Contacts of the helix formed by residues 762 - 775 (chain B) in PDB entry 2W3S
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 THR 762 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LYS* 3.9 20.4 - - + -
640B ASN* 4.8 0.2 - - - -
676B THR 3.4 16.4 + - - +
677B THR* 4.7 2.0 - - - -
679B GLU* 3.7 27.4 + - + +
760B PRO* 3.0 20.7 + - + -
761B ALA* 1.3 78.8 - - - +
763B PRO* 1.4 71.6 - - + +
764B GLU* 3.8 9.5 + - - +
765B ALA* 3.2 20.0 + - - +
766B VAL* 2.8 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 763 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A SER 3.8 14.6 - - - +
355A LYS* 3.5 33.7 - - + +
434A TYR* 3.6 15.7 - - - +
637B THR 4.0 1.6 - - - -
638B GLY* 3.3 33.9 - - - +
639B GLU* 3.8 9.9 - - + +
640B ASN* 4.2 13.0 - - - +
677B THR* 5.5 2.2 - - + -
762B THR* 1.4 85.6 - - + +
764B GLU* 1.3 53.6 + - - +
766B VAL 3.0 1.6 + - - -
767B LEU* 2.7 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 764 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG 5.0 0.2 - - - +
430A ALA* 3.6 10.2 - - - -
431A SER* 2.7 48.9 + - - -
434A TYR* 3.5 42.2 - - + +
762B THR* 3.3 9.1 + - - +
763B PRO* 1.3 78.9 - - - +
765B ALA* 1.3 59.9 + - - +
767B LEU* 3.2 2.8 + - - +
768B ALA* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 765 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B LEU* 3.3 12.5 - - + +
758B GLN* 4.2 15.1 + - + +
760B PRO 3.7 18.8 - - - +
761B ALA* 4.1 3.8 - - - -
762B THR* 3.2 19.9 + - - +
764B GLU* 1.3 81.0 - - + +
766B VAL* 1.3 61.9 + - - +
768B ALA* 3.7 7.1 + - - +
769B ALA* 3.2 16.8 + - - +
772B ARG* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 766 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ILE* 3.9 33.2 - - + -
634B ASP 5.5 0.2 - - - +
638B GLY* 3.7 22.7 - - - +
640B ASN* 4.7 2.9 - - - +
743B LEU* 4.1 17.0 - - + -
747B CYS* 4.1 5.3 - - - -
757B LEU* 3.9 10.8 - - + -
761B ALA* 3.7 25.6 - - + +
762B THR 2.8 19.4 + - - +
763B PRO 3.6 3.6 - - - +
765B ALA* 1.3 75.0 - - - +
767B LEU* 1.3 60.2 + - - +
769B ALA* 3.2 2.9 + - - +
770B VAL* 2.8 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 767 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TYR* 3.5 28.5 - - + -
437A ASN* 3.2 28.0 - - - +
438A ALA* 5.4 1.1 - - + +
634B ASP 4.9 0.2 - - - +
635B ARG 3.4 21.1 - - - +
636B LEU 3.2 27.8 - - - +
637B THR* 3.6 9.6 - - - +
638B GLY* 4.0 2.9 - - - +
763B PRO 2.7 16.8 + - - +
764B GLU 3.5 8.5 - - - +
766B VAL* 1.3 73.5 - - - +
768B ALA* 1.3 56.2 + - - +
770B VAL* 3.1 8.4 + - + +
771B ARG* 2.9 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 768 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B GLU* 3.0 18.3 + - + +
765B ALA* 3.9 8.1 - - - +
767B LEU* 1.3 75.7 - - - +
769B ALA* 1.3 58.4 + - - +
771B ARG* 3.2 9.0 + - - +
772B ARG* 3.0 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 769 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B CYS* 4.0 9.4 - - - -
755B PRO* 3.3 29.6 - - + +
757B LEU* 3.6 28.9 - - + +
765B ALA 3.2 14.6 + - - +
766B VAL 3.2 4.1 + - - +
768B ALA* 1.3 75.3 - - - +
770B VAL* 1.3 65.2 + - - +
772B ARG* 3.2 14.1 - - - +
773B ALA* 3.3 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 770 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ILE* 3.4 33.4 - - + -
634B ASP 5.8 0.4 - - - +
635B ARG* 4.1 29.6 - - + +
638B GLY* 6.4 0.2 - - - -
747B CYS* 3.6 10.3 - - - +
750B CYS* 4.1 8.1 - - + -
766B VAL* 2.8 21.7 + - + +
767B LEU* 3.5 8.1 - - + +
769B ALA* 1.3 74.6 - - - +
771B ARG* 1.3 62.7 + - + +
773B ALA* 3.0 8.7 + - - +
774B GLU* 2.9 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 771 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ASN* 4.0 26.3 - - - +
635B ARG 5.7 0.4 - - - +
767B LEU* 2.9 37.8 + - + +
768B ALA* 3.2 7.9 + - - +
770B VAL* 1.3 78.3 - - + +
772B ARG* 1.3 50.0 + - - +
774B GLU* 3.4 14.9 + - - +
775B GLY 2.6 29.5 + - - -
776B ARG* 2.7 72.5 + - + +
777B ALA* 3.9 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 772 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B HIS* 3.3 13.7 - - - +
754B TRP 4.0 7.6 - - - +
755B PRO 2.9 32.9 + - - +
756B ASP* 3.0 27.3 + - - +
757B LEU* 4.5 1.0 - - - +
758B GLN* 5.1 9.3 - - - +
765B ALA 4.8 1.2 + - - -
768B ALA* 3.0 32.8 + - - +
769B ALA* 3.2 21.8 - - - +
771B ARG* 1.3 74.6 - - - +
773B ALA* 1.3 56.4 + - - +
775B GLY* 2.7 24.8 + - - +
776B ARG 4.9 0.9 - - - +
777B ALA 5.1 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 773 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B CYS 3.4 25.4 - - - +
748B ALA* 4.8 0.2 - - - -
750B CYS 4.6 0.2 - - - -
751B GLY* 2.8 33.2 - - - +
752B PRO* 3.3 5.7 - - - +
753B HIS* 3.3 29.5 + - - +
755B PRO* 4.1 8.5 - - + +
769B ALA 3.3 11.5 + - - +
770B VAL 3.0 9.5 + - - +
772B ARG* 1.3 78.5 - - - +
774B GLU* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 774 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B ARG* 2.9 36.0 + - - +
750B CYS* 3.0 25.4 - - + +
751B GLY* 4.3 1.6 - - - -
752B PRO* 5.0 2.8 - - - +
753B HIS* 4.3 5.2 + - - -
770B VAL* 2.9 22.6 + - - +
771B ARG* 3.6 15.7 - - - +
773B ALA* 1.3 76.0 - - - +
775B GLY* 1.3 61.9 + - - +
776B ARG* 3.3 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 775 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B HIS* 4.0 16.8 - - - -
771B ARG 2.6 10.9 + - - -
772B ARG* 2.7 17.1 + - - -
774B GLU* 1.3 77.8 - - - +
776B ARG* 1.3 57.7 + - - +
777B ALA 4.3 0.9 - - - -
----------------------------------------------------------
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