Contacts of the helix formed by residues 602 - 609 (chain A) in PDB entry 2WNT
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 ILE 602 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PRO* 5.4 1.1 - - + -
598A TRP* 3.0 36.2 + - + +
599A SER* 3.3 12.6 - - - +
601A GLY* 1.3 74.6 - - - +
603A LEU* 1.3 64.9 + - + +
605A TYR* 3.3 8.2 + - - +
606A THR* 2.9 33.8 + - - -
613A PRO* 4.0 12.9 - - + +
614A PHE* 4.1 11.4 - - + -
656A LEU* 3.7 19.5 - - + -
698A MET* 3.7 17.0 - - - -
701A THR* 4.8 7.9 - - + -
702A TYR* 3.3 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 3.6 35.4 - - + -
498A LEU* 4.3 9.6 - - + -
515A VAL* 4.7 11.4 - - + -
516A LEU* 6.0 4.0 - - + -
519A ILE* 5.3 4.7 - - + -
536A LEU 5.8 1.3 - - - +
538A PRO* 4.0 24.9 - - + -
541A ILE* 4.0 19.7 - - + -
599A SER 3.1 12.8 + - - +
600A LEU* 3.6 16.2 - - + +
602A ILE* 1.3 76.5 - - + +
604A LEU* 1.3 66.2 + - - +
606A THR* 3.2 4.3 + - - -
607A MET* 3.0 43.6 + - + +
698A MET* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 4.1 8.5 - - + +
600A LEU 2.9 18.2 + - - +
601A GLY* 3.5 6.5 - - - +
603A LEU* 1.3 77.2 - - - +
605A TYR* 1.3 62.2 + - - +
607A MET* 3.3 19.2 + - + +
608A LEU* 3.1 39.2 + - + +
648A ALA 4.8 0.7 - - - +
651A LEU* 3.7 29.8 - - + -
652A VAL* 3.5 26.9 - - + -
655A MET* 3.8 16.2 - - - -
674A TRP* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLY 2.9 19.7 + - - +
602A ILE 3.5 5.8 - - - +
603A LEU 3.3 0.4 - - - -
604A LEU* 1.3 73.6 - - - +
606A THR* 1.3 56.7 + - - +
608A LEU* 3.3 2.1 + - - +
609A ALA* 2.8 37.2 + - + +
611A TYR* 3.3 40.7 + + - -
613A PRO* 3.5 41.2 + - + +
634A PHE* 3.8 15.7 - + - -
635A THR* 2.6 38.2 + - - -
636A LEU* 4.0 1.3 - - + -
641A TRP* 3.3 19.6 + + - -
652A VAL* 3.9 27.1 - - + -
656A LEU* 4.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 4.6 12.8 - - + -
502A LEU* 5.3 5.2 - - + +
602A ILE 2.9 17.6 + - - -
603A LEU* 3.2 6.9 + - - -
605A TYR* 1.3 73.8 - - - +
607A MET* 1.3 61.0 + - - +
610A GLY* 2.7 31.0 + - - -
611A TYR 3.4 15.0 - - - +
612A THR* 3.7 14.1 - - - +
694A VAL* 3.6 31.6 - - + -
698A MET* 3.3 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 5.2 0.2 - - - -
501A ILE* 3.5 25.1 - - + -
502A LEU* 5.5 4.9 - - - +
507A PHE* 3.8 31.0 - - + -
512A ALA* 3.9 22.4 - - + +
515A VAL* 3.7 29.4 - - + -
516A LEU* 4.6 7.6 - - + +
603A LEU* 3.0 29.3 + - + +
604A LEU* 3.7 34.5 - - + +
606A THR* 1.3 76.6 - - - +
608A LEU* 1.3 62.0 + - + +
610A GLY* 4.3 2.4 + - - -
686A LEU* 3.5 22.4 - - - +
687A SER 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 4.2 18.2 - - + -
512A ALA* 4.6 6.7 - - + -
604A LEU* 3.1 26.7 + - + +
605A TYR 3.7 2.7 - - - +
607A MET* 1.3 80.9 - - - +
609A ALA* 1.3 60.4 + - - +
610A GLY 3.5 0.2 - - - -
640A ASN* 4.8 4.3 + - - +
641A TRP* 4.1 20.0 - - + -
644A VAL* 4.1 14.8 - - + +
648A ALA* 3.9 20.9 - - + +
652A VAL* 3.6 31.0 - - + -
674A TRP* 3.8 26.2 - - + -
686A LEU* 3.7 21.9 - - + +
687A SER 4.4 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A TYR* 2.8 27.5 + - + +
608A LEU* 1.3 74.7 - - - +
610A GLY* 1.3 62.6 + - - +
611A TYR* 3.4 26.5 - - + +
640A ASN* 3.4 24.6 + - - +
641A TRP* 3.2 35.4 - - + -
644A VAL* 5.9 0.2 - - - -
687A SER 3.5 2.8 - - - +
688A HIS* 4.7 0.5 - - - -
689A GLN* 5.8 0.2 - - - +
----------------------------------------------------------
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