Contacts of the helix formed by residues 837 - 858 (chain A) in PDB entry 3ZW3
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 ASP 837 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLN* 4.4 3.6 - - - +
836A ASP* 1.3 69.6 - - - +
838A LEU* 1.3 56.8 + - - +
839A ARG* 3.1 53.3 + - - +
840A GLN* 3.2 51.2 + - - +
841A ASP* 3.6 6.6 - - - +
871A SER* 4.8 0.7 + - - -
875A LYS* 3.6 27.8 + - + +
966A GLY* 4.0 6.5 + - - -
1038A GLY 4.1 6.4 - - - +
1040A PRO* 5.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A LYS* 4.3 22.4 - - + +
836A ASP* 3.2 13.0 + - + +
837A ASP* 1.3 69.0 + - - +
839A ARG* 1.3 58.1 + - - +
840A GLN 3.2 2.0 - - - -
841A ASP* 3.3 27.5 + - - +
842A MET* 2.9 31.7 + - - +
869A CYS* 4.1 18.4 - - - -
870A ILE 4.6 0.2 - - - +
871A SER* 4.1 19.1 + - - +
875A LYS* 5.4 0.8 - - - +
876A ILE 4.1 1.8 - - - +
877A GLY* 3.5 44.4 - - - +
878A MET 4.1 1.3 - - - +
879A ILE* 4.3 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LYS* 5.5 1.4 - - - +
701A SER* 3.7 7.6 - - - +
702A GLU* 3.2 36.0 + - - +
705A GLN* 3.2 47.1 + - - +
706A SER* 4.8 3.4 - - - -
837A ASP* 3.1 30.1 + - - +
838A LEU* 1.3 76.8 - - - +
840A GLN* 1.3 59.6 + - + +
842A MET* 3.4 17.2 + - + +
843A LEU* 3.3 32.2 + - + +
871A SER* 3.5 21.7 - - - +
874A ASP* 5.8 0.8 + - - -
1038A GLY* 5.4 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A ASP* 3.4 29.5 + - - +
838A LEU 3.2 0.6 - - - -
839A ARG* 1.3 73.2 - - - +
841A ASP* 1.3 63.6 + - - +
843A LEU* 3.4 3.8 + - - +
844A ILE* 3.1 28.5 + - - +
966A GLY* 3.4 28.2 + - - -
969A LEU* 3.5 23.1 - - + +
970A GLY* 3.4 18.2 - - - +
1038A GLY 3.5 25.4 - - - +
1039A MET* 3.7 28.6 - - + +
1040A PRO* 5.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A ASP* 5.1 0.7 - - - +
837A ASP 3.6 4.2 - - - +
838A LEU* 3.3 30.2 + - - +
840A GLN* 1.3 73.9 - - - +
842A MET* 1.4 62.9 + - - +
844A ILE* 3.3 2.4 + - - +
845A LEU* 3.0 36.1 + - + +
867A TYR* 4.2 5.0 + - + +
869A CYS* 4.0 14.6 - - - -
964A ASP* 3.7 8.8 + - - +
965A PHE* 2.9 36.4 + - + +
966A GLY* 2.9 26.9 + - - +
2191A ZW3 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU* 3.7 28.0 - - + +
665A GLN* 6.1 0.9 - - - +
698A PHE* 5.0 17.9 - - + -
701A SER* 4.1 10.5 - - - +
702A GLU* 5.6 2.7 - - - +
838A LEU 2.9 15.1 + - - +
839A ARG* 3.4 37.5 - - + +
840A GLN 3.3 0.2 - - - -
841A ASP* 1.4 74.7 - - - +
843A LEU* 1.3 57.9 + - + +
845A LEU* 3.5 7.6 + - - +
846A GLN* 3.0 29.3 + - - +
849A ARG* 5.1 1.2 + - - -
869A CYS* 3.6 22.4 - - - +
870A ILE* 4.1 9.2 - - - -
871A SER* 3.5 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU* 3.8 26.2 - - + -
662A GLN* 3.9 29.1 - - + +
665A GLN* 4.4 14.6 - - + +
839A ARG* 3.3 15.5 + - + +
840A GLN 3.8 6.1 - - - +
841A ASP 3.4 0.2 - - - -
842A MET* 1.3 77.0 - - + +
844A ILE* 1.3 64.2 + - - +
846A GLN* 3.3 4.1 + - + +
847A ILE* 3.1 26.7 + - + +
