Contacts of the helix formed by residues 557 - 569 (chain A) in PDB entry 2WXL
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 557 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 6.4 0.2 - - - -
383A ASP* 3.2 14.8 - - - +
554A LYS* 3.3 26.5 + - + +
555A TRP 3.4 1.0 + - - -
556A ASN* 1.3 109.9 - - - +
558A HIS* 1.3 66.5 + - - +
559A GLU* 3.3 3.6 - - + +
560A ASP* 3.2 17.1 + - - +
561A VAL* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 4.6 28.9 - + + +
382A CYS* 3.4 33.1 - - - +
383A ASP* 2.7 34.7 + - - +
384A LEU 5.9 0.7 - - - +
485A PHE* 6.2 4.5 - - + -
494A LEU* 3.9 20.7 - - + +
557A LYS* 1.3 70.0 - - - +
559A GLU* 1.3 68.4 + - + +
561A VAL* 3.8 8.2 - - - +
562A ALA* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU* 4.2 35.2 - - + +
557A LYS* 3.3 2.8 - - + +
558A HIS* 1.3 89.2 + - + +
560A ASP* 1.3 67.6 + - - +
562A ALA* 3.4 3.3 + - - +
563A GLN* 3.0 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A TRP* 3.2 32.7 + - + -
553A THR* 4.8 1.5 - - - -
554A LYS* 3.8 35.1 + - + +
557A LYS* 3.2 22.5 + - - +
559A GLU* 1.3 85.9 - - - +
561A VAL* 1.3 59.1 + - - +
563A GLN* 3.0 12.9 - - - +
564A MET* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PRO* 5.0 8.7 - - + -
485A PHE* 5.8 8.5 - - + -
553A THR* 4.8 1.8 - - - +
554A LYS 3.6 1.8 - - - +
555A TRP* 3.6 53.8 - - + +
557A LYS 3.1 18.1 + - - +
558A HIS* 3.8 7.4 - - - +
559A GLU 3.4 0.2 - - - -
560A ASP* 1.3 74.5 - - - +
562A ALA* 1.3 58.2 + - - +
564A MET* 3.0 6.7 + - - +
565A LEU* 2.8 58.6 + - + +
589A ASP* 5.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 3.7 43.6 - - + +
494A LEU* 3.9 25.5 - - + -
558A HIS 2.9 18.9 + - - +
559A GLU 3.5 5.6 - - - +
561A VAL* 1.3 75.8 - - - +
563A GLN* 1.3 58.2 + - - +
565A LEU* 3.9 1.0 - - - +
566A TYR* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU 4.3 16.4 + - - -
532A TRP* 3.5 12.5 + - + -
535A ARG* 3.2 42.8 + - - +
559A GLU* 3.0 37.4 + - - +
560A ASP* 3.0 14.4 - - - +
562A ALA* 1.3 74.5 - - - +
564A MET* 1.3 66.5 + - - +
566A TYR* 3.3 7.9 + - - +
567A LEU* 3.3 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A TRP* 4.0 7.9 - - + -
546A LEU* 4.8 6.5 - - - -
549A LEU* 3.0 49.4 - - + +
550A LEU* 3.7 27.6 - - + +
553A THR* 2.9 38.6 - - + +
555A TRP* 4.4 8.7 - - + -
560A ASP 3.0 8.8 + - - +
561A VAL* 3.0 8.9 + - - +
563A GLN* 1.3 79.5 - - - +
565A LEU* 1.3 62.8 + - + +
567A LEU* 3.1 13.0 + - - +
568A LEU* 2.8 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A PHE* 5.7 4.0 - - + -
488A LEU* 5.1 2.9 - - + -
491A ILE* 3.6 31.0 - - + -
492A LEU* 5.3 1.1 - - - -
555A TRP* 4.2 17.0 - - + -
561A VAL* 2.8 51.9 + - + +
562A ALA 3.9 3.8 - - - +
564A MET* 1.3 75.4 - - + +
566A TYR* 1.3 61.9 + - - +
568A LEU* 3.1 12.2 + - + +
569A CYS* 3.0 32.6 + - - -
589A ASP* 4.6 9.2 - - - +
591A TYR* 3.5 42.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
491A ILE* 5.4 0.4 - - - +
492A LEU* 4.0 46.0 - - + +
494A LEU 6.2 1.3 - - - -
536A HIS* 5.6 7.2 - + - -
562A ALA 3.0 19.0 + - - +
563A GLN* 3.5 7.9 - - - +
564A MET 3.2 0.4 - - - -
565A LEU* 1.3 76.3 - - - +
567A LEU* 1.3 76.7 + - + +
569A CYS* 3.6 8.3 + - - +
570A SER* 3.9 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ARG* 3.5 54.1 - - + +
536A HIS* 3.7 30.5 - - + +
539A GLN* 3.0 39.7 + - - +
549A LEU* 4.4 8.5 - - + -
563A GLN 3.3 9.6 + - - +
564A MET* 3.1 10.8 + - - +
566A TYR* 1.3 87.0 - - + +
568A LEU* 1.3 65.5 + - - +
570A SER 3.0 8.7 + - - -
571A TRP* 3.3 18.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A LEU* 4.0 24.5 - - + -
550A LEU* 5.2 2.7 - - + -
564A MET* 2.8 19.0 + - + +
565A LEU* 3.1 17.5 + - + +
567A LEU* 1.3 76.3 - - - +
569A CYS* 1.3 59.9 + - - +
571A TRP* 3.0 29.9 + - + +
589A ASP* 5.1 0.2 - - - +
591A TYR* 3.7 40.8 - - + +
592A VAL* 3.8 20.0 - - + +
595A PHE* 3.8 34.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU* 4.0 34.8 - - - -
492A LEU* 4.1 17.7 - - + -
565A LEU* 3.0 19.8 + - - +
566A TYR 4.1 5.6 - - - +
567A LEU 3.1 0.4 + - - -
568A LEU* 1.3 80.8 - - - +
570A SER* 1.3 57.6 + - - +
571A TRP 3.5 0.4 - - - -
591A TYR* 5.3 8.1 - - - -
----------------------------------------------------------
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