Contacts of the helix formed by residues 559 - 569 (chain A) in PDB entry 2XER
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 LYS 559 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A MET* 3.2 12.3 + - + +
556A ASP* 3.1 38.1 + - - +
557A ASP 4.9 0.2 - - - -
558A ARG* 1.3 76.9 - - - +
560A HIS* 1.3 65.0 + - + +
561A LYS 3.0 5.2 + - - -
562A ILE* 3.2 25.1 + - - +
563A CYS* 3.6 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASP 3.2 26.6 + - - -
558A ARG 3.1 1.4 + - - -
559A LYS* 1.3 85.0 - - + +
561A LYS* 1.3 84.5 + - + +
563A CYS* 4.2 9.4 - - - +
564A SER* 3.0 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 4.0 25.9 - - + +
535A ASP* 3.0 31.2 + - + +
536A VAL* 4.2 19.5 - - + -
557A ASP 4.1 8.9 + - - -
558A ARG* 2.9 30.4 + - - +
560A HIS* 1.3 104.7 - - + +
562A ILE* 1.3 66.5 + - - +
563A CYS 3.3 0.2 - - - -
564A SER* 3.1 8.2 + - - -
565A MET* 3.0 28.7 + - - +
527C GLU* 5.7 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL* 3.9 26.5 - - + -
555A MET* 6.3 4.5 - - + -
558A ARG* 4.4 7.9 - - + +
559A LYS* 3.2 17.2 + - - +
561A LYS* 1.3 76.3 - - - +
563A CYS* 1.3 63.7 + - - +
565A MET* 3.1 12.3 + - - +
566A TYR* 3.0 21.0 + - - +
603A PHE* 3.2 52.9 - - + +
604A LEU* 3.8 16.8 - - + +
605A SER 5.2 0.2 - - - +
608A GLN* 4.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LYS 3.6 10.6 + - - +
560A HIS* 4.3 9.9 - - - +
561A LYS 3.3 0.2 - - - -
562A ILE* 1.3 79.9 - - - +
564A SER* 1.3 52.6 + - - +
566A TYR* 3.2 8.6 + - + +
567A ASP* 2.8 48.3 + - - +
608A GLN* 4.0 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 3.8 18.2 - - - -
560A HIS* 3.0 23.7 + - - -
561A LYS* 3.1 12.8 + - - -
563A CYS* 1.3 79.8 - - - +
565A MET* 1.3 56.3 + - - +
567A ASP* 3.5 8.2 + - - +
568A ASN* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A THR* 3.8 18.5 - - + +
532A LEU* 3.9 20.2 - - + +
533A LEU* 3.4 41.7 - - + +
536A VAL* 4.5 11.7 - - - -
561A LYS 3.0 19.9 + - - +
562A ILE* 3.1 15.0 + - - +
564A SER* 1.3 73.2 - - - +
566A TYR* 1.3 66.3 + - - +
568A ASN* 3.2 3.5 + - - +
569A LEU* 3.0 30.0 + - - +
600A ILE* 3.4 50.0 - - + -
603A PHE* 5.5 2.7 - - - -
604A LEU* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ILE 3.0 12.8 + - - +
563A CYS* 3.2 10.1 + - - +
565A MET* 1.3 76.7 - - - +
567A ASP* 1.3 73.1 + - - +
569A LEU* 3.0 17.8 + - - +
570A ARG* 3.0 22.7 + - + +
604A LEU* 4.2 16.9 - - + +
607A GLU 4.8 0.2 + - - -
608A GLN* 3.6 58.6 - - + +
611A ASP* 2.5 33.8 + - - +
612A ILE* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A CYS* 2.8 34.1 + - - +
564A SER* 3.6 8.9 - - - +
566A TYR* 1.3 83.0 - - - +
568A ASN* 1.3 64.5 + - - +
570A ARG 3.0 0.7 + - - -
571A GLY* 2.6 41.6 + - - +
572A LYS 5.5 1.8 + - - -
583A HIS* 4.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 3.5 15.3 + - + +
528A LYS* 4.3 13.3 - - - +
529A THR* 3.0 39.1 + - - +
532A LEU* 4.5 8.3 - - - +
564A SER* 2.9 23.7 + - - +
565A MET 3.6 4.0 - - - +
566A TYR 3.2 0.4 - - - -
567A ASP* 1.3 80.1 - - - +
569A LEU* 1.3 58.3 + - - +
570A ARG 3.4 0.2 - - - -
583A HIS* 2.7 29.8 + - - -
587A ILE* 3.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A THR* 4.6 4.5 - - + +
565A MET 3.0 20.2 - - - +
566A TYR* 3.0 10.8 + - - +
568A ASN* 1.3 79.4 - - - +
570A ARG* 1.3 60.5 + - - +
583A HIS* 3.9 2.2 - - - -
584A PHE* 3.2 42.8 + - + +
587A ILE* 3.9 20.6 - - + -
596A MET* 4.3 21.1 - - + -
597A VAL* 4.3 23.3 - - + -
600A ILE* 4.1 28.7 - - + -
604A LEU* 5.0 4.5 - - + -
612A ILE* 4.4 22.9 - - + -
----------------------------------------------------------
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