Contacts of the helix formed by residues 892 - 909 (chain A) in PDB entry 3POZ
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 THR 892 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834A VAL* 3.5 21.0 - - - +
884A GLU* 4.6 3.6 + - - -
890A ILE* 4.0 19.4 - - + +
891A TYR* 1.3 80.1 - - - +
893A HIS* 1.3 63.0 + - - +
894A GLN* 3.1 14.4 + - - +
895A SER* 2.8 33.5 + - - -
896A ASP 3.1 6.8 + - - -
955A ALA* 5.2 1.9 - - - +
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Residues in contact with HIS 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SO4 5.1 0.4 + - - -
825A MET 5.5 0.2 + - - -
828A LEU* 5.8 0.2 - - - +
829A GLU* 3.5 59.0 + - + +
832A ARG* 3.8 16.6 - - - +
833A LEU 3.4 38.8 + - - -
834A VAL* 3.7 12.4 - - + +
892A THR* 1.3 75.8 - - - +
894A GLN* 1.3 61.6 + - + +
896A ASP* 3.3 13.1 + - - +
897A VAL* 3.0 28.3 + - - +
961A PHE* 3.6 5.4 - - + -
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Residues in contact with GLN 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A GLU* 4.9 5.4 - - - +
892A THR* 3.1 10.8 + - - +
893A HIS* 1.3 83.1 - - + +
895A SER* 1.3 61.1 + - - +
896A ASP 3.2 0.4 - - - -
897A VAL* 3.3 22.7 + - - +
898A TRP 3.3 6.8 + - - -
955A ALA* 3.1 39.0 + - + +
956A ASP* 4.9 6.7 - - - +
958A ARG* 3.0 33.2 + - - +
959A PRO 3.2 20.5 + - - -
960A LYS* 3.3 34.4 + - - +
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Residues in contact with SER 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 4.7 0.9 - - - +
882A ALA* 3.7 7.9 + - - +
884A GLU* 3.6 14.1 + - - -
885A SER* 3.5 21.5 + - - -
890A ILE 4.2 2.0 - - - -
891A TYR* 3.3 12.0 - - - +
892A THR* 2.8 38.4 + - - -
894A GLN* 1.3 72.7 - - - +
896A ASP* 1.3 65.4 + - - +
898A TRP* 3.2 13.2 + - - +
899A SER* 3.2 15.3 + - - -
958A ARG* 3.7 8.9 - - - +
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Residues in contact with ASP 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A MET* 3.5 26.1 - - + +
833A LEU 4.4 1.0 - - - +
834A VAL* 3.6 10.9 - - - +
835A HIS* 2.8 27.6 + - - +
836A ARG* 3.1 26.2 + - - -
837A ASP 4.8 0.2 + - - -
838A LEU* 4.3 5.1 + - - +
892A THR 3.1 13.0 + - - +
893A HIS* 3.3 17.8 + - - +
894A GLN 3.2 0.2 - - - -
895A SER* 1.3 79.1 + - - +
897A VAL* 1.3 55.6 + - - +
899A SER* 3.2 9.1 + - - +
900A TYR* 2.8 28.1 + - - +
961A PHE* 3.6 6.2 - - + -
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Residues in contact with VAL 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A HIS 3.0 19.3 + - - +
894A GLN* 3.4 20.6 - - - +
895A SER 3.2 0.2 - - - -
896A ASP* 1.3 73.5 - - - +
898A TRP* 1.3 65.1 + - - +
900A TYR* 3.2 3.4 + - - +
901A GLY 2.9 18.2 + - - -
950A CYS* 3.5 24.6 - - + +
958A ARG* 4.0 12.6 - - + -
959A PRO* 3.3 29.8 - - + +
961A PHE* 3.6 31.6 - - + +
964A LEU* 4.2 6.7 - - + -
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Residues in contact with TRP 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A LYS 5.3 0.8 + - - -
880A TRP 3.6 18.0 + - - -
