Contacts of the helix formed by residues 661 - 666 (chain B) 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 PHE 661 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A TRP* 4.5 1.1 - + - -
690A LEU* 3.0 47.6 - - + -
694A PHE* 3.1 25.4 - + - -
738A TYR* 3.7 17.9 - - - -
657B TRP* 3.3 42.8 - + - -
658B ALA* 2.7 25.4 + - - -
660B GLY* 1.3 66.4 - - - +
662B MET* 1.3 64.8 + - - +
663B PHE 2.7 9.5 - - - +
664B LEU* 3.0 8.6 - - + +
665B ILE* 2.5 28.6 + - + +
713B PHE* 5.1 4.3 - + - -
1786B CLA 4.7 4.9 - + + -
1787B CLA 2.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B THR* 4.3 4.9 - - - +
660B GLY 2.9 7.8 + - - +
661B PHE* 1.3 80.5 - - - +
663B PHE* 1.3 69.4 + - + +
664B LEU 2.5 4.7 + - - -
665B ILE 2.7 8.8 + - - -
666B SER* 2.8 24.7 + - - +
671B TRP* 3.2 31.2 - - + -
1771B CLA 3.9 13.2 - - + -
1773B PQN 2.8 40.4 - - + +
1787B CLA 2.8 80.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B THR* 3.8 11.9 - - - -
660B GLY 2.5 30.8 - - - +
661B PHE 2.7 1.6 - - - +
662B MET* 1.3 80.2 - - + +
664B LEU* 1.3 74.1 + - - +
700B LEU* 4.4 13.7 - - + -
705B ALA* 3.5 17.7 - - + +
708B VAL* 4.6 7.4 - - + -
709B GLY 3.4 27.4 - - - +
712B HIS* 4.6 12.3 - + - -
1771B CLA 4.0 43.1 - + + -
1773B PQN 3.0 65.2 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A LEU 3.8 2.9 - - - +
694A PHE* 3.6 44.8 - - + -
577B TYR* 3.4 26.2 - - + +
581B PHE* 4.4 5.6 - - + -
660B GLY* 3.7 6.5 - - - -
661B PHE* 3.0 25.8 - - + +
662B MET 2.5 5.9 + - - -
663B PHE* 1.3 85.9 - - - +
665B ILE* 1.3 53.9 + - - +
666B SER 4.1 0.8 - - - +
667B TRP* 2.4 39.9 - - - -
705B ALA 4.4 5.4 + - - +
706B ARG* 4.1 5.6 - - - +
709B GLY* 3.0 33.7 - - - +
713B PHE* 4.6 12.1 - - + -
1773B PQN 4.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN* 3.3 12.9 - - - +
599A PHE* 3.7 13.7 - - + -
600A LEU* 3.6 9.7 - - - +
603A PHE* 3.4 32.8 - - + -
693A LEU* 3.6 38.4 - - + +
694A PHE* 3.6 16.2 - - + -
738A TYR* 4.8 3.6 - - + -
661B PHE* 2.5 30.1 + - + +
662B MET 2.7 1.6 + - - -
664B LEU* 1.3 75.1 - - - +
666B SER* 1.3 62.6 + - - +
667B TRP* 3.8 5.6 - - - -
1787B CLA 3.5 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN* 3.1 18.1 - - - +
600A LEU* 4.4 7.6 - - - +
662B MET* 2.8 34.0 + - - +
665B ILE* 1.3 83.6 + - - +
667B TRP* 1.3 82.1 + - - +
671B TRP* 3.0 32.9 + - - -
1773B PQN 3.7 4.0 - - - -
1787B CLA 4.3 11.6 - - - +
----------------------------------------------------------
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