644A ASN* 3.7 1.5 - - - +
645A ASP* 2.8 26.2 + - - -
646A SER 3.1 10.3 + - - +
648A PHE* 4.3 12.8 - - + -
681A ARG* 1.3 81.0 - - - +
683A ARG* 1.3 65.3 + - - +
684A MET* 5.1 11.0 - - + -
770A VAL* 5.2 0.2 - - - -
771A GLN* 3.4 27.1 - - + +
772A THR* 4.3 2.7 - - - +
773A VAL* 5.4 0.4 - - + +
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Residues in contact with ARG 683 (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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644A ASN* 3.3 4.7 - - - +
645A ASP* 3.3 32.5 + - - +
681A ARG* 3.0 41.5 - - - +
682A LEU* 1.3 74.4 - - - +
684A MET* 1.3 65.4 + - - +
770A VAL* 4.5 11.7 - - + +
771A GLN 3.5 3.4 + - - +
772A THR* 2.9 37.5 + - - +
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Residues in contact with MET 684 (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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426A VAL* 4.0 26.2 - - + -
430A LEU* 5.4 0.7 - - + -
640A LEU* 3.7 29.4 - - + -
644A ASN* 3.2 28.6 + - + +
682A LEU* 5.1 10.5 - - + -
683A ARG* 1.3 80.2 - - - +
685A SER* 1.3 66.9 + - - +
686A ALA* 3.5 3.3 + - - +
688A ALA* 6.4 1.8 - - + -
689A ILE* 4.9 15.6 - - + +
710A CYS* 5.0 20.4 - - + +
713A ALA* 6.2 0.4 - - + -
714A ALA* 5.5 0.7 - - + -
772A THR* 4.3 1.8 - - - -
773A VAL* 4.0 40.4 - - + +
778A VAL* 6.0 2.9 - - + -
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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