Contacts of the helix formed by residues 881 - 901 (chain A) in PDB entry 6MZL
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 SER 881 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A LEU* 5.2 1.6 - - - -
789A PHE* 5.5 0.3 - - - -
877A ARG 4.6 3.6 - - - -
878A ALA 5.4 0.2 + - - -
880A VAL* 1.3 86.2 - - - +
882A PRO* 1.3 70.9 - - - +
883A GLU* 3.5 17.8 + - - +
884A GLN* 3.2 40.8 + - - +
885A CYS* 3.6 5.8 + - - -
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Residues in contact with PRO 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A HIS* 4.2 19.1 - - + +
595A ALA 3.7 26.7 - - - +
596A VAL* 4.5 11.0 - - + +
598A LEU* 5.2 2.0 - - + -
603A PHE* 3.6 26.7 - - + -
696A MET* 3.8 19.7 - - + -
880A VAL 4.5 2.2 - - - +
881A SER* 1.3 86.7 - - - +
883A GLU* 1.3 65.7 + - - +
885A CYS* 3.4 4.5 + - + +
886A CYS* 3.4 26.9 + - - -
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Residues in contact with GLU 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A HIS* 2.7 33.5 + - - -
696A MET* 4.5 3.1 - - + -
746A ASN* 3.3 42.4 + - + +
747A LEU* 3.7 33.4 - - + +
789A PHE* 3.6 23.6 - - + -
881A SER* 3.2 20.3 + - - +
882A PRO* 1.3 81.7 - - - +
884A GLN* 1.3 63.1 + - - +
886A CYS 3.4 1.4 + - - -
887A ALA 3.3 15.9 + - - -
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Residues in contact with GLN 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A PHE* 3.8 12.7 - - + -
798A ARG* 3.4 28.7 + - - +
802A HIS* 3.2 30.2 + - + +
879A MET 4.1 7.0 + - - +
880A VAL* 3.9 10.6 - - + +
881A SER* 3.2 33.7 + - - +
882A PRO 3.3 0.6 - - - -
883A GLU* 1.3 74.4 - - - +
885A CYS* 1.3 66.0 + - - +
887A ALA* 3.5 3.8 + - - +
888A TYR* 3.3 15.8 + - - +
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Residues in contact with CYS 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A LEU* 3.8 18.4 - - - -
603A PHE* 4.7 7.9 - - + -
802A HIS* 3.4 17.3 - - + -
806A PHE* 4.3 10.5 - - - -
880A VAL* 3.7 27.6 - - - -
881A SER 3.6 5.1 + - - -
882A PRO* 3.8 9.0 - - + +
883A GLU 3.3 0.4 - - - -
884A GLN* 1.3 79.6 - - - +
886A CYS* 1.3 52.5 + - - +
888A TYR* 3.2 2.3 + - - +
889A TYR* 2.7 60.4 + - + -
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Residues in contact with CYS 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PHE* 5.4 0.4 - - - -
615A PHE* 5.6 0.7 - - - -
690A LEU* 3.9 5.6 - - + +
691A MET 3.2 29.1 + - - +
693A GLN* 4.1 17.3 - - - -
696A MET* 3.6 25.4 - - - -
747A LEU* 4.2 11.7 - - + -
882A PRO 3.4 14.8 - - - -
883A GLU 3.4 7.5 + - - +
884A GLN 3.3 0.6 - - - -
885A CYS* 1.3 77.4 - - - +
887A ALA* 1.3 58.2 + - - +
889A TYR* 3.7 7.9 - - - +
890A SER* 2.9 30.7 + - - -
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Residues in contact with ALA 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A LEU* 3.8 12.0 - - + +
789A PHE* 3.6 33.2 - - + -
790A GLU 3.6 15.0 - - - +
791A VAL* 3.5 9.1 - - - +
792A PRO* 3.4 21.0 - - + +
798A ARG* 4.7 2.0 - - - +
883A GLU 3.3 3.2 + - - -
884A GLN 3.7 5.6 - - - +
885A CYS 3.3 0.6 - - - -
886A CYS* 1.3 79.9 - - - +
888A TYR* 1.3 59.6 + - - +
890A SER 3.7 0.2 + - - -
