Contacts of the helix formed by residues 867 - 885 (chain A) in PDB entry 1WER
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 PRO 867 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801A TYR* 5.8 1.3 - - - +
805A THR* 3.3 36.8 - - - +
806A ALA* 4.5 7.6 - - - -
808A GLN* 6.0 2.9 - - - +
809A PHE* 5.1 1.1 - - + +
865A ILE 3.3 7.6 - - - +
866A LEU* 1.3 96.2 - - + +
868A PRO* 1.3 75.6 - - + +
869A THR* 3.3 5.6 - - - +
870A LEU* 3.2 15.5 + - + +
871A ARG* 3.1 18.2 + - - +
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Residues in contact with PRO 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A LEU 4.2 2.9 - - - +
867A PRO* 1.3 87.4 - - + +
869A THR* 1.3 58.7 + - - +
871A ARG* 3.3 10.5 + - + +
872A TYR* 2.8 28.4 + - - +
977A VAL* 3.8 13.8 - - + +
981A PRO* 3.5 26.0 - - + -
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Residues in contact with THR 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A GLU* 3.8 13.8 + - - +
767A SER* 3.4 24.0 - - - +
801A TYR* 3.4 20.4 - - - +
867A PRO* 3.3 3.3 - - - +
868A PRO* 1.3 79.6 - - - +
870A LEU* 1.3 58.2 + - - +
872A TYR* 3.1 9.3 + - - +
873A ILE* 2.9 30.4 + - + +
980A LEU* 4.6 9.2 - - + -
981A PRO* 4.0 4.7 - - - +
982A ASP* 3.9 22.9 + - - +
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Residues in contact with LEU 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A MET* 4.4 7.0 - - + -
801A TYR* 4.0 27.8 + - + +
802A MET* 4.0 23.1 - - + -
805A THR* 4.7 4.9 - - - +
806A ALA* 4.2 13.5 - - + -
866A LEU* 3.9 25.1 - - + -
867A PRO* 3.2 20.0 + - + +
869A THR* 1.3 79.2 - - - +
871A ARG* 1.3 56.9 + - - +
873A ILE* 3.2 6.7 + - + +
874A TYR* 2.9 69.2 + - + +
904A LEU* 5.6 0.4 - - + -
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Residues in contact with ARG 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A SER* 3.6 30.5 + - - -
864A GLU* 2.9 30.5 + - - +
866A LEU* 3.5 31.6 - - + +
867A PRO 3.1 13.4 + - - +
868A PRO* 3.3 8.7 + - - +
870A LEU* 1.3 75.7 - - - +
872A TYR* 1.3 58.0 + - - +
874A TYR* 3.2 8.7 + - - +
875A GLY 2.9 23.9 + - - -
973A GLU* 3.0 28.3 + - - +
974A LEU* 3.0 25.3 + - - +
975A GLY* 3.4 8.2 - - - +
976A ASN* 4.7 4.6 - - - +
977A VAL* 3.7 24.9 - - + +
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Residues in contact with TYR 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A SER* 4.1 12.1 - - - -
771A CYS* 4.3 9.5 - - - -
868A PRO 2.8 14.0 + - - +
869A THR 3.2 8.5 - - - +
871A ARG* 1.3 76.6 - - - +
873A ILE* 1.3 59.5 + - - +
875A GLY* 3.2 2.1 + - - -
876A CYS* 3.0 54.7 + - - -
977A VAL* 3.3 30.2 - - + +
978A PRO 3.4 19.1 - - - -
979A GLU 3.5 12.8 - - - -
980A LEU* 3.6 41.0 - - + +
981A PRO* 4.1 4.5 - - + -
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Residues in contact with ILE 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A GLU 4.8 0.4 - - - +
767A SER* 4.0 20.6 - - - +
770A LEU* 3.5 31.6 - - + -
771A CYS* 3.9 24.9 - - - -
774A ASN* 4.0 12.7 + - - +
798A MET* 3.9 31.4 - - + -
801A TYR* 3.8 21.1 - - + -
869A THR* 2.9 17.0 + - + +
870A LEU* 3.2 8.7 + - + +
872A TYR* 1.3 73.0 - - + +
874A TYR* 1.3 63.2 + - + +
876A CYS* 3.2 5.0 + - - +
877A LEU* 3.1 20.8 + - + +
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Residues in contact with TYR 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A MET* 3.9 16.2 - - + -
802A MET* 3.2 25.6 - - - -
866A LEU* 3.5 30.7 - - + -
870A LEU* 2.9 38.1 + - + +
871A ARG* 3.3 10.8 - - - +
873A ILE* 1.3 75.3 - - - +
875A GLY* 1.3 64.5 + - - +
877A LEU* 3.1 21.6 + - + +
878A GLN* 3.0 25.2 + - - +
896A VAL* 4.1 16.7 - - + +
899A PHE* 4.0 11.0 - - + -
900A VAL* 3.7 21.0 + - + +
904A LEU* 5.1 0.2 - - - +
974A LEU* 4.0 22.7 - - + -
975A GLY* 4.0 10.8 - - - -
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Residues in contact with GLY 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ARG 2.9 14.6 + - - -
872A TYR 3.2 5.1 + - - -
874A TYR* 1.3 71.8 - - - +
876A CYS* 1.3 58.0 + - - +
878A GLN* 3.3 12.8 + - - +
879A LYS* 3.0 32.9 + - - +
975A GLY* 3.2 23.2 + - - -
977A VAL 5.1 2.2 - - - -
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Residues in contact with CYS 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A CYS* 3.8 27.4 - - + +
