Contacts of the helix formed by residues 582 - 591 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578C GLN* 5.4 0.7 - - - -
581C HIS* 1.3 73.1 - - - +
583C GLU* 1.3 60.4 + - - +
584C ARG* 3.9 5.1 + - - +
585C HIS* 3.3 15.9 + - - +
586C VAL* 3.0 31.6 + - - +
673C HIS* 2.8 36.2 + - - -
674C SER* 3.2 23.5 - - - -
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Residues in contact with GLU 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C GLN* 4.1 26.3 - - + +
582C SER* 1.3 73.1 - - - +
584C ARG* 1.3 61.9 + - - +
586C VAL* 3.4 6.0 + - - +
587C LEU* 2.9 38.3 + - + +
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Residues in contact with ARG 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C SER* 3.4 5.0 + - - +
583C GLU* 1.3 74.8 - - - +
585C HIS* 1.3 61.1 + - - +
587C LEU* 3.9 7.9 - - - +
588C LEU* 2.9 47.1 + - + +
674C SER* 5.6 8.1 + - - -
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Residues in contact with HIS 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C HIS* 3.2 30.4 + + + -
582C SER* 3.3 22.9 + - - +
584C ARG* 1.3 80.2 - - - +
586C VAL* 1.3 56.1 + - - +
588C LEU* 4.7 1.3 - - - -
589C TYR* 3.0 58.6 + + - +
673C HIS 4.0 7.9 - - - +
674C SER* 3.8 5.7 - - - -
675C THR* 3.6 17.7 + - - -
676C ALA* 3.6 22.9 + - + -
681C PHE 2.7 29.5 + - - -
682C PHE* 3.5 12.4 - + - -
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Residues in contact with VAL 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C LEU* 3.8 39.3 - - + +
577C LEU* 3.6 42.8 - - + +
578C GLN* 3.9 9.6 - - + +
581C HIS* 3.9 9.9 - - + +
582C SER 3.0 22.4 + - - +
583C GLU* 3.8 5.4 - - - +
585C HIS* 1.3 74.6 - - - +
587C LEU* 1.3 58.4 + - + +
590C GLY* 2.7 34.3 + - - -
591C THR* 4.8 0.7 - - - +
682C PHE* 4.4 7.0 - - + -
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Residues in contact with LEU 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B PHE* 5.3 11.7 - - - +
519B THR* 6.3 5.2 - - + -
574C LEU* 5.3 8.3 - - + -
583C GLU* 2.9 24.7 + - + +
584C ARG* 3.9 6.7 - - - +
586C VAL* 1.3 79.5 - - + +
588C LEU* 1.3 63.2 + - - +
589C TYR 3.4 0.2 + - - -
591C THR* 2.8 40.8 + - + +
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Residues in contact with LEU 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584C ARG* 2.9 36.3 + - + +
585C HIS* 3.9 3.1 - - - +
587C LEU* 1.3 77.9 - - - +
589C TYR* 1.3 95.0 + - + +
591C THR 3.8 9.4 - - - +
629C TRP* 4.3 7.1 - - - -
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Residues in contact with TYR 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C HIS* 3.0 51.4 + + - +
588C LEU* 1.3 106.0 - - + +
590C GLY* 1.3 54.4 + - - +
591C THR 3.5 1.6 - - - -
623C VAL* 3.2 38.9 - - + +
629C TRP* 3.5 34.6 - + + -
635C SER* 2.7 30.0 + - - -
676C ALA* 3.8 14.0 + - + +
681C PHE* 4.3 9.0 - + + -
682C PHE* 3.6 25.9 - - + -
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Residues in contact with GLY 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C LEU* 3.8 2.3 - - - +
577C LEU* 4.4 5.4 - - - -
586C VAL 2.7 23.2 + - - -
589C TYR* 1.3 71.6 - - - +
591C THR* 1.3 64.9 + - - +
635C SER* 3.3 9.2 + - - -
639C ARG* 2.8 41.9 + - - -
682C PHE* 3.8 8.4 - - - -
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Residues in contact with THR 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B ARG 4.4 0.7 - - - +
656B GLU* 3.9 33.4 - - + +
574C LEU* 4.0 24.9 - - + -
586C VAL 4.8 2.0 - - - +
587C LEU* 2.8 36.5 + - + +
588C LEU 3.8 10.6 - - - +
589C TYR 3.5 0.9 - - - -
590C GLY* 1.3 85.9 - - - +
592C ASN* 1.3 74.5 + - - +
629C TRP* 5.2 2.6 - - - -
635C SER* 4.1 5.7 + - - -
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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