Contacts of the helix formed by residues 877 - 892 (chain A) 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 877 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A PRO* 3.7 31.0 + - + -
768A PRO 2.9 27.8 + - - +
769A MET* 3.5 17.0 - - - -
773A GLU* 2.9 20.0 + - - +
875A LYS 3.7 2.1 + - - -
876A PRO* 1.3 77.5 - - - +
878A LEU* 1.3 63.6 + - - +
879A ASN* 2.8 23.8 + - - +
880A ALA* 3.1 11.3 + - - +
881A ILE* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A PRO* 5.3 3.2 - - + +
877A ASN* 1.3 75.7 - - - +
879A ASN* 1.3 61.7 + - - +
881A ILE* 3.5 19.5 + - + -
882A ARG* 3.0 72.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ALA 3.5 16.2 - - - +
763A GLY* 3.6 25.1 + - - +
764A GLY 4.6 1.7 - - - +
766A ASP 3.6 8.0 - - - +
767A PRO* 3.4 26.8 - - - +
769A MET* 4.0 6.7 - - + -
877A ASN* 2.8 9.2 + - - +
878A LEU* 1.3 77.0 - - - +
880A ALA* 1.3 57.6 + - - +
882A ARG* 3.5 20.4 + - - +
883A SER* 2.7 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A TRP* 3.4 26.9 - - + -
769A MET* 4.1 3.3 - - - +
773A GLU* 3.2 37.5 - - + +
876A PRO* 4.6 4.3 - - + -
877A ASN* 3.1 12.4 + - - +
879A ASN* 1.3 74.2 - - - +
881A ILE* 1.3 61.4 + - - +
883A SER* 3.5 0.9 - - - -
884A LEU* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A LYS* 6.0 1.3 - - + -
876A PRO* 3.6 35.4 - - + +
877A ASN 3.1 12.9 + - - +
878A LEU* 3.8 20.4 - - + +
879A ASN 3.3 0.4 - - - -
880A ALA* 1.3 77.6 - - - +
882A ARG* 1.3 57.5 + - + +
884A LEU* 3.5 9.1 + - + +
885A GLU* 2.8 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A LEU* 3.0 59.2 + - + +
879A ASN* 3.9 18.3 - - - +
880A ALA 3.4 0.2 - - - -
881A ILE* 1.3 74.2 - - + +
883A SER* 1.3 66.1 + - - +
885A GLU* 3.3 9.0 + - + +
886A ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 883 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 4.7 2.1 - - - +
759A VAL* 5.8 0.9 - - - -
760A ALA 3.8 14.5 + - - -
761A TRP* 3.7 18.9 - - - -
762A ALA* 3.1 29.6 + - - +
879A ASN 2.7 23.0 + - - -
880A ALA 3.5 5.4 - - - -
882A ARG* 1.3 76.8 - - - +
884A LEU* 1.3 61.3 + - - +
886A ALA* 3.2 9.7 + - - +
887A VAL* 3.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A VAL* 3.6 31.0 - - + -
761A TRP* 4.1 8.7 - - + -
773A GLU 4.7 0.2 - - - +
776A ALA* 4.1 16.8 - - + +
777A ALA* 4.0 29.4 - - + +
780A ILE* 4.3 13.7 - - + -
781A VAL* 3.7 21.8 - - + -
876A PRO* 6.1 0.9 - - + -
880A ALA* 2.9 24.3 + - + +
881A ILE* 3.9 6.3 - - + +
883A SER* 1.3 73.4 - - - +
885A GLU* 1.3 59.8 + - - +
887A VAL* 3.1 5.1 + - + +
888A ILE* 2.9 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A ILE* 2.8 22.1 + - + +
882A ARG* 3.5 10.5 - - - +
883A SER 3.3 0.2 - - - -
884A LEU* 1.3 76.9 - - - +
886A ALA* 1.3 57.4 + - - +
888A ILE* 3.4 7.6 + - - +
889A ARG* 3.0 29.2 + - + +
900A ARG* 2.7 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 886 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 3.7 17.5 - - + -
882A ARG 3.0 12.9 + - - +
883A SER* 3.5 10.5 - - - +
884A LEU 3.2 0.2 - - - -
885A GLU* 1.3 74.3 - - - +
887A VAL* 1.3 63.7 + - - +
889A ARG* 3.4 6.7 + - - +
890A VAL* 3.2 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 887 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 3.6 14.4 - - + -
757A VAL* 4.0 26.5 - - + -
758A ASN 3.6 21.1 - - - +
759A VAL* 3.9 16.4 - - + -
760A ALA 4.5 0.9 - - - +
781A VAL* 4.1 20.9 - - + -
785A ILE* 5.7 0.2 - - + -
883A SER 3.1 15.4 + - - +
884A LEU* 3.1 13.2 + - - +
886A ALA* 1.3 75.7 - - - +
888A ILE* 1.3 57.0 + - - +
890A VAL* 3.4 0.3 + - - +
891A HIS* 3.0 37.7 + - + +
898A MET* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 888 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A ILE* 3.7 28.7 - - + -
781A VAL* 4.7 3.6 - - + -
884A LEU* 2.9 26.5 + - + +
885A GLU* 3.7 7.6 - - - +
887A VAL* 1.3 75.3 - - - +
889A ARG* 1.3 64.2 + - - +
891A HIS 3.9 0.2 - - - -
892A SER* 3.1 24.1 + - - -
898A MET* 3.5 45.4 - - - +
900A ARG* 3.5 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 889 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A GLU* 3.0 18.7 + - + +
886A ALA* 3.7 8.5 - - - +
887A VAL 3.4 0.2 - - - -
888A ILE* 1.3 77.4 - - - +
890A VAL* 1.3 59.7 + - + +
892A SER* 3.0 20.4 + - - -
893A LYS* 4.7 0.5 + - - +
900A ARG* 4.5 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 890 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 3.4 28.3 - - + +
745A ASP* 4.6 11.0 - - - +
747A VAL* 3.3 34.5 - - + -
886A ALA* 3.2 17.6 + - + +
887A VAL 3.9 3.1 - - - +
888A ILE 3.3 0.2 - - - -
889A ARG* 1.3 80.0 - - + +
891A HIS* 1.3 63.6 + - + +
892A SER 3.3 1.3 + - - -
893A LYS* 3.6 19.2 + - - +
894A TYR* 4.1 4.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 891 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 4.7 5.7 + - + -
747A VAL* 4.0 14.4 - - + +
754A GLY* 3.4 23.3 + - - -
756A ASN 3.1 27.9 + - - -
757A VAL* 3.5 28.7 - - + +
758A ASN 4.7 1.9 + - - -
785A ILE* 4.9 2.5 - - + -
887A VAL* 3.0 24.9 + - + +
890A VAL* 1.3 83.7 - - + +
892A SER* 1.3 55.5 + - - +
893A LYS 3.1 5.6 - - - -
894A TYR* 3.1 9.0 + - - -
895A TRP* 2.9 50.1 + + + -
898A MET* 3.6 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 892 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A ILE* 3.1 15.0 + - - -
889A ARG* 3.0 19.8 + - - -
891A HIS* 1.3 76.3 - - - +
893A LYS* 1.3 58.0 + - - +
894A TYR 3.2 0.2 - - - -
898A MET* 3.4 25.6 - - - -
899A GLN* 2.9 38.0 - - - +
900A ARG 5.2 0.7 - - - -
----------------------------------------------------------
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