Contacts of the strand formed by residues 585 - 591 (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 HIS 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A ASP* 4.6 9.6 - - - -
407A VAL* 4.4 2.6 - - - +
437A ASN* 2.8 31.5 + - - -
439A THR* 3.4 32.6 - - + +
443A CYS* 3.4 23.9 - - + +
580A GLY 3.6 0.3 - - - +
581A TYR* 3.4 7.9 - - - -
582A THR* 2.4 54.6 + - - +
583A ARG* 3.6 30.9 + - - +
584A GLY* 1.3 72.3 - - - +
586A PHE* 1.3 70.6 + - - +
587A SER* 3.9 13.9 + - - -
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Residues in contact with PHE 586 (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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437A ASN* 3.0 13.7 + - - -
443A CYS* 3.4 23.7 - - - +
444A LEU* 3.9 31.9 - - + -
447A SER* 3.0 19.2 + - - +
521A LEU 4.1 15.9 - - - -
526A ILE* 3.5 33.9 - - + -
539A VAL* 4.5 7.6 - - + -
558A PHE* 3.8 13.9 - + - -
579A LEU* 4.2 17.7 - - + -
580A GLY 3.3 8.1 - - - -
581A TYR* 3.7 33.2 - + + -
584A GLY 5.6 0.9 - - - -
585A HIS* 1.3 81.3 - - - +
587A SER* 1.3 62.5 + - - +
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Residues in contact with SER 587 (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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404A ASP* 5.0 1.6 - - - +
407A VAL* 3.8 37.2 - - - +
434A ALA* 4.3 5.3 - - - +
435A LEU 4.0 15.3 + - - -
437A ASN* 4.1 3.4 - - - +
447A SER* 3.2 7.6 - - - -
579A LEU* 3.2 4.9 - - - -
580A GLY* 2.7 43.4 + - - -
582A THR* 5.4 0.2 + - - -
585A HIS* 3.9 9.1 + - - -
586A PHE* 1.3 75.2 + - - +
588A ALA* 1.3 65.6 + - - +
589A LEU* 5.2 0.4 - - - -
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Residues in contact with ALA 588 (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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433A TYR 3.3 1.6 - - - +
434A ALA* 3.4 4.5 - - - -
435A LEU* 3.0 44.0 + - + +
437A ASN* 4.8 0.8 - - - +
447A SER* 3.2 32.0 + - - +
450A GLN* 4.1 11.6 + - + +
451A ALA* 3.9 20.0 - - + +
578A ALA 4.0 4.7 - - - -
579A LEU* 4.1 2.5 - - - -
587A SER* 1.3 71.7 - - - +
589A LEU* 1.3 58.8 + - - +
590A VAL* 4.0 1.6 - - + -
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A LEU* 4.5 6.3 - - + -
418A ILE* 3.7 44.0 - - + -
432A LEU* 4.4 14.9 - - + +
433A TYR 3.3 3.4 - - - +
434A ALA* 3.6 32.3 - - + +
451A ALA* 5.4 0.9 - - - +
540A TYR* 3.9 12.6 - - + -
578A ALA* 2.9 38.6 + - + +
579A LEU 3.7 6.3 - - - +
580A GLY* 3.5 33.2 - - - +
587A SER* 3.4 0.9 + - - +
588A ALA* 1.3 71.7 - - - +
590A VAL* 1.3 62.5 + - - +
665A GLN* 5.4 3.5 + - - -
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Residues in contact with VAL 590 (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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381A PHE* 3.7 27.6 - - + +
383A LEU* 3.9 20.9 - - + -
432A LEU* 3.5 4.4 - - - -
433A TYR* 2.8 42.3 + - - +
435A LEU* 3.8 45.3 - - + -
451A ALA* 4.2 21.8 - - + +
588A ALA* 4.4 0.4 - - + -
589A LEU* 1.3 80.7 - - - +
591A ALA* 1.3 62.1 + - - +
665A GLN* 5.8 2.2 - - - +
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Residues in contact with ALA 591 (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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381A PHE 4.8 2.2 + - - -
382A THR* 3.4 11.1 - - + +
383A LEU* 3.0 23.9 + - - +
429A ASP 5.2 0.2 - - - +
430A SER* 4.8 5.6 - - - +
431A ARG 3.5 15.5 - - - +
432A LEU* 4.3 2.6 - - + +
433A TYR* 4.3 3.1 - - - -
590A VAL* 1.3 77.0 - - - +
592A MET* 1.3 65.2 + - - +
615A THR* 3.5 40.2 - - + +
665A GLN* 5.1 5.8 + - - +
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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