891A MET* 3.4 14.9 + - - +
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Residues in contact with TYR 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A THR 6.0 1.6 - - - -
792A PRO* 4.4 7.1 - - + +
798A ARG* 6.0 0.9 - - - +
799A ALA* 4.7 9.0 - - + -
802A HIS* 3.6 34.3 - + + +
803A ILE* 3.5 44.5 - - + +
884A GLN 3.3 3.3 + - - +
885A CYS 3.2 6.1 + - - +
887A ALA* 1.3 78.3 - - - +
889A TYR* 1.3 80.9 + + - +
891A MET* 3.2 29.3 + - + +
892A ILE* 3.2 53.5 + - + +
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Residues in contact with TYR 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PHE* 3.7 11.5 - + - +
604A PRO* 2.4 51.9 + - + -
605A THR 5.7 2.0 - - - -
607A MET* 3.7 20.0 - - + +
615A PHE* 3.6 24.3 - + + -
693A GLN* 4.0 27.6 - - + -
802A HIS* 6.0 0.7 - + - -
806A PHE* 4.5 8.1 - + - -
885A CYS* 2.7 43.8 + - + +
886A CYS* 3.7 9.2 - - - +
888A TYR* 1.3 91.3 - + - +
890A SER* 1.3 61.3 + - - +
892A ILE* 3.6 6.9 - - + +
893A ALA* 3.3 24.9 + - - +
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Residues in contact with SER 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A PHE* 4.7 8.7 - - - -
688A GLY 4.1 4.5 + - - -
689A PRO* 2.8 32.2 + - - +
690A LEU* 4.7 1.8 - - - -
691A MET* 5.8 1.8 - - - -
791A VAL* 4.4 3.4 - - - -
886A CYS 2.9 17.8 + - - -
887A ALA* 3.9 6.1 - - - -
888A TYR 3.3 0.2 - - - -
889A TYR* 1.3 77.6 - - - +
891A MET* 1.3 62.0 + - - +
893A ALA* 4.1 2.2 - - - +
894A ALA* 3.2 24.9 + - - +
897A ARG* 4.7 2.6 + - - -
931A PRO* 3.4 16.6 - - - +
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Residues in contact with MET 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A VAL* 4.4 5.1 - - + +
792A PRO* 3.3 26.5 - - + +
794A PRO* 3.7 29.2 - - + -
795A ASN 4.7 1.3 - - - +
799A ALA* 4.1 16.4 - - + -
803A ILE* 5.8 0.4 - - + -
887A ALA 3.4 12.1 + - - +
888A TYR* 3.2 40.6 + - + +
890A SER* 1.3 78.7 - - - +
892A ILE* 1.3 56.9 + - + +
894A ALA* 3.2 3.6 + - - +
895A GLU* 2.8 61.5 + - - +
931A PRO* 5.0 0.2 - - - -
932A TRP* 4.1 14.4 - - + -
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Residues in contact with ILE 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A MET* 3.8 30.1 - - + +
612A LEU* 3.4 28.2 - - + +
888A TYR* 3.4 61.2 - - + +
889A TYR* 3.6 8.7 - - + +
891A MET* 1.3 89.4 - - + +
893A ALA* 1.3 62.6 + - - +
895A GLU* 3.8 9.1 - - - +
896A GLN 3.1 17.0 + - - -
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Residues in contact with ALA 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A LEU* 3.8 26.4 - - + +
615A PHE* 3.8 23.8 - - + -
889A TYR 3.3 18.9 + - - +
890A SER* 4.1 3.6 - - - +
891A MET 3.3 0.4 - - - -
892A ILE* 1.3 78.9 - - - +
894A ALA* 1.3 60.9 + - - +
896A GLN* 3.3 5.2 + - - +
897A ARG* 3.2 38.1 + - - +
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Residues in contact with ALA 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A SER 3.2 17.7 + - - +
891A MET 3.8 2.5 - - - +
893A ALA* 1.3 76.7 - - - +
895A GLU* 1.3 61.0 + - - +
897A ARG* 3.3 28.1 + - - +
898A LEU* 3.0 34.5 + - + +
930A ALA* 5.4 1.8 - - + -
931A PRO* 3.7 24.9 - - + -