881A MET 3.3 15.2 + - - -
882A ALA* 3.4 17.3 - - + -
883A LEU* 4.0 12.6 - - + -
894A GLN 3.3 3.0 + - - -
895A SER 3.2 11.2 + - - +
897A VAL* 1.3 77.7 - - - +
899A SER* 1.3 62.2 + - - +
901A GLY 3.0 10.6 + - - -
902A VAL* 3.1 20.7 + - + +
915A TYR* 4.9 5.6 + - - -
927A LEU* 3.7 43.5 - - + +
932A ARG* 4.2 6.1 - - - -
950A CYS 3.3 12.5 + - - +
951A TRP* 3.2 60.2 + + + -
952A MET 3.8 7.6 - - - -
953A ILE* 4.4 5.8 - - + -
958A ARG* 3.5 25.6 - - - +
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Residues in contact with SER 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A ARG 5.5 4.3 + - - -
837A ASP* 5.8 0.2 - - - -
838A LEU* 3.5 32.2 + - - +
880A TRP* 2.7 27.7 + - - +
881A MET* 4.5 3.3 - - - +
882A ALA 4.8 0.2 + - - -
895A SER 3.2 10.1 + - - -
896A ASP* 3.2 12.6 + - - -
898A TRP* 1.3 77.7 - - - +
900A TYR* 1.3 57.0 + - - +
902A VAL* 3.2 6.3 + - - +
903A THR* 2.8 32.1 + - - -
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Residues in contact with TYR 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A CYS* 2.7 27.4 + - - +
821A ILE* 3.7 24.0 - - + -
822A ALA* 3.7 31.4 - - + +
838A LEU* 3.7 10.9 - - + +
896A ASP 2.8 13.4 + - - +
897A VAL 3.3 8.5 - - - +
899A SER* 1.3 76.3 - - - +
901A GLY* 1.3 58.5 + - - +
903A THR* 3.1 5.2 + - - -
904A VAL* 2.8 49.3 + - + +
946A ILE* 5.4 0.4 - - + -
950A CYS* 4.4 7.6 - - - -
961A PHE* 3.6 22.7 - + + -
964A LEU* 3.8 26.0 - - + -
968A PHE* 3.4 27.1 - + - -
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Residues in contact with GLY 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A VAL 2.9 12.1 + - - -
898A TRP 3.0 5.8 + - - -
900A TYR* 1.3 78.3 - - - +
902A VAL* 1.3 55.6 + - - +
904A VAL* 3.4 2.3 + - - -
905A TRP* 3.0 22.7 + - - +
947A MET* 3.7 11.4 - - - +
950A CYS* 3.9 17.7 - - - -
951A TRP* 3.5 23.5 - - - -
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Residues in contact with VAL 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A LYS 3.9 21.3 - - - +
880A TRP* 3.4 34.1 - - + +
898A TRP* 3.1 24.8 + - + +
899A SER 3.2 6.5 + - - +
901A GLY* 1.3 74.4 - - - +
903A THR* 1.3 57.5 + - - +
905A TRP* 3.2 4.8 + - + +
906A GLU* 2.8 28.7 + - + +
914A PRO* 4.2 9.0 - - + -
915A TYR* 5.0 2.0 - - - +
933A LEU* 4.0 20.2 - - + -
951A TRP* 3.6 20.9 - - - +
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Residues in contact with THR 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A LEU* 6.0 0.2 - - + -
821A ILE* 4.3 25.1 - - + -
838A LEU* 3.7 8.7 - - + +
839A ALA* 3.3 26.8 + - - +
840A ALA* 3.8 21.8 - - + +
843A VAL* 4.5 5.2 - - + -
880A TRP* 4.6 0.2 - - - -
899A SER 2.8 13.4 + - - -
900A TYR* 3.4 12.8 - - + -
902A VAL* 1.3 77.3 - - - +
904A VAL* 1.3 63.8 + - + +
906A GLU* 3.1 13.8 + - - +
907A LEU* 3.0 25.7 + - + +
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Residues in contact with VAL 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A CYS* 3.8 28.7 - - + -
821A ILE* 6.0 1.1 - - + -
900A TYR* 2.8 56.4 + - + +
