Contacts of the helix formed by residues 582 - 591 (chain B) in PDB entry 3ZNS
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 SER 582 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578B GLN* 4.7 0.7 - - - -
581B HIS* 1.3 76.2 - - - +
583B GLU* 1.3 65.1 + - - +
584B ARG* 3.4 31.0 - - - +
585B HIS* 3.3 22.1 + - - +
586B VAL* 3.1 22.9 + - - +
673B HIS* 2.9 34.7 + - - -
674B SER* 3.6 6.2 - - - -
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Residues in contact with GLU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B GLN* 3.8 30.7 + - - +
582B SER* 1.3 71.2 - - - +
584B ARG* 1.3 61.8 + - - +
586B VAL* 3.2 2.3 + - - +
587B LEU* 2.9 41.2 + - + +
603B LYS* 2.9 40.6 + - - +
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Residues in contact with ARG 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B SER* 3.4 20.6 + - - +
583B GLU* 1.3 77.4 - - - +
585B HIS* 1.3 61.8 + - + +
587B LEU* 3.4 10.4 + - - +
588B LEU* 3.0 30.8 + - - +
607B LEU* 5.4 0.9 - - - +
610B GLN* 4.9 8.3 - - - +
673B HIS* 4.9 4.9 + - - -
674B SER* 3.2 30.9 + - - -
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Residues in contact with HIS 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B HIS* 3.6 28.0 + + + -
582B SER* 3.3 18.8 + - - +
583B GLU 3.2 0.6 - - - -
584B ARG* 1.3 84.1 - - + +
586B VAL* 1.3 57.4 + - - +
588B LEU* 4.4 5.4 - - - -
589B TYR* 3.1 62.3 + + - +
673B HIS 4.1 9.0 - - - +
674B SER* 3.8 7.3 + - - -
675B THR* 3.7 15.1 + - - -
676B ALA* 3.5 19.5 + - + -
681B PHE 2.8 27.1 + - - -
682B PHE* 3.6 11.7 - + - -
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Residues in contact with VAL 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B LEU* 3.6 43.3 - - + +
577B LEU* 3.7 26.5 - - + -
578B GLN* 3.5 26.9 - - + +
581B HIS* 4.1 10.5 - - + -
582B SER 3.1 17.9 + - - +
583B GLU* 3.7 4.9 - - + +
585B HIS* 1.3 73.7 - - - +
587B LEU* 1.3 61.6 + - + +
590B GLY* 2.8 32.7 + - - -
591B THR* 4.5 0.5 - - - +
682B PHE* 4.3 8.3 - - + -
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B LEU* 5.3 5.4 - - + -
583B GLU* 2.9 32.3 + - + +
584B ARG* 3.7 8.3 - - - +
586B VAL* 1.3 78.3 - - + +
588B LEU* 1.3 61.6 + - - +
591B THR* 2.8 36.3 + - + -
599B LEU* 3.6 40.2 - - + -
603B LYS* 4.0 35.4 - - + +
607B LEU* 4.1 22.6 - - + +
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Residues in contact with LEU 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B ARG 3.0 17.6 + - - +
585B HIS* 3.6 7.4 - - - +
586B VAL 3.2 0.4 - - - -
587B LEU* 1.3 79.8 - - - +
589B TYR* 1.3 97.4 + - + +
591B THR 4.3 6.9 - - - +
607B LEU* 4.6 9.2 - - + -
610B GLN* 3.2 45.5 - - + +
629B TRP* 4.4 6.2 - - - -
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Residues in contact with TYR 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B HIS* 3.1 54.9 + + - -
588B LEU* 1.3 106.5 - - + +
590B GLY* 1.3 54.0 + - - +
591B THR 3.6 1.6 - - - -
623B VAL* 3.7 33.3 - - + +
629B TRP* 3.4 34.3 - + + -
635B SER* 2.7 33.4 + - - -
638B ALA* 5.4 0.2 - - - +
676B ALA* 3.8 16.8 + - + +
681B PHE* 4.1 10.5 - + + -
682B PHE* 3.6 22.6 - - + -
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Residues in contact with GLY 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B LEU* 3.8 8.0 - - - +
577B LEU* 4.7 0.7 - - - -
586B VAL 2.8 16.3 + - - -
589B TYR* 1.3 76.9 - - - +
591B THR* 1.3 66.2 + - - +
597B LEU* 5.2 0.3 - - - +
635B SER* 3.2 9.4 + - - -
639B ARG* 3.3 39.0 + - - -
682B PHE* 3.8 9.3 - - - -
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Residues in contact with THR 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B LEU* 4.2 14.1 - - + -
586B VAL 4.5 0.2 - - - +
587B LEU* 2.8 40.2 + - + +
588B LEU 4.3 10.0 - - - +
589B TYR 4.5 0.2 - - - -
590B GLY* 1.3 82.6 - - - +
592B ASN* 1.3 71.9 + - - +
593B PRO* 4.4 3.0 - - - +
595B SER* 4.2 3.8 - - - -
597B LEU* 3.4 32.3 - - + -
599B LEU* 4.9 4.3 - - + +
607B LEU* 4.7 9.2 - - - +
629B TRP* 5.1 2.1 - - - -
635B SER* 3.8 6.7 + - - -
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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