1034A MET* 3.8 25.8 - - + +
1037A THR* 4.4 4.9 - - - +
1038A GLY* 3.6 31.2 - - - +
1039A MET* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A GLN 3.1 12.5 + - - +
841A ASP 3.8 5.4 - - - +
843A LEU* 1.3 73.5 - - - +
845A LEU* 1.3 57.9 + - - +
847A ILE* 3.1 7.3 + - + +
848A LEU* 3.0 34.4 + - + +
942A LEU* 4.3 16.1 - - + +
944A ILE* 3.9 25.1 - - + -
965A PHE* 3.7 40.4 - - + -
969A LEU* 3.5 32.8 - - + -
1034A MET* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A ASP* 3.0 26.9 + - + +
842A MET* 3.9 4.5 - - - +
844A ILE* 1.3 74.6 - - - +
846A GLN* 1.3 61.3 + - - +
848A LEU* 3.4 11.4 + - + +
849A ARG* 3.2 39.8 + - - +
865A LEU 4.8 0.4 - - - +
866A PRO* 3.6 29.2 - - + +
867A TYR* 3.6 40.2 - - + +
869A CYS* 3.7 24.5 - - + -
965A PHE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU 4.2 5.7 + - - +
658A HIS* 2.8 42.5 + - - +
659A TYR* 5.6 0.4 - - - -
661A LEU* 4.3 27.1 - - + +
662A GLN* 5.7 7.0 - - + +
698A PHE* 5.7 4.5 - - - -
842A MET 3.0 17.3 + - - +
843A LEU* 3.7 6.1 - - + +
844A ILE 3.3 0.2 - - - -
845A LEU* 1.3 71.7 - - - +
847A ILE* 1.3 66.7 + - + +
849A ARG* 3.0 44.7 + - - +
850A ILE* 3.1 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLN* 4.3 14.6 - - - +
843A LEU* 3.1 8.2 + - + +
844A ILE* 3.1 8.7 + - - +
846A GLN* 1.3 76.3 - - + +
848A LEU* 1.3 58.1 + - - +
850A ILE* 3.1 10.2 + - + +
851A MET* 2.9 38.5 + - + +
942A LEU* 3.9 29.6 - - + -
1027A LEU* 4.7 13.5 - - + -
1030A LEU* 4.4 22.2 - - + +
1031A PHE 4.7 1.8 - - - +
1034A MET* 3.5 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A ILE* 3.0 19.8 + - + +
845A LEU* 3.5 28.5 - - + +
847A ILE* 1.3 75.5 - - - +
849A ARG* 1.4 55.1 + - - +
851A MET* 3.2 12.1 + - + +
852A GLU* 3.0 31.1 + - - +
864A LEU* 3.7 13.6 - - + +
866A PRO* 4.4 9.2 - - + -
935A TYR* 4.1 29.6 - - + +
938A ALA* 3.8 29.4 - - + -
939A THR* 6.1 0.7 - - - +
942A LEU* 4.2 15.7 - - + -
944A ILE* 5.9 1.8 - - + -
965A PHE* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A HIS* 4.4 13.7 + - + +
842A MET 5.1 1.2 + - - -
845A LEU* 3.2 33.2 + - - +
846A GLN* 3.0 44.2 + - - +
848A LEU* 1.4 73.6 - - - +
850A ILE* 1.3 62.6 + - - +
852A GLU* 3.3 10.3 + - - +
853A SER* 3.1 21.8 + - - -
866A PRO* 3.0 41.5 + - + +
867A TYR 3.5 15.0 + - - -
868A GLY* 4.4 5.5 - - - +
869A CYS 5.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A HIS* 3.7 27.1 - - + +
659A TYR* 3.7 39.0 - - + +
662A GLN* 4.8 4.9 - - + +
846A GLN* 3.1 22.8 + - + +
847A ILE* 3.1 11.9 + - - +
849A ARG* 1.3 75.2 - - - +
851A MET* 1.4 58.5 + - - +
853A SER* 2.8 26.0 + - - +
854A ILE* 3.0 28.9 + - + +
1026A LEU* 4.4 3.4 - - + -
1027A LEU* 5.0 3.8 - - + -
1030A LEU* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 851 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ILE* 2.9 26.7 + - + +
848A LEU* 3.5 18.8 - - + +
850A ILE* 1.4 75.5 - - - +
