Contacts of the helix formed by residues 584 - 592 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C LEU* 3.6 35.4 - - + -
495C ARG* 4.2 7.2 - - - +
544C LEU* 5.3 7.2 - - + -
580C ARG* 3.3 40.8 - - + +
581C LEU* 3.1 12.6 + - + +
582C PHE 4.6 0.7 - - - -
583C SER* 1.3 78.1 - - - +
585C ASP* 1.3 71.5 + - - +
586C TRP* 3.7 11.9 - - + +
587C TYR* 3.8 13.0 - - + +
588C MET* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 585 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ARG* 2.9 37.0 + - - +
583C SER 3.9 3.8 + - - -
584C VAL* 1.3 72.5 - - - +
586C TRP* 1.3 80.3 + - - +
588C MET* 3.4 6.1 + - - +
589C ASP* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C LEU* 5.1 3.8 - - + -
494C LEU* 3.4 69.5 + - + -
495C ARG* 4.5 15.9 - - + +
544C LEU* 4.8 2.2 - - + -
547C GLU* 4.1 13.9 - - + -
551C ARG* 4.3 9.2 - - - +
584C VAL* 3.3 8.5 - - + -
585C ASP* 1.3 90.1 + - - +
587C TYR* 1.3 74.5 + + + +
589C ASP* 3.2 9.3 + - + +
590C ARG* 3.1 74.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C VAL* 3.7 28.5 - - + +
544C LEU* 4.0 20.6 - - + -
547C GLU* 3.6 24.6 + - + -
561C VAL* 3.9 6.4 + - - +
581C LEU* 3.6 45.3 - - + +
582C PHE* 4.5 4.3 - + - -
584C VAL* 3.3 12.8 + - + +
586C TRP* 1.3 86.1 - + + +
588C MET* 1.3 67.4 + - - +
590C ARG* 3.1 1.8 + - + +
591C ILE* 3.0 50.8 + - + +
595C GLN* 2.4 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582C PHE* 3.1 39.3 - - - +
584C VAL 3.1 14.3 + - - +
585C ASP* 3.8 7.0 - - - +
587C TYR* 1.3 76.2 - - - +
589C ASP* 1.3 62.7 + - - +
591C ILE* 3.9 12.6 - - - +
592C LYS* 3.1 22.9 + - - -
593C GLY* 4.7 4.9 + - - +
631C TYR* 3.7 30.3 - - + +
632C GLY 5.7 0.2 - - - +
633C VAL* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 589 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C ASP 3.0 14.1 + - - +
586C TRP* 3.4 13.5 - - + +
587C TYR 3.2 0.2 - - - -
588C MET* 1.3 77.0 - - - +
590C ARG* 1.3 61.6 + - - +
592C LYS* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 590 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C GLU* 2.8 55.8 + - - +
550C GLN* 4.9 1.2 - - - +
551C ARG* 4.6 18.0 - - - +
558C PRO* 3.5 36.9 - - - +
559C LEU 5.7 0.9 - - - -
586C TRP* 3.1 45.7 + - + +
587C TYR* 3.1 7.1 + - - +
589C ASP* 1.3 77.1 - - - +
591C ILE* 1.3 68.7 + - + +
592C LYS* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 591 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C GLU* 5.0 1.3 - - - +
560C PRO* 6.6 0.2 - - + -
561C VAL 6.4 0.7 - - - +
582C PHE* 4.0 20.2 - - + -
587C TYR* 3.0 63.6 + - + +
588C MET* 3.9 18.6 - - - +
590C ARG* 1.3 81.4 - - + +
592C LYS* 1.3 70.6 + - - +
593C GLY 3.2 4.7 + - - +
594C LYS* 3.3 36.2 + - - +
595C GLN* 4.1 4.7 - - + +
633C VAL* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 592 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C MET 3.1 13.1 + - - +
589C ASP* 3.2 23.7 + - - +
590C ARG* 3.3 18.9 + - - +
591C ILE* 1.3 76.5 - - - +
593C GLY* 1.3 59.8 + - - +
594C LYS* 3.6 9.0 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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