Contacts of the helix formed by residues 882 - 898 (chain C) in PDB entry 4OIN
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 LEU 882 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C HIS* 3.2 20.9 + - + +
876C VAL* 3.7 26.9 - - + -
880C MET 5.0 0.2 - - - -
881C ASN* 1.3 71.1 - - - +
883C GLY* 1.3 65.1 + - - +
884C GLN 3.1 3.1 - - - -
885C ILE* 2.9 27.1 + - + +
886C LEU* 3.1 14.4 + - - +
949D ILE* 4.8 6.5 - - + -
950D GLY 5.7 1.3 - - - +
951D ILE* 4.2 16.8 - - + -
954D ALA* 4.9 8.1 - - + -
1020D LEU* 6.5 0.4 - - + -
1038D LEU* 3.7 37.2 - - + +
1061D PHE* 4.0 4.0 - - + +
1062D ARG* 4.0 30.7 - - + +
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Residues in contact with GLY 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PHE* 3.7 24.8 - - - -
552C HIS* 3.9 5.7 - - - +
553C ASP* 2.8 16.2 + - - -
843C HIS* 3.3 16.8 - - - -
882C LEU* 1.3 78.3 - - - +
884C GLN* 1.3 55.4 + - - +
886C LEU* 3.4 1.6 + - - -
887C GLU* 2.8 29.8 + - - +
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Residues in contact with GLN 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 6.1 0.6 - - - +
841C ASN* 3.0 18.6 + - - +
843C HIS* 3.4 30.3 - - + -
845C ASN* 2.9 31.2 + - - +
871C LEU* 4.7 0.9 - - - +
875C GLY 5.0 1.6 + - - -
876C VAL* 4.0 18.6 - - - +
881C ASN* 3.1 45.8 + - - +
883C GLY* 1.3 74.0 - - - +
885C ILE* 1.3 64.9 + - + +
887C GLU* 3.5 4.4 - - - +
888C THR* 2.6 37.7 + - - -
992C MET* 3.9 13.1 - - + +
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Residues in contact with ILE 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ILE* 3.6 22.4 - - + -
876C VAL* 4.0 22.9 - - + -
882C LEU* 2.9 33.4 + - + +
884C GLN* 1.3 82.5 - - + +
886C LEU* 1.3 60.3 + - - +
888C THR* 2.9 8.4 + - - -
889C HIS* 2.8 50.8 + - + +
988C VAL* 5.2 0.9 - - + -
949D ILE* 3.6 29.2 - - + +
950D GLY 3.8 1.3 - - - -
951D ILE* 3.5 18.6 - - + +
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Residues in contact with LEU 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PHE* 3.8 25.2 - - + -
552C HIS* 3.5 49.6 - - + +
882C LEU 3.1 8.4 + - - +
883C GLY 3.7 6.5 - - - +
885C ILE* 1.3 77.4 - - - +
887C GLU* 1.3 64.8 + - - +
889C HIS* 2.9 9.5 + - + +
890C LEU* 2.9 25.5 + - - +
909C ALA 5.5 1.3 - - - +
911C GLU* 4.6 10.8 - - + -
914C ILE* 4.2 18.5 - - + +
951D ILE* 3.7 39.3 - - + -
1062D ARG 5.1 0.4 - - - +
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Residues in contact with GLU 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C PRO* 5.1 0.9 - - + -
549C PHE* 3.7 16.2 - - + -
579C VAL* 4.1 16.9 + - + +
841C ASN* 5.1 0.9 - - - +
842C ARG* 3.2 25.6 + - - +
843C HIS* 2.6 39.6 + - - +
883C GLY 2.8 20.1 + - - +
884C GLN* 3.5 4.3 - - - +
886C LEU* 1.3 71.5 - - - +
888C THR* 1.3 57.8 + - - +
890C LEU* 4.1 1.3 - - - +
891C GLY* 2.8 23.7 + - - -
991C GLN 3.3 10.4 - - - +
992C MET* 3.7 10.6 - - - +
993C PHE* 2.8 32.4 + - - +
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Residues in contact with THR 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674C VAL* 3.9 13.0 - - + -
676C ILE* 4.4 4.7 - - + +
884C GLN 2.6 21.7 + - - -
885C ILE* 2.9 10.9 + - - -
887C GLU* 1.3 74.8 - - - +
889C HIS* 1.3 54.8 + - - +
891C GLY* 2.9 3.1 + - - -
892C LEU 2.7 31.0 + - - -
988C VAL* 4.1 17.3 - - + -
989C VAL 4.0 4.7 - - - -
990C GLY* 3.5 34.3 - - - +
991C GLN 3.7 7.4 - - - -
992C MET* 3.2 19.8 - - - +
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Residues in contact with HIS 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C ILE* 2.8 29.8 + - + +
886C LEU* 2.9 12.1 + - + +
888C THR* 1.3 75.4 - - - +
890C LEU* 1.3 62.6 + - - +
892C LEU* 2.9 23.4 + - - +
893C ALA 3.2 4.7 + - - -
914C ILE* 4.2 15.7 - - + -
918C LEU* 3.7 14.9 - - + +
968C LEU 6.1 0.2 - - - -
969C GLN 3.6 21.4 + - - -
970C GLY* 3.8 13.9 + - - -
988C VAL* 3.8 19.6 - - + +
989C VAL 5.5 0.4 + - - -
950D GLY* 3.6 8.9 - - - -
951D ILE* 3.0 48.7 + - + +
