Contacts of the helix formed by residues 582 - 586 (chain D) in PDB entry 6UZA
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 ALA 582 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D PRO 3.3 14.8 - - - +
473D ASN* 3.7 14.1 - - - +
474D GLU 3.4 23.6 - - - +
475D THR* 4.2 7.5 + - - +
484D PHE* 4.2 7.0 - - - -
581D LEU* 1.3 76.4 - - - +
583D ARG* 1.3 67.0 + - - +
584D ILE* 3.2 10.1 + - + -
585D LYS* 3.2 11.0 + - + +
586D TRP* 3.1 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 583 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 3.7 47.5 - - - +
659A TYR* 3.7 30.2 + - - -
695A TYR* 4.1 4.5 - - + -
697A HIS* 3.2 27.1 + - + -
470D LEU* 5.7 6.5 - - + -
471D LEU 5.3 2.2 + - - +
472D PRO* 3.0 23.5 + - + +
484D PHE* 4.9 6.9 - - + -
582D ALA* 1.3 75.0 - - - +
584D ILE* 1.3 61.3 + - - +
585D LYS 3.3 0.4 + - - -
586D TRP* 3.5 52.6 + - + +
592D GLN* 5.1 0.6 - - - +
593D ILE* 3.8 5.3 - - - +
596D GLU* 2.6 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 584 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A TYR* 3.4 45.4 - - + +
697A HIS* 5.0 3.3 + - - -
472D PRO 3.3 12.2 + - - +
473D ASN* 4.4 13.0 - - + +
582D ALA* 4.2 9.2 - - + -
583D ARG* 1.3 78.2 - - - +
585D LYS* 1.3 93.1 + - + +
586D TRP 3.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 585 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D TYR* 4.2 10.0 - - - -
581D LEU* 4.0 34.9 - - + +
582D ALA* 3.2 10.5 + - + +
584D ILE* 1.3 108.6 - - + +
586D TRP* 1.3 67.2 + - - +
587D ASP 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 586 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A HIS* 3.9 13.2 + + - +
484D PHE* 4.3 12.1 - + - -
485D ARG* 3.6 40.1 - - - +
488D THR* 5.1 7.2 - - + -
578D TYR* 3.9 9.9 - + - +
581D LEU* 3.0 25.5 + - + +
582D ALA 3.1 17.1 + - - -
583D ARG* 3.5 67.0 + - + +
584D ILE 3.5 4.8 - - - +
585D LYS* 1.3 83.2 - - - +
587D ASP* 1.3 70.6 + - - +
588D PRO* 3.8 3.5 - - - +
590D ASP* 4.0 7.2 - - + -
592D GLN* 3.7 27.4 - - + -
593D ILE* 3.7 18.4 - - + -
----------------------------------------------------------
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