Contacts of the helix formed by residues 62 - 69 (chain 2) in PDB entry 2WSC
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 62 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 GLY 4.8 0.7 - - - +
592 ALA* 2.8 34.1 - - + +
602 ALA 2.8 4.2 + - - -
612 GLY* 1.3 84.8 - - - +
632 PHE* 1.3 65.9 + - - +
652 PRO* 3.4 5.4 - - + -
662 GLU* 3.1 46.1 + - + +
1722 LEU* 3.9 14.4 - - + -
12172 CLA 4.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 ALA 3.6 5.2 - - - +
602 ALA* 3.3 39.0 - - + -
622 ILE* 1.3 82.7 - - - +
642 ILE* 1.3 89.1 + - + +
662 GLU* 5.8 0.4 - - - -
672 PHE* 3.1 40.8 + - + +
1642 ILE* 6.2 1.1 - - + -
1682 ARG* 3.2 35.0 - - - -
1712 MET* 3.7 32.8 - - + -
1722 LEU* 4.3 7.4 - - + -
12132 CLA 3.6 45.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 ALA 4.5 2.5 - - - +
612 GLY* 6.0 0.2 - - - -
632 PHE* 1.3 102.1 - - + +
652 PRO* 1.3 67.2 - - + +
662 GLU 3.3 0.4 - - - -
672 PHE* 4.6 3.4 - - + +
682 LEU* 2.3 77.6 + - + +
12132 CLA 3.6 45.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 65 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 ALA 4.0 1.1 - - - +
612 GLY* 3.3 26.0 - - - +
622 ILE* 3.4 20.2 - - + +
642 ILE* 1.3 100.5 - - + +
662 GLU* 1.3 61.4 + - - +
682 LEU* 4.0 8.1 - - + +
692 THR* 3.6 11.1 + - - +
12172 CLA 4.7 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 ILE* 3.1 34.4 + - + +
632 PHE* 4.3 1.1 - - - +
652 PRO* 1.3 73.9 - - - +
672 PHE* 1.3 93.5 + - + +
682 LEU 3.1 3.4 - - - -
692 THR* 2.8 36.8 + - + +
1822 ILE* 4.2 13.0 - - - +
12172 CLA 5.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632 PHE* 3.1 24.8 + - + +
642 ILE* 4.6 6.0 - - + +
662 GLU* 1.3 101.3 - - + +
682 LEU* 1.3 62.0 + - - +
692 THR* 3.3 5.6 + - + -
1752 MET* 5.3 22.0 - - + -
1782 TRP* 5.5 7.9 - + + -
1822 ILE* 3.6 27.1 - - + -
2052 PHE* 5.1 14.1 - + - -
2062 ALA 6.4 0.7 - - - -
2072 ALA* 6.1 4.7 - - + -
12132 CLA 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 ILE* 2.3 62.9 + - + +
652 PRO* 4.0 8.3 - - + +
672 PHE* 1.3 79.0 - - - +
692 THR* 1.3 80.3 + - - +
702 LYS* 3.1 7.0 + - - +
12132 CLA 5.9 0.7 - - + -
12172 CLA 3.1 67.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 PRO 3.6 6.2 + - - +
662 GLU* 2.8 27.9 + - + +
672 PHE* 4.3 5.0 + - + -
682 LEU* 1.3 94.0 + - - +
702 LYS* 1.3 87.8 + - - +
712 LEU* 3.7 11.6 + - - +
2052 PHE* 6.3 2.5 - - + -
12172 CLA 4.9 1.2 - - - +
----------------------------------------------------------
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