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Residues in contact with LEU 890 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 4.4 2.2 - - + -
549C PHE* 4.0 21.8 - - + -
579C VAL* 4.2 11.9 - - + -
886C LEU 2.9 17.3 + - - +
887C GLU 4.1 2.5 - - - +
889C HIS* 1.3 72.5 - - - +
891C GLY* 1.3 63.2 + - - +
893C ALA* 3.0 8.4 + - + +
894C GLY 2.9 20.8 + - - -
901C TYR* 3.5 46.5 - - + +
903C SER* 5.1 0.9 - - - -
909C ALA* 4.3 15.9 - - + -
914C ILE* 3.8 23.8 - - + +
917C LEU* 3.7 25.4 - - + -
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Residues in contact with GLY 891 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578C VAL* 4.4 13.0 - - - -
579C VAL* 4.7 1.3 - - - +
887C GLU 2.8 18.9 + - - -
888C THR 2.9 6.0 + - - -
890C LEU* 1.3 76.7 - - - +
892C LEU* 1.3 59.1 + - - +
894C GLY 3.7 0.5 + - - -
895C TYR* 3.1 17.7 + - - +
991C GLN* 3.4 36.5 - - - +
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Residues in contact with LEU 892 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673C LEU* 5.5 2.0 - - + -
861C LEU* 6.2 1.3 - - + -
888C THR 2.7 10.9 + - - +
889C HIS* 2.9 10.3 + - - +
891C GLY* 1.3 70.3 - - - +
893C ALA* 1.3 67.2 + - - +
895C TYR* 2.9 22.3 + - + +
896C PHE* 3.4 37.7 + - + -
918C LEU* 3.9 11.4 - - + -
967C PHE* 3.8 28.3 - - + -
970C GLY* 4.0 24.0 - - - +
972C VAL* 4.5 8.1 - - + -
989C VAL* 3.3 37.5 - - + +
990C GLY* 3.8 6.3 - - - -
991C GLN 3.6 0.4 - - - +
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Residues in contact with ALA 893 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889C HIS 3.2 2.7 + - - +
890C LEU* 3.0 14.0 + - + +
892C LEU* 1.3 77.1 - - - +
894C GLY* 1.3 58.3 + - - +
895C TYR 2.9 3.3 + - - -
896C PHE* 3.0 4.3 + - - -
897C LEU* 2.9 29.6 + - + +
901C TYR* 3.8 10.8 - - - +
914C ILE 4.9 0.2 - - - +
917C LEU* 3.9 28.3 - - + +
918C LEU* 3.7 19.2 - - + +
921C ALA* 3.7 12.9 - - - +
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Residues in contact with GLY 894 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C VAL* 5.1 1.1 - - - -
890C LEU 2.9 11.8 + - - -
891C GLY 3.9 2.7 - - - -
893C ALA* 1.3 75.2 - - - +
895C TYR* 1.3 56.6 + - - +
898C GLY* 3.0 21.0 + - - -
899C GLN* 3.1 29.4 + - - +
901C TYR* 3.2 21.4 + - - -
991C GLN* 4.1 6.2 - - - +
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Residues in contact with TYR 895 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG* 5.3 3.3 + - - -
673C LEU* 4.0 30.5 - - + +
861C LEU* 5.2 1.3 - - + -
865C THR* 3.7 25.2 + - + +
891C GLY 3.1 13.4 + - - +
892C LEU* 2.9 15.7 + - + +
893C ALA 2.9 0.4 + - - -
894C GLY* 1.3 81.1 - - - +
896C PHE* 1.3 97.8 + + + +
898C GLY* 3.6 6.9 + - - -
991C GLN* 3.5 35.9 - - + +
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Residues in contact with PHE 896 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861C LEU* 4.2 14.6 - - + -
863C ASP* 5.2 6.7 - - - -
892C LEU* 3.4 35.4 + - + -
893C ALA 3.0 2.6 + - - -
895C TYR* 1.3 103.9 - + - +
897C LEU* 1.3 62.3 + - - +
898C GLY 3.3 0.4 - - - -
921C ALA* 3.7 23.1 - - + +
924C VAL* 3.3 26.2 - - + +
925C TYR* 3.4 43.1 - + + -
967C PHE* 3.8 23.3 - + - -
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Residues in contact with LEU 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893C ALA 2.9 15.7 + - - +
896C PHE* 1.3 75.7 - - - +
898C GLY* 1.3 62.8 + - - +
899C GLN* 3.3 40.9 + - + +
901C TYR* 4.1 5.6 - - - +
917C LEU* 3.7 24.0 - - + +
920C GLN* 3.9 23.8 - - + +
921C ALA* 3.7 25.8 - - + +
924C VAL* 3.8 16.2 - - + -
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Residues in contact with GLY 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.7 23.9 - - - +
2C GLU 4.6 1.6 + - - -
894C GLY 3.0 10.6 + - - -
895C TYR 3.6 5.8 + - - -
896C PHE 3.3 3.8 - - - -
897C LEU* 1.3 80.3 - - - +
899C GLN* 1.3 57.8 + - - +
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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