852A GLU* 1.3 56.4 + - - +
854A ILE* 3.2 9.9 + - - +
855A TRP* 3.0 54.4 + - + -
864A LEU* 4.4 1.6 - - + -
938A ALA* 2.9 49.6 - - + +
941A VAL* 5.4 3.6 - - - -
942A LEU* 4.7 4.5 - - - -
1020A LEU* 3.9 25.1 - - + -
1027A LEU* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 852 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 5.2 0.3 + - - -
298A LYS* 5.2 4.8 + - - -
848A LEU 3.0 16.6 + - - +
849A ARG* 3.5 11.9 - - - +
850A ILE 3.3 0.4 - - - -
851A MET* 1.3 76.6 - - - +
853A SER* 1.3 55.1 + - - +
855A TRP* 3.5 11.7 + - + +
856A GLU* 3.0 27.8 + - - +
860A LEU 4.8 1.2 - - - +
861A ASP* 4.1 7.6 - - - +
862A LEU 4.5 3.1 + - - -
863A CYS* 4.0 7.4 + - - -
864A LEU* 3.2 50.9 + - + +
866A PRO* 4.0 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 853 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 5.8 6.3 - - - -
658A HIS* 4.2 25.0 + - - -
659A TYR* 5.5 1.7 + - - -
849A ARG 3.1 11.4 + - - -
850A ILE* 2.8 24.3 + - - +
852A GLU* 1.3 72.5 - - - +
854A ILE* 1.4 65.6 + - - +
856A GLU* 3.2 14.9 + - - +
857A THR* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A ILE* 3.0 34.1 + - + +
851A MET* 3.4 9.0 - - - +
853A SER* 1.4 78.2 + - - +
855A TRP* 1.3 64.6 + - + +
857A THR* 2.6 31.5 + - - -
858A GLU* 3.6 5.0 - - - +
1019A ALA* 3.9 15.5 - - + +
1020A LEU* 4.1 23.3 - - + -
1023A HIS* 3.4 50.5 - - + +
1026A LEU* 4.4 7.0 - - + -
1027A LEU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A MET* 3.0 42.2 + - + +
852A GLU* 3.8 11.0 - - + +
853A SER 3.4 0.2 - - - -
854A ILE* 1.3 74.8 - - - +
856A GLU* 1.3 60.6 + - - +
858A GLU* 3.0 13.1 + - - +
860A LEU* 2.9 42.1 + - + +
862A LEU* 3.5 35.2 - - + +
864A LEU* 3.8 23.1 - - + -
934A GLY* 3.7 20.2 - - - -
937A VAL* 4.0 12.6 - - + -
938A ALA* 4.4 0.2 - - + -
1016A ALA* 3.0 33.9 + - + +
1019A ALA* 3.8 20.0 - - + -
1020A LEU* 3.6 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 4.6 17.4 - - - +
206A PRO 4.1 5.0 - - - +
208A PRO* 3.7 27.6 - - + +
210A TYR* 3.2 26.5 + - - +
294A ARG* 4.1 13.0 + - - -
298A LYS* 5.5 1.9 + - - -
852A GLU 3.0 14.6 + - - +
853A SER* 3.3 17.1 - - - +
854A ILE 3.2 0.2 - - - -
855A TRP* 1.3 75.5 - - - +
857A THR* 1.4 56.5 + - + +
858A GLU 3.0 0.2 - - - -
859A SER* 2.9 21.6 + - - +
860A LEU 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 6.2 4.7 - - + -
853A SER* 3.1 19.0 + - - +
854A ILE* 2.6 21.0 + - - +
856A GLU* 1.4 75.5 - - + +
858A GLU* 1.3 67.6 + - - +
859A SER* 3.5 1.8 + - - -
1023A HIS* 4.2 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A ILE 3.6 7.9 - - - +
855A TRP 3.0 6.0 + - - +
857A THR* 1.3 91.5 + - - +
859A SER* 1.3 69.6 + - - +
860A LEU* 3.3 20.5 + - + +
1019A ALA* 3.7 30.0 - - + +
1022A HIS* 3.3 34.4 + - - +
1023A HIS* 4.2 6.2 + - - -
----------------------------------------------------------
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