Contacts of the helix formed by residues 584 - 592 (chain D) in PDB entry 6V3O
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 584 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491D LEU* 3.4 36.8 - - + -
495D ARG* 4.2 5.2 - - - +
544D LEU* 5.5 6.5 - - + -
580D ARG* 3.5 41.5 - - - +
581D LEU* 3.2 10.3 + - - +
582D PHE 3.2 1.2 - - - -
583D SER* 1.3 79.0 - - - +
585D ASP* 1.3 70.6 + - - +
586D TRP 3.7 10.1 - - - +
587D TYR* 3.2 13.3 + - + +
588D MET* 3.1 25.2 + - - +
1003D SO4 4.9 4.5 - - - +
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Residues in contact with ASP 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D ARG* 2.8 39.4 + - - +
583D SER 3.9 3.0 + - - -
584D VAL* 1.3 71.7 - - - +
586D TRP* 1.3 79.5 + - - -
588D MET* 3.4 5.2 + - - +
589D ASP* 3.1 31.2 + - - +
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Residues in contact with TRP 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D LEU* 4.6 8.1 - - + -
494D LEU* 3.3 65.5 + - + -
495D ARG* 4.4 13.9 - - + -
544D LEU* 4.8 3.4 - - + -
547D GLU* 4.0 25.6 - - + -
551D ARG* 4.3 11.0 - - + +
584D VAL* 3.3 7.3 - - + +
585D ASP* 1.3 87.8 + - - +
587D TYR* 1.3 80.3 + + + +
589D ASP* 3.3 10.4 + - + +
590D ARG* 3.1 52.4 + - + +
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Residues in contact with TYR 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D VAL* 3.7 28.6 - - + +
544D LEU* 4.0 21.1 - - + -
547D GLU* 3.6 25.2 + - + -
561D VAL* 4.0 5.5 + - - +
581D LEU* 3.6 44.6 - - + +
582D PHE* 4.6 4.5 - + - -
584D VAL* 3.2 13.2 + - + +
586D TRP* 1.3 87.4 - + + +
588D MET* 1.3 66.1 + - - +
590D ARG* 3.1 2.1 + - + +
591D ILE* 3.0 49.5 + - + +
595D GLN* 2.5 36.4 + - - -
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Residues in contact with MET 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D PHE* 3.1 46.4 - - - +
584D VAL 3.1 17.0 + - - +
585D ASP* 3.8 6.5 - - - +
586D TRP 3.3 0.2 - - - -
587D TYR* 1.3 75.9 - - - +
589D ASP* 1.3 64.4 + - - +
591D ILE* 4.0 8.9 - - - +
592D LYS* 3.2 21.7 + - - -
593D GLY* 4.5 3.7 + - - +
631D TYR* 3.6 31.9 - - + +
633D VAL* 3.9 18.6 - - + -
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Residues in contact with ASP 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D ASP* 3.1 19.6 + - - +
586D TRP* 3.6 12.3 - - + +
587D TYR 3.3 0.2 - - - -
588D MET* 1.3 78.8 - - - +
590D ARG* 1.3 62.4 + - - +
592D LYS* 4.0 14.1 + - - +
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Residues in contact with ARG 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D GLU* 3.5 31.4 + - - +
558D PRO* 3.9 46.9 + - - +
559D LEU 5.4 3.0 + - - -
560D PRO* 5.7 2.4 - - - +
586D TRP* 3.1 39.2 + - + +
587D TYR* 3.1 8.8 + - - +
589D ASP* 1.3 78.9 + - - +
591D ILE* 1.3 67.0 + - + +
592D LYS* 3.4 4.9 + - - +
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Residues in contact with ILE 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D GLU* 4.8 2.0 - - - +
560D PRO* 6.6 0.2 - - + -
561D VAL 6.4 0.4 - - - +
582D PHE* 4.0 21.5 - - + -
587D TYR* 3.0 63.5 + - + +
588D MET* 4.0 15.0 - - - +
590D ARG* 1.3 80.3 - - + +
592D LYS* 1.3 71.0 + - - +
593D GLY 3.1 5.5 + - - +
594D LYS* 3.2 38.4 + - - +
595D GLN* 4.1 3.6 - - - +
633D VAL* 4.3 8.5 - - + -
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Residues in contact with LYS 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588D MET 3.2 14.5 + - - -
589D ASP 4.2 11.2 - - - +
590D ARG 3.3 6.1 - - - +
591D ILE* 1.3 79.4 - - - +
593D GLY* 1.3 59.3 + - - +
594D LYS* 3.6 10.0 + - - +
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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