901A GLY* 3.8 5.6 - - - +
903A THR* 1.3 72.5 - - + +
905A TRP* 1.3 58.1 + - - +
907A LEU* 3.1 10.4 + - + +
908A MET* 2.9 48.7 + - + +
947A MET* 4.1 19.7 - - + -
968A PHE* 4.2 11.7 - - + -
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Residues in contact with TRP 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A GLY 3.0 13.9 + - - +
902A VAL* 3.3 12.8 - - - +
904A VAL* 1.3 76.3 - - - +
906A GLU* 1.3 72.0 + - + +
908A MET* 3.3 2.7 + - - +
909A THR* 3.0 41.9 + - + +
912A SER* 3.5 42.0 - - - -
913A LYS 3.8 10.1 - - - -
914A PRO* 3.6 19.7 - - + -
915A TYR 5.0 0.7 - - - -
933A LEU* 3.6 32.5 - - + +
934A PRO* 2.7 48.1 + - + -
936A PRO* 3.7 16.6 - - + +
944A TYR* 5.2 0.4 - + - -
947A MET* 3.8 16.8 - - - -
951A TRP* 4.2 6.3 - + + -
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Residues in contact with GLU 906 (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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799A LEU* 3.7 21.6 - - + +
802A VAL* 4.3 1.1 - - - +
840A ALA* 2.9 39.7 + - + +
841A ARG 4.8 0.3 + - - -
880A TRP* 2.9 45.1 + - + +
902A VAL* 2.8 15.7 + - + +
903A THR* 3.1 12.2 + - - +
905A TRP* 1.3 82.6 - - + +
907A LEU* 1.3 60.3 + - - +
909A THR* 3.2 8.2 + - - -
911A GLY* 2.7 31.6 + - - -
912A SER 4.1 16.3 - - - +
914A PRO* 4.8 1.7 - - + +
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Residues in contact with LEU 907 (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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798A LEU* 3.6 33.7 - - + -
802A VAL* 4.0 17.5 - - + +
814A LEU* 3.5 26.4 - - + +
817A TRP* 4.2 17.0 - - + -
818A CYS* 4.4 17.0 - - - -
821A ILE* 4.0 26.0 - - + -
840A ALA* 4.3 14.6 - - + -
903A THR* 3.0 21.2 + - + +
904A VAL* 3.1 8.3 + - - +
906A GLU* 1.3 76.5 - - - +
908A MET* 1.3 59.5 + - + +
910A PHE* 3.0 22.7 + - - -
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Residues in contact with MET 908 (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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814A LEU* 4.3 13.0 - - + -
815A LEU* 4.3 8.1 - - + -
818A CYS* 3.7 29.6 - - - -
904A VAL* 2.9 31.0 + - + +
905A TRP 4.0 0.2 - - - +
907A LEU* 1.3 77.4 - - + +
909A THR* 1.3 58.9 + - - +
910A PHE* 3.3 6.7 + - - -
936A PRO* 3.8 14.3 - - + +
937A PRO* 5.5 1.2 - - - +
938A ILE* 3.4 30.6 + - + +
939A CYS* 3.7 24.2 - - - -
943A VAL* 4.2 9.2 - - + -
947A MET* 4.3 2.0 - - + -
968A PHE* 4.6 0.4 - - + -
979A LEU* 3.8 43.5 - - + -
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Residues in contact with THR 909 (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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806A LYS* 5.8 0.5 - - - -
905A TRP* 3.0 45.8 + - + +
906A GLU* 3.2 5.5 + - - -
908A MET* 1.3 75.0 - - - +
910A PHE* 1.3 72.1 + - - +
911A GLY 3.2 0.3 + - - -
912A SER* 3.1 41.6 + - - +
936A PRO* 3.8 22.7 - - + -
937A PRO* 5.0 6.5 - - + -
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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