872A TYR* 3.0 47.3 + - - -
873A ILE 3.4 9.0 - - - +
874A TYR 3.1 0.2 - - - -
875A GLY* 1.3 75.7 - - - +
877A LEU* 1.3 64.3 + - - +
879A LYS* 3.4 7.1 + - - +
880A SER* 3.0 27.8 + - - -
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Residues in contact with LEU 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A ASN* 3.6 39.5 - - + +
778A ILE* 4.0 5.6 - - + +
788A PHE* 3.8 23.8 - - + -
798A MET* 4.7 1.6 - - + -
873A ILE 3.1 15.0 + - - +
874A TYR* 3.3 28.9 - - + +
876A CYS* 1.3 74.4 - - - +
878A GLN* 1.3 57.5 + - - +
880A SER* 3.3 5.5 + - - -
881A VAL* 3.0 34.0 + - - +
895A VAL* 4.0 21.3 - - + +
896A VAL* 5.0 1.8 - - + -
899A PHE* 3.5 29.8 - - + -
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Residues in contact with GLN 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A TYR 3.0 15.7 + - - +
875A GLY* 3.4 10.9 - - - +
877A LEU* 1.3 73.8 - - - +
879A LYS* 1.3 65.4 + - - +
880A SER 3.3 0.2 + - - -
881A VAL* 3.3 10.0 + - - +
882A GLN* 3.1 30.2 + - - +
892A ARG* 3.2 59.8 + - + +
895A VAL* 4.4 0.7 - - + -
896A VAL* 3.6 11.1 - - + +
971A LEU 3.4 12.3 + - - -
972A ASP* 3.1 25.2 + - - +
975A GLY* 3.6 22.4 - - - +
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Residues in contact with LYS 879 (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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875A GLY 3.0 20.8 + - - +
876A CYS* 3.4 7.2 + - - +
878A GLN* 1.3 74.4 - - + +
880A SER* 1.3 62.5 + - - +
882A GLN* 3.5 22.1 + - - +
883A HIS* 3.2 23.7 + - - +
892A ARG* 5.4 4.5 - - - +
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Residues in contact with SER 880 (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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775A ASP* 3.0 32.5 + - - +
778A ILE* 3.5 29.0 - - - +
876A CYS* 3.0 20.1 + - - +
877A LEU* 3.5 1.3 - - - -
879A LYS* 1.3 78.8 - - - +
881A VAL* 1.3 61.4 + - - +
883A HIS* 3.4 7.6 + - - +
884A LYS* 3.1 22.3 + - - +
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Residues in contact with VAL 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A ILE* 3.8 19.7 - - + -
787A LEU* 3.9 22.7 - - + -
877A LEU 3.0 15.5 + - - +
878A GLN 3.4 10.8 - - - +
880A SER* 1.3 73.1 - - - +
882A GLN* 1.3 62.9 + - - +
885A TRP* 2.9 45.8 + - + +
888A ASN 5.5 0.4 - - - +
891A MET* 3.7 41.5 - - + +
892A ARG* 3.8 9.0 - - + +
895A VAL* 4.0 10.3 - - + -
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Residues in contact with GLN 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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878A GLN 3.1 16.9 + - - +
879A LYS* 3.7 27.7 - - - +
881A VAL* 1.3 76.9 - - + +
883A HIS* 1.3 61.3 + - - +
885A TRP 4.6 4.0 - - - -
886A PRO* 3.3 28.2 - - - +
888A ASN 5.7 2.9 - - - +
892A ARG* 2.8 48.6 + - + +
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Residues in contact with HIS 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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879A LYS 3.2 14.7 + - - +
880A SER* 3.6 8.1 - - - +
882A GLN* 1.3 80.0 - - - +
884A LYS* 1.3 63.7 + - - +
886A PRO* 3.4 16.2 - - - +
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Residues in contact with LYS 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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778A ILE* 3.3 24.2 - - + +
779A SER* 2.9 28.9 + - - -
781A GLU 3.0 27.4 + - - -
782A ASP* 5.0 1.4 - - - +
880A SER 3.1 14.1 + - - +
881A VAL 3.3 3.1 + - - +
883A HIS* 1.3 85.4 - - + +
885A TRP* 1.3 92.6 + - + +
886A PRO* 3.4 6.8 - - - +
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Residues in contact with TRP 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A ILE* 4.2 5.8 - - + -
781A GLU* 3.7 37.6 + - + -
782A ASP* 5.4 2.2 - - - +
783A GLU 4.4 1.4 - - - +
784A ALA* 3.6 38.9 - - + +
787A LEU* 4.0 25.4 - - + -
881A VAL* 2.9 37.2 + - + +
882A GLN* 3.7 4.8 - - - +
884A LYS* 1.3 109.1 - - + +
886A PRO* 1.3 59.2 - - - +
887A THR* 3.3 3.4 - - - -
888A ASN* 3.1 42.0 + - + +
891A MET* 4.0 13.0 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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