Contacts of the strand formed by residues 925 - 932 (chain A) in PDB entry 3NZ0
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 925 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A PHE* 5.1 7.4 - - - -
915A CYS* 3.6 0.3 - - - -
916A TYR* 2.8 39.5 + - + +
924A GLY* 1.3 71.2 - - - -
926A MET* 1.3 72.3 + - - +
927A VAL* 3.7 11.9 + - + +
963A LYS* 3.2 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A ILE* 2.6 39.0 - - + -
913A LEU* 3.7 13.9 - - + -
914A TYR 3.4 13.9 - - - +
915A CYS* 3.7 23.1 - - - -
924A GLY 4.2 4.5 - - - +
925A GLU* 1.3 80.9 - - - +
927A VAL* 1.3 63.1 + - - +
963A LYS* 5.5 1.0 - - - -
980A TYR* 3.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A PHE* 4.4 9.2 - - + -
897A LEU* 5.8 1.6 - - + -
913A LEU* 3.7 4.4 - - - +
914A TYR* 2.9 44.2 + - + +
916A TYR* 4.3 17.0 - - + -
925A GLU* 4.1 18.4 - - + +
926A MET* 1.3 80.1 - - - +
928A ALA* 1.3 59.3 + - - +
929A VAL* 4.0 18.7 + - + -
963A LYS* 3.9 24.7 - - + -
977A VAL* 3.9 15.3 - - + -
978A MET 3.8 7.0 - - - +
980A TYR* 4.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A IZA 3.2 45.3 - - + +
903A LEU* 4.3 4.7 - - + -
911A VAL* 3.9 11.0 - - + -
912A SER 3.5 6.3 - - - +
927A VAL* 1.3 72.7 - - - +
929A VAL* 1.3 60.3 + - - +
930A LYS 4.2 0.2 - - - -
976A LEU 3.7 0.3 - - - +
977A VAL* 3.4 3.1 - - - +
978A MET* 2.7 39.4 + - + +
979A GLU 3.6 6.7 - - - +
980A TYR* 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A LEU* 4.3 13.0 - - + -
910A LYS 3.7 1.7 - - - +
911A VAL* 3.5 2.0 - - - -
912A SER* 2.9 34.0 + - - -
914A TYR* 3.5 31.5 - - + -
927A VAL* 4.0 16.4 - - + -
928A ALA* 1.3 79.6 - - - +
930A LYS* 1.3 62.1 + - - +
931A ALA* 4.3 0.3 + - - +
975A GLN* 3.4 46.1 + - + +
976A LEU 3.2 6.5 - - - +
977A VAL* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A IZA 4.6 3.0 - - - +
906A GLY* 4.7 2.2 - - - -
908A PHE 5.5 0.2 - - - +
909A GLY* 3.7 33.7 - - - +
910A LYS 3.4 6.5 - - - +
911A VAL* 3.8 21.1 - - + +
928A ALA 4.2 0.4 - - - -
929A VAL* 1.3 74.4 - - - +
931A ALA* 1.3 62.7 + - - +
944A TRP* 3.4 19.5 - - + -
947A GLU* 2.7 30.4 + - - +
975A GLN* 3.4 7.1 - - - +
976A LEU* 2.7 38.9 + - + +
978A MET* 3.9 22.2 - - + +
1041A ASP* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A GLY* 2.9 20.8 - - - -
910A LYS* 3.0 17.1 + - + +
929A VAL 5.5 0.2 - - - +
930A LYS* 1.3 74.7 - - - +
932A LEU* 1.3 70.1 + - - +
933A LYS* 4.2 0.2 - - - -
944A TRP* 4.0 4.5 - - - -
974A LEU 4.9 0.9 - - - +
975A GLN* 3.8 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 932 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A PHE* 3.4 17.7 - - + +
909A GLY* 4.3 1.1 - - - -
931A ALA* 1.3 77.0 - - - +
933A LYS* 1.3 67.3 + - - +
934A ALA* 3.5 2.4 + - - -
936A CYS* 3.4 46.4 - - + +
937A GLY 4.6 3.6 - - - +
940A HIS* 4.2 8.7 - - + -
941A ARG* 4.1 36.8 - - + +
944A TRP* 3.8 36.6 - - + +
973A SER* 4.5 13.8 + - - +
974A LEU 4.8 1.4 + - - -
----------------------------------------------------------
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