Contacts of the helix formed by residues 579 - 584 (chain A) in PDB entry 1XR2
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 PRO 579 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A MET* 4.3 11.4 - - + -
535A THR* 3.2 27.6 - - + +
539A TRP* 4.2 13.7 - - + +
577A ASP* 3.4 14.8 - - + +
578A GLU* 1.3 88.3 - - - +
580A ALA* 1.3 54.7 + - - +
583A GLU* 3.3 21.6 - - - +
618A HIS 4.6 2.9 - - - +
619A MET* 4.9 3.8 - - + -
620A CYS* 5.9 3.8 - - + +
621A TYR* 2.4 27.2 + - + +
1200A C2F 3.9 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.6 10.8 - - + +
535A THR* 3.3 27.8 + - + +
538A SER* 3.2 28.9 - - - +
539A TRP* 5.1 2.4 - - - +
578A GLU 3.1 1.6 - - - -
579A PRO* 1.3 74.8 - - - +
581A PHE* 1.3 67.8 + - - +
582A ARG 3.1 3.1 - - - -
583A GLU* 3.6 11.2 - - + -
584A LYS* 2.9 21.6 + - + +
595A TYR* 3.2 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 4.9 2.7 - - + -
578A GLU* 3.1 33.1 + - + +
579A PRO 3.2 0.2 - - - -
580A ALA* 1.3 74.6 - - - +
582A ARG* 1.3 58.2 + - - +
595A TYR* 2.7 32.8 + - - -
596A PHE* 3.7 35.3 - + - -
599A ALA* 4.2 16.4 - - + -
600A ILE* 4.1 10.1 - - + -
603A PHE* 5.6 1.8 - - + -
619A MET* 4.0 10.5 - - + -
621A TYR* 3.4 4.7 - - - +
627A ILE* 4.5 8.1 - - + -
630A TYR* 4.0 21.1 - - + -
631A ILE* 3.4 34.1 - - + -
634A LEU* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A PHE* 1.3 77.5 - - - +
583A GLU* 1.3 65.2 + - - +
584A LYS 3.3 2.2 - - - -
585A ALA* 2.9 36.5 + - + +
586A PRO 5.5 1.0 + - - -
589A LYS* 3.3 28.7 - - - +
592A TRP* 3.4 21.8 - - + -
596A PHE* 4.6 3.1 - - + -
621A TYR* 3.0 32.8 + - + -
623A ASP 6.2 0.2 - - - -
626A GLU* 4.2 7.5 + - - +
627A ILE* 3.9 30.1 - - + +
1205A MRY 4.9 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 2.9 49.5 + - + +
107A ASN* 4.4 17.7 - - - +
539A TRP* 5.0 2.1 + - - -
579A PRO* 3.3 22.3 + - - +
580A ALA* 3.2 7.8 + - + -
582A ARG* 1.3 82.2 + - + +
584A LYS* 1.3 59.5 + - - +
585A ALA 3.2 5.2 + - - +
621A TYR* 4.5 12.0 - - + -
1200A C2F 2.9 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 5.4 5.6 - - - +
283A ARG* 5.9 3.0 - - - +
534A VAL* 4.1 15.9 - - + +
537A MET* 4.3 9.9 - - + -
538A SER* 3.5 34.0 - - - +
542A TYR* 3.0 29.3 + - - -
548A GLU* 3.3 19.0 + - - -
580A ALA* 2.9 19.7 + - + +
583A GLU* 1.3 71.3 - - - +
585A ALA* 1.3 66.8 + - - +
586A PRO* 3.5 3.1 - - - +
595A TYR* 3.8 16.3 - - + +
598A TRP* 4.3 15.7 - - + -
----------------------------------------------------------
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