Contacts of the helix formed by residues 680 - 687 (chain B) in PDB entry 6WCZ
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 LEU 680 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ARG* 3.4 26.7 - - - +
677B ALA 4.2 1.8 - - - +
678B HIS* 3.8 7.4 + - + -
679B ALA* 1.3 90.9 - - - +
681B ARG* 1.3 66.5 + - + +
682B PHE* 3.5 2.1 - - - -
683B LEU* 4.0 15.1 - - + +
684B ASN* 2.6 41.8 + - - +
690B ARG* 3.6 26.2 - - - +
696B TRP* 3.5 26.0 - - + +
697B LYS 3.5 26.2 - - - +
698B PRO* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B GLU* 4.8 12.9 + - - +
633B MET* 3.3 56.9 - - + +
636B LEU* 6.1 3.1 - - + -
678B HIS 5.4 5.0 + - - -
679B ALA* 6.1 0.6 - - - +
680B LEU* 1.3 77.6 - - + +
682B PHE* 1.3 61.3 + - + +
683B LEU 3.1 1.1 - - - -
684B ASN* 2.9 25.6 + - - +
685B ASP* 2.9 15.0 + - - +
696B TRP* 3.8 25.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B THR* 5.0 4.5 - - + +
619B VAL 4.9 1.1 - - - -
622B ILE* 3.8 26.0 - - + -
623B ARG* 3.6 37.5 - - + -
626B GLU* 3.5 32.8 - - + -
631B LEU* 5.3 10.8 - - + -
636B LEU* 4.8 19.0 - - + +
679B ALA 3.4 37.0 - - - -
680B LEU* 3.5 0.9 - - - -
681B ARG* 1.3 82.9 - - + +
683B LEU* 1.3 73.0 + - + +
685B ASP* 3.0 12.9 + - - +
686B MET* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASP* 5.2 3.4 - - - +
619B VAL* 5.1 14.1 - - + +
620B GLN* 6.3 1.3 - - + -
623B ARG* 3.7 41.7 - - + +
679B ALA 4.6 2.2 - - - +
680B LEU* 4.0 15.7 - - + +
681B ARG 3.1 1.0 - - - -
682B PHE* 1.3 89.0 - - + +
684B ASN* 1.3 65.5 + - - +
686B MET* 3.2 15.3 + - + +
687B GLY 2.6 29.5 + - - -
688B LYS* 3.3 40.2 + - + +
689B VAL* 5.2 0.4 - - - -
690B ARG* 5.3 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B LEU* 2.6 24.1 + - - +
681B ARG 2.9 8.3 + - - +
683B LEU* 1.3 86.6 - - - +
685B ASP* 1.3 64.4 + - - +
687B GLY* 3.4 13.5 + - - +
688B LYS 4.8 0.2 - - - +
689B VAL* 4.4 19.2 - - + +
690B ARG* 5.9 0.9 + - - +
695B GLU* 3.1 38.6 + - + +
696B TRP* 3.7 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PRO 5.1 2.3 - - - +
367B PRO* 3.3 30.8 - - - +
368B GLN* 3.7 23.4 + - - +
371B THR* 2.9 27.6 + - - +
636B LEU* 5.5 9.6 - - + -
681B ARG 2.9 8.1 + - - +
682B PHE* 3.0 18.8 + - - +
684B ASN* 1.3 76.5 - - - +
686B MET* 1.3 64.0 + - - +
687B GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PRO 5.5 1.6 - - - +
367B PRO* 4.5 15.6 - - + +
371B THR* 3.9 19.5 - - + -
375B MET* 3.6 32.3 - - + +
542B ARG* 4.6 4.3 + - - +
544B SER* 5.6 4.2 + - - -
547B ASP* 6.0 1.8 - - - +
619B VAL* 3.7 32.5 - - + -
622B ILE* 4.5 7.0 - - + -
682B PHE* 2.9 37.5 + - + +
683B LEU* 3.5 13.7 - - - +
685B ASP* 1.3 77.1 - - - +
687B GLY* 1.3 62.9 + - - +
688B LYS* 4.2 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ARG* 3.5 42.7 + - - +
683B LEU 2.6 14.2 + - - -
684B ASN* 3.4 13.4 + - - -
685B ASP 3.2 2.0 - - - -
686B MET* 1.3 75.1 - - - +
688B LYS* 1.3 64.7 + - - +
689B VAL* 3.7 8.3 + - - -
----------------------------------------------------------
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