Contacts of the helix formed by residues 782 - 792 (chain K) in PDB entry 3ZPV
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 782 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776K ARG* 3.6 1.6 - - - +
780K GLY 4.7 0.9 - - - +
781K LEU* 1.3 76.8 - - - +
783K GLU* 1.3 64.7 + - - +
784K ALA* 4.1 0.9 - - - +
785K ALA* 3.0 19.4 + - - +
786K PHE* 3.0 21.5 + - - +
332L ASN* 2.7 38.6 + - + +
335L ALA* 4.6 2.1 - - - +
782Q THR* 5.8 8.1 - - + -
336R GLU* 3.2 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 783 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762K GLU* 4.8 10.4 - - - +
776K ARG* 3.5 31.6 + - - +
782K THR* 1.3 73.8 - - - +
784K ALA* 1.3 61.0 + - - +
786K PHE* 3.5 7.4 + - + +
787K GLN* 3.1 46.2 + - - +
336R GLU* 3.2 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 784 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782K THR* 3.2 1.3 - - - +
783K GLU* 1.3 78.2 - - - +
785K ALA* 1.3 64.6 + - - +
787K GLN* 3.3 13.0 + - - +
788K MET* 3.0 35.1 + - + +
335L ALA* 4.0 8.7 - - + -
339L LEU* 3.9 25.4 - - + -
336R GLU* 3.4 20.6 + - - +
340R SER* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 785 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781K LEU* 4.2 3.8 - - + -
782K THR* 3.0 11.9 + - - +
784K ALA* 1.3 76.0 - - - +
786K PHE* 1.3 57.5 + - - +
788K MET* 3.3 3.2 + - - +
789K LEU* 2.9 36.1 + - - +
331L ALA* 3.4 30.1 - - + +
332L ASN* 3.2 28.0 - - - +
335L ALA* 3.6 10.2 - - + +
346L ILE* 5.2 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 786 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791I LYS* 4.2 17.5 - - + -
762K GLU* 3.8 38.1 - - + -
763K ALA 3.4 34.5 - - - -
764K VAL* 4.0 17.0 - - + -
776K ARG* 3.4 28.9 - - + -
781K LEU* 4.5 7.7 - - + +
782K THR 3.0 16.8 + - - +
783K GLU* 3.6 8.3 - - + +
785K ALA* 1.3 78.3 - - - +
787K GLN* 1.3 63.7 + - + +
789K LEU* 3.8 3.6 - - - +
790K ASN* 3.0 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 787 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783K GLU* 3.1 40.9 + - - +
784K ALA* 3.3 12.1 + - - +
786K PHE* 1.3 87.1 - - + +
788K MET* 1.3 60.8 + - + +
790K ASN* 3.5 5.5 + - - +
791K LYS* 3.1 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 788 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784K ALA* 3.0 21.4 + - + +
785K ALA* 3.9 3.6 - - - +
787K GLN* 1.3 76.1 - - + +
789K LEU* 1.3 65.0 + - - +
791K LYS* 3.8 28.0 - - - +
792K GLU* 3.1 31.6 + - + +
335L ALA* 3.8 33.9 - - + +
338L VAL* 3.7 34.1 - - + -
339L LEU* 4.1 19.7 - - + -
345L THR* 6.1 0.2 - - - -
346L ILE* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 789 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764K VAL* 5.1 4.7 - - + -
781K LEU* 4.1 23.6 - - + -
785K ALA 2.9 20.8 + - - +
786K PHE* 3.8 4.7 - - - +
788K MET* 1.3 77.1 - - - +
790K ASN* 1.3 67.3 + - - +
791K LYS 3.3 0.2 + - - -
792K GLU 3.4 17.0 - - - +
795K ALA* 4.1 13.9 - - + +
796K GLU* 4.5 10.1 - - - +
797K TRP* 4.1 17.7 - - + -
326L PHE* 3.8 35.9 - - + -
331L ALA* 3.8 20.2 - - + -
346L ILE* 3.9 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 790 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790I ASN* 3.2 49.8 + - + +
791I LYS* 4.0 8.4 + - - +
763K ALA 5.1 1.8 + - - +
764K VAL* 5.0 5.0 - - - +
786K PHE* 3.0 59.2 + - - +
787K GLN* 3.9 5.5 - - - +
789K LEU* 1.3 82.9 - - - +
791K LYS* 1.3 60.1 + - + +
792K GLU 4.8 1.9 - - - -
793K VAL* 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 791 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761I ASP 5.3 3.6 - - - +
762I GLU* 5.6 1.0 - - + +
763I ALA 4.9 4.2 + - - +
786I PHE* 4.2 17.5 - - + -
790I ASN* 3.8 19.5 + - + +
787K GLN* 3.1 20.8 + - + +
788K MET* 3.3 38.8 + - - +
789K LEU 3.2 0.6 - - - -
790K ASN* 1.3 75.9 - - + +
792K GLU* 1.3 76.0 + - - +
793K VAL 3.5 3.3 + - - -
338L VAL* 6.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 792 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759I ASP* 2.8 28.6 - - - +
760I ASN* 4.9 1.6 - - - -
761I ASP 4.9 5.7 - - - +
788K MET* 3.1 20.7 + - + +
789K LEU 3.4 10.2 - - - +
790K ASN 4.8 1.8 - - - -
791K LYS* 1.3 90.6 - - + +
793K VAL* 1.3 65.2 + - - +
794K PHE* 3.1 1.6 - - - +
795K ALA* 3.0 28.3 + - + +
345L THR* 3.5 26.0 - - - +
346L ILE* 4.1 14.1 - - + +
347L ILE* 3.5 15.7 - - + +
----------------------------------------------------------
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