Contacts of the helix formed by residues 584 - 592 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491H LEU* 3.6 40.2 - - + -
495H ARG* 3.9 13.7 - - - +
544H LEU* 5.4 7.0 - - + -
580H ARG* 3.0 40.6 - - - +
581H LEU* 3.2 13.2 + - + +
583H SER* 1.3 78.2 - - - +
585H ASP* 1.3 67.6 + - - +
586H TRP* 4.0 9.2 - - + +
587H TYR* 4.2 10.1 - - + +
588H MET* 3.2 24.7 + - - +
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Residues in contact with ASP 585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495H ARG* 4.5 13.4 - - - +
583H SER 3.8 8.0 + - - +
584H VAL* 1.3 75.0 - - - +
586H TRP* 1.3 63.6 + - - +
588H MET* 3.3 7.4 + - - +
589H ASP* 3.1 31.9 + - - +
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Residues in contact with TRP 586 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491H LEU* 5.3 2.7 - - + -
494H LEU* 3.4 71.1 + - + -
495H ARG* 4.3 20.9 - - + +
544H LEU* 4.9 2.0 - - + -
547H GLU* 4.1 25.8 - - + -
551H ARG* 4.2 13.8 - - + +
584H VAL* 3.3 10.3 - - + +
585H ASP* 1.3 79.2 - - - +
587H TYR* 1.3 77.5 + + + +
589H ASP* 3.2 10.6 + - + +
590H ARG* 3.1 48.0 + - + +
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Residues in contact with TYR 587 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543H VAL* 3.8 26.8 - - + +
544H LEU* 4.0 20.6 - - + -
547H GLU* 3.6 25.8 + - + -
561H VAL* 4.1 4.5 + - - +
581H LEU* 3.5 47.5 - - + +
582H PHE* 4.6 3.1 - + - -
584H VAL* 3.4 10.9 + - + +
585H ASP 3.3 0.8 - - - -
586H TRP* 1.3 86.9 - + + +
588H MET* 1.3 67.6 + - - +
590H ARG* 3.1 2.6 + - + +
591H ILE* 3.0 50.1 + - + +
595H GLN* 2.4 36.8 + - - -
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Residues in contact with MET 588 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582H PHE* 3.1 44.2 - - - +
584H VAL 3.2 11.1 + - - +
585H ASP* 3.7 9.4 - - - +
587H TYR* 1.3 76.2 - - - +
589H ASP* 1.3 63.9 + - - +
591H ILE* 3.8 10.0 - - - +
592H LYS* 3.2 22.2 + - - +
593H GLY* 4.5 4.1 + - - +
631H TYR* 3.6 32.3 - - + +
633H VAL* 4.0 19.1 - - + -
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Residues in contact with ASP 589 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585H ASP* 3.1 21.3 + - - +
586H TRP* 3.5 12.4 - - + +
587H TYR 3.2 0.2 - - - -
588H MET* 1.3 80.0 - - - +
590H ARG* 1.3 59.1 + - - +
592H LYS* 3.1 34.9 + - - +
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Residues in contact with ARG 590 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547H GLU* 2.9 33.7 + - - +
558H PRO* 4.6 25.9 + - + +
559H LEU 3.9 4.8 + - - -
560H PRO* 3.5 36.2 - - - +
561H VAL 3.7 6.7 - - - +
586H TRP* 3.1 41.5 + - + +
587H TYR* 3.1 10.1 + - - +
589H ASP* 1.3 79.2 - - - +
591H ILE* 1.3 80.3 + - + +
592H LYS* 3.4 8.0 + - - +
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Residues in contact with ILE 591 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582H PHE* 3.9 23.3 - - + -
587H TYR* 3.0 62.8 + - + +
588H MET* 3.8 15.5 - - - +
590H ARG* 1.3 94.4 - - - +
592H LYS* 1.3 71.2 + - - +
593H GLY 3.0 5.6 + - - +
594H LYS* 3.1 36.4 + - - +
595H GLN* 4.1 7.0 - - + +
633H VAL* 4.3 7.4 - - + -
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Residues in contact with LYS 592 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588H MET 3.2 11.6 + - - +
589H ASP* 3.1 27.0 + - - +
590H ARG 3.7 8.0 + - - +
591H ILE* 1.3 78.3 - - - +
593H GLY* 1.3 58.7 + - - +
594H LYS* 3.6 11.8 + - - +
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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