Contacts of the strand formed by residues 661 - 668 (chain A) in PDB entry 3ZRH
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 LEU 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A PRO* 3.6 1.6 - - - +
619A LEU* 2.9 39.9 + - + -
620A VAL* 4.1 14.8 + - + +
626A LEU* 3.6 30.5 - - + -
644A GLU* 4.3 21.5 - - + +
647A LEU* 5.0 3.6 - - + -
648A ARG* 3.8 30.1 - - - +
653A CYS* 4.3 12.6 - - + -
654A CYS 3.7 13.5 - - - +
655A VAL* 4.2 8.5 - - + +
659A GLY 3.6 4.6 + - - -
660A VAL* 1.3 74.8 - - - +
662A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 662 (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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424A LEU* 3.8 29.2 - - + -
616A PHE* 3.9 20.0 - - + -
617A LEU 3.2 16.6 - - - +
618A PRO* 3.8 9.4 - - + -
619A LEU* 3.9 6.1 - - - +
653A CYS* 3.2 7.6 - - - +
654A CYS* 3.0 56.9 + - - +
656A THR* 4.3 6.5 - - + -
660A VAL* 4.0 10.8 - - + +
661A LEU* 1.3 80.5 - - - +
663A ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 663 (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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538A ILE* 4.3 9.2 - - + -
576A PRO* 4.4 5.8 - - + -
615A THR 3.5 1.2 - - - +
616A PHE* 3.6 1.6 - - - -
617A LEU* 2.7 38.6 + - + +
619A LEU* 3.8 26.5 - - + +
651A LEU* 4.2 26.0 - - + -
652A ASP 3.8 4.7 - - - +
653A CYS* 4.4 1.1 - - - +
662A VAL* 1.3 74.3 - - - +
664A MET* 1.3 62.7 + - - +
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Residues in contact with MET 664 (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 LYS 4.6 0.9 - - - +
575A SER* 4.3 5.5 - - - -
576A PRO* 3.6 14.3 - - - +
614A ILE* 3.8 12.3 - - + -
615A THR 3.4 3.4 - - - -
616A PHE* 3.6 36.3 - - + -
652A ASP* 3.0 60.3 + - - +
653A CYS 4.3 10.3 - - - +
654A CYS* 4.4 13.5 - - + -
662A VAL 5.2 0.2 - - - +
663A ALA* 1.3 74.9 - - - +
665A GLN* 1.3 60.9 + - - +
666A LYS* 3.9 26.7 + - - +
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Residues in contact with GLN 665 (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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380A THR* 4.0 21.9 + - - +
381A PHE 4.7 3.8 + - - +
382A THR* 4.6 11.3 - - - +
451A ALA 5.9 0.2 + - - -
575A SER* 3.5 17.9 - - - +
576A PRO* 2.8 29.2 + - + +
577A ILE* 3.9 12.9 - - - +
578A ALA* 4.7 2.4 - - - +
589A LEU 5.4 3.8 + - - -
590A VAL* 5.8 2.0 - - - +
591A ALA* 5.1 5.4 + - - +
613A THR 3.5 3.1 - - - +
615A THR* 2.8 61.2 + - - +
617A LEU* 4.4 15.8 - - + +
663A ALA 3.9 0.2 + - - -
664A MET* 1.3 72.2 - - - +
666A LYS* 1.3 62.3 + - - +
667A SER* 3.9 2.5 + - - +
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Residues in contact with LYS 666 (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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378A LEU* 5.6 3.1 - - - +
380A THR* 5.1 4.2 - - - +
575A SER* 3.8 17.7 + - - -
612A VAL* 4.5 10.8 - - + -
613A THR 3.3 3.6 - - - +
614A ILE* 3.6 28.7 - - + -
652A ASP* 3.2 26.1 + - - +
664A MET* 3.9 31.1 + - + +
665A GLN* 1.3 75.9 - - - +
667A SER* 1.3 61.5 + - - +
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Residues in contact with SER 667 (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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380A THR* 4.4 23.6 - - - -
382A THR* 3.7 19.2 + - - +
612A VAL* 3.4 7.0 - - - +
613A THR* 2.7 55.1 + - - -
665A GLN* 3.9 2.9 + - - +
666A LYS* 1.3 75.2 - - - +
668A SER* 1.3 62.2 + - - +
672A ASN* 5.1 6.1 - - - -
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Residues in contact with SER 668 (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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611A ASP 3.9 9.3 + - - -
612A VAL* 4.7 10.7 - - - +
667A SER* 1.3 77.6 - - - +
669A ARG* 1.3 64.2 + - - +
670A ARG* 3.0 26.9 + - - +
671A ARG* 3.1 24.4 + - - +
672A ASN* 3.3 17.1 + - - +
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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