932A TRP* 4.5 6.3 - - + -
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Residues in contact with GLU 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A PRO* 3.7 24.7 - - + +
795A ASN* 5.3 3.8 + - - -
891A MET* 2.8 40.5 + - - +
892A ILE* 3.8 11.7 - - - +
893A ALA 3.3 0.2 - - - -
894A ALA* 1.3 71.4 - - - +
896A GLN* 1.3 63.7 + - - +
898A LEU* 3.5 6.3 + - - +
899A LYS* 3.1 50.5 + - - +
905A GLU* 4.2 8.5 - - - +
908A PHE* 3.8 23.7 - - + -
932A TRP* 4.5 5.8 - - - -
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Residues in contact with GLN 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A PRO* 3.4 43.2 - - - +
612A LEU* 3.9 26.0 - - + +
613A ARG* 3.5 10.3 + - + -
892A ILE 3.1 14.3 + - - +
893A ALA 3.5 9.2 - - - +
894A ALA 3.2 0.2 - - - -
895A GLU* 1.3 77.7 - - - +
897A ARG* 1.3 56.2 + - + +
899A LYS* 3.4 17.3 + - - +
900A ASP* 3.0 54.2 + - - +
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Residues in contact with ARG 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A LEU 4.8 7.0 + - - +
613A ARG* 5.8 7.2 - - + -
615A PHE* 5.4 4.6 - - - +
687A ASN* 3.4 50.5 + - - +
688A GLY 5.4 2.8 + - - -
890A SER* 4.7 2.6 + - - -
893A ALA* 3.2 29.0 + - - +
894A ALA* 3.3 35.1 + - - +
896A GLN* 1.3 77.2 - - + +
898A LEU* 1.3 59.9 - - + +
900A ASP* 3.5 10.8 + - - +
901A ALA* 3.1 26.7 + - - +
931A PRO* 5.1 4.6 - - - +
151J THR* 5.6 0.7 - - - +
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Residues in contact with LEU 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894A ALA* 3.0 19.2 + - + +
895A GLU 3.9 3.8 - - - +
897A ARG* 1.3 75.6 - - + +
899A LYS* 1.3 64.9 + - - +
901A ALA* 3.2 10.2 + - + -
902A GLY 3.3 0.3 + - - -
903A TYR* 2.9 46.9 + - + +
908A PHE* 4.1 19.7 - - + -
926A GLU* 3.9 37.2 - - + +
927A VAL* 4.8 8.1 - - + -
930A ALA* 4.5 9.4 - - + -
932A TRP* 3.6 35.7 - - + -
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Residues in contact with LYS 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895A GLU* 3.1 44.8 + - + +
896A GLN* 3.7 18.6 - - - +
897A ARG 3.4 0.2 - - - -
898A LEU* 1.3 77.1 - - - +
900A ASP* 1.3 61.1 + - - +
902A GLY* 3.2 12.6 + - - -
903A TYR 3.5 14.8 - - - +
904A GLY* 5.5 2.0 - - - -
905A GLU* 3.7 29.6 + - - -
908A PHE* 4.9 3.6 - - + -
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Residues in contact with ASP 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A ARG* 2.5 56.0 + - - +
896A GLN* 3.0 28.1 + - - +
897A ARG* 3.6 9.4 - - - +
899A LYS* 1.3 76.9 - - - +
901A ALA* 1.3 57.2 + - - +
902A GLY 3.2 1.7 + - - -
153J LYS* 4.6 9.7 + - - +
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Residues in contact with ALA 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897A ARG 3.1 17.1 + - - +
898A LEU* 3.7 10.8 - - + +
899A LYS 3.2 1.0 - - - -
900A ASP* 1.3 74.9 - - - +
902A GLY* 1.3 58.7 + - - +
903A TYR* 3.4 10.5 + - + -
926A GLU* 5.5 0.4 - - + -
151J THR* 3.9 26.5 - - + -
152J ALA 4.6 5.2 - - - +
153J LYS* 3.8 20.2 - - + +
154J LYS* 3.4 23.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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