Contacts of the strand formed by residues 756 - 761 (chain B) in PDB entry 3ZNS
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 ASN 756 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B GLN* 3.1 41.6 + - - +
718B PHE 5.8 1.4 - - - +
719B TYR* 4.1 8.7 - - + +
726B TYR* 3.4 28.9 - - - +
746B GLU 2.8 25.5 + - - +
747B VAL* 3.2 26.4 + - - +
748B GLY* 3.8 6.5 - - - +
752B GLY 5.3 0.2 - - - +
754B GLY 3.4 0.8 - - - -
755B PHE* 1.3 79.2 - - - +
757B VAL* 1.3 63.2 + - - +
758B ASN* 3.4 7.5 + - - +
891B HIS* 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 757 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B LEU* 4.3 17.9 - - + -
726B TYR* 2.8 13.7 + - - +
727B ILE* 3.3 17.3 - - + +
728B SER 2.9 27.7 + - - +
754B GLY 4.4 3.4 - - - +
756B ASN* 1.3 73.6 - - - +
758B ASN* 1.3 64.6 + - - +
759B VAL* 4.5 3.6 - - + -
781B VAL* 4.1 15.7 - - + -
785B ILE* 4.1 16.4 - - + -
887B VAL* 4.1 17.5 - - + -
891B HIS* 3.5 36.3 - - + +
895B TRP* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 758 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B HIS* 3.1 24.8 + - - -
715B GLN* 2.9 21.7 + - - +
726B TYR* 4.5 1.4 - - - -
728B SER* 3.6 10.0 - - - -
730B HIS* 3.6 2.6 + - - +
742B GLY* 3.4 28.9 - - - +
743B ALA 3.1 24.0 + - - +
744B VAL* 3.8 13.4 + - - +
746B GLU* 3.5 8.6 + - - +
756B ASN* 3.4 13.4 + - - +
757B VAL* 1.3 72.0 - - - +
759B VAL* 1.3 60.8 + - - +
760B ALA 3.0 6.6 + - - -
887B VAL* 3.6 14.2 - - - +
891B HIS* 4.7 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B ILE* 4.6 6.1 - - + -
728B SER 2.7 17.1 + - - +
729B LEU* 3.5 19.6 - - + -
730B HIS* 3.2 22.5 + - - -
757B VAL* 4.5 7.2 - - + -
758B ASN* 1.3 68.8 - - - +
760B ALA* 1.3 57.9 + - - +
761B TRP* 3.4 31.4 + - + -
777B ALA* 4.5 0.7 - - + -
781B VAL* 4.0 30.1 - - + -
782B VAL* 5.1 2.0 - - + -
883B SER* 5.8 1.1 - - - -
884B LEU* 3.9 23.6 - - + -
887B VAL* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B HIS* 3.7 9.6 - - + -
732B HIS* 3.6 19.7 - - + +
742B GLY 3.5 24.5 - - - +
744B VAL* 4.1 21.0 - - + +
758B ASN 3.0 5.9 + - - +
759B VAL* 1.3 69.1 - - - +
761B TRP* 1.3 67.2 + - - +
762B ALA* 3.3 6.1 + - - +
883B SER* 3.7 13.8 + - - +
887B VAL* 4.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 761 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B LEU* 4.2 5.8 - - + +
730B HIS 3.0 41.1 + - - +
732B HIS* 2.9 26.6 + - - +
733B ASP* 3.1 9.7 + - - +
759B VAL* 4.0 19.5 - - + -
760B ALA* 1.3 69.4 - - - +
762B ALA* 1.3 60.2 + - - +
769B MET* 3.8 15.9 - - + -
773B GLU* 3.5 28.9 - - + -
774B TYR* 3.3 33.5 + + - -
777B ALA* 3.9 16.4 - - + -
813B TYR* 3.5 31.0 - + - +
880B ALA* 3.5 43.5 - - + -
883B SER* 3.7 9.2 - - - -
884B LEU* 4.4 8.5 - - + -
----------------------------------------------------------
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