Contacts of the helix formed by residues 687 - 692 (chain B) in PDB entry 6UZA
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 GLU 687 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A LEU* 4.9 5.4 - - + -
687A GLU* 5.3 8.5 - - - +
665B ASN* 5.6 2.9 + - - -
685B LEU 4.4 8.9 - - - +
686B SER* 1.3 80.1 - - - +
688B VAL* 1.3 61.6 + - - +
689B LYS* 3.2 30.8 - - + +
690B SER* 2.9 25.8 + - - -
708B TYR* 4.0 5.6 - - - -
687C GLU* 5.3 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A TRP* 3.8 35.4 - - + +
685A LEU* 3.7 45.5 - - + +
687B GLU* 1.3 73.4 - - - +
689B LYS* 1.3 58.8 + - - +
690B SER* 3.1 6.2 + - - -
691B VAL* 3.3 19.8 - - + +
692B VAL* 4.0 5.2 - - - +
705B TYR* 3.6 29.0 + - + +
708B TYR* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B GLN* 3.6 50.0 + - + +
665B ASN* 3.5 23.7 - - - +
687B GLU* 3.8 26.2 - - + +
688B VAL* 1.3 78.0 - - - +
690B SER* 1.3 57.2 + - - +
691B VAL 3.3 4.0 + - - -
692B VAL* 3.7 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LYS* 2.7 27.2 + - - -
665B ASN* 3.4 24.2 - - - -
667B ALA* 3.8 16.1 - - - +
668B PHE* 3.4 17.3 - - - -
677B THR* 3.9 16.2 - - - +
686B SER* 6.0 0.2 - - - -
687B GLU* 2.9 23.4 + - - -
688B VAL 3.1 0.4 - - - -
689B LYS* 1.3 77.6 - - - +
691B VAL* 1.3 56.9 + - - +
708B TYR* 4.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B MET* 5.3 0.4 - - - -
656B TYR* 2.5 32.9 + - + +
663B LYS* 3.5 5.4 - - - +
668B PHE* 4.0 17.5 - - + -
688B VAL* 3.3 20.2 - - + +
690B SER* 1.3 84.9 - - - +
692B VAL* 1.3 59.6 + - - +
693B ILE 3.9 0.2 + - - -
701B GLU* 3.6 11.8 - - - +
704B GLY 4.0 19.5 - - - +
705B TYR* 3.8 35.9 - - + +
708B TYR* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LYS* 3.5 8.1 + - - +
664B GLN* 3.2 42.7 + - + +
688B VAL 4.0 11.9 - - - +
689B LYS* 3.7 15.0 + - + +
690B SER 3.6 0.6 - - - -
691B VAL* 1.3 81.2 - - - +
693B ILE* 1.3 73.7 + - - +
694B ASN* 5.4 0.4 - - - +
698B LYS* 5.3 1.1 - - - +
701B GLU* 4.2 17.3 - - - +
705B TYR* 3.6 23.6 - - + +
----------------------------------------------------------
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