Contacts of the helix formed by residues 888 - 905 (chain B) in PDB entry 2B7A
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 888 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886B HIS* 3.1 37.7 + - + +
887B SER* 1.3 78.7 - - - +
889B GLU* 1.3 59.9 + - - +
890B GLU* 3.8 6.6 + - - +
891B HIS* 3.1 30.2 + - + -
892B LEU* 2.9 30.1 + - - +
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Residues in contact with GLU 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B THR* 1.3 74.1 - - - +
890B GLU* 1.3 59.2 + - + +
892B LEU* 3.5 11.4 + - + +
893B ARG* 3.1 35.2 + - - +
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Residues in contact with GLU 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B THR* 3.2 6.5 + - - +
889B GLU* 1.3 77.6 - - + +
891B HIS* 1.3 63.9 + - + +
893B ARG* 3.3 33.4 + - - +
894B ASP* 3.1 36.0 + - - +
1011B LYS* 6.1 0.9 - - - +
1013B PRO* 4.9 13.3 - - - +
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Residues in contact with HIS 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B PHE* 5.1 21.1 - + + -
884B LEU* 3.6 15.1 - - + +
886B HIS* 3.0 56.4 - + + +
888B THR* 3.1 20.1 + - - +
890B GLU* 1.3 76.1 - - + +
892B LEU* 1.3 60.1 + - - +
894B ASP* 3.4 12.9 + - - +
895B PHE* 3.0 29.8 + - - +
1013B PRO* 5.7 10.5 - - + -
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Residues in contact with LEU 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884B LEU* 4.1 15.5 - - + -
887B SER* 3.7 28.7 - - - +
888B THR 2.9 23.5 + - - +
889B GLU* 3.8 10.1 - - + +
891B HIS* 1.3 74.3 - - - +
893B ARG* 1.3 59.7 + - - +
895B PHE* 3.3 3.9 + - + +
896B GLU* 3.0 36.5 + - + +
924B ASN* 6.2 1.8 - - - +
925B LEU* 5.2 19.9 - - + +
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Residues in contact with ARG 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B GLU* 3.1 31.8 + - - +
890B GLU* 3.3 35.1 + - - +
891B HIS 3.3 0.2 - - - -
892B LEU* 1.3 77.4 - - - +
894B ASP* 1.3 62.9 + - - +
896B GLU* 3.4 8.7 + - - +
897B ARG* 3.1 50.9 + - + +
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Residues in contact with ASP 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B PHE* 5.7 8.4 - - + -
890B GLU* 3.1 20.7 + - - +
891B HIS* 3.7 14.1 + - - +
892B LEU 3.3 0.2 - - - -
893B ARG* 1.3 77.2 + - - +
895B PHE* 1.3 52.0 + - - +
897B ARG* 2.8 36.0 + - - +
898B GLU* 2.8 34.7 + - - +
996B GLY 5.3 9.0 - - - +
999B LYS* 4.1 12.9 + - - -
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Residues in contact with PHE 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882B LYS* 3.4 42.4 - - + -
883B LYS* 4.6 2.9 - - - -
884B LEU* 3.9 34.8 - - + -
891B HIS 3.0 17.4 + - - +
892B LEU* 3.7 6.3 - - + +
893B ARG 3.3 0.2 - - - -
894B ASP* 1.3 74.3 - - - +
896B GLU* 1.3 64.7 + - - +
898B GLU* 3.2 28.5 + - - +
899B ILE* 3.0 34.3 + - + +
925B LEU* 3.3 44.4 - - + -
926B LYS* 4.1 1.3 - - - -
927B LEU* 3.6 21.1 - - + -
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Residues in contact with GLU 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892B LEU* 3.0 21.2 + - + +
893B ARG* 3.6 10.5 - - - +
895B PHE* 1.3 75.0 - - - +
897B ARG* 1.3 64.2 + - + +
899B ILE* 3.4 9.9 + - - +
900B GLU* 3.2 30.0 + - - +
918B TYR* 3.8 17.5 + - - -
925B LEU* 3.3 27.2 - - + +
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Residues in contact with ARG 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B ARG* 3.1 43.7 + - + +
894B ASP* 2.8 34.6 + - - +
896B GLU* 1.3 74.3 - - + +
898B GLU* 1.3 60.1 + - - +
900B GLU* 3.3 8.2 + - - +
901B ILE* 2.9 40.9 + - + +
999B LYS* 3.8 17.4 - - - +
1008B PTR 3.5 31.3 + - - -
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Residues in contact with GLU 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B PHE* 5.4 4.2 - - - -
882B LYS* 2.7 35.3 + - - +
894B ASP 2.8 14.4 + - - +
895B PHE* 3.3 31.1 - - - +
897B ARG* 1.3 73.9 - - - +
899B ILE* 1.3 65.3 + - - +
901B ILE* 3.3 12.4 + - - +
902B LEU* 3.0 24.7 + - + +
927B LEU* 3.9 11.2 - - + +
994B ASP* 4.3 1.0 - - - +
995B PHE* 3.4 27.7 + - + +
996B GLY* 3.4 23.2 + - - +
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Residues in contact with ILE 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B PHE* 3.0 32.2 + - + +
896B GLU* 3.7 9.2 - - - +
897B ARG 3.3 0.2 - - - -
898B GLU* 1.3 76.6 - - - +
900B GLU* 1.3 66.1 + - - +
902B LEU* 3.3 2.8 + - - +
903B LYS* 2.9 29.9 + - + +
913B TYR* 3.7 18.3 - - + +
916B VAL* 3.6 24.7 - - + -
925B LEU* 3.6 39.9 - - + -
927B LEU* 4.0 30.1 - - + -
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Residues in contact with GLU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896B GLU* 3.2 16.9 + - + +
897B ARG* 3.7 9.4 - - - +
898B GLU 3.3 0.2 - - - -
899B ILE* 1.3 82.7 - - - +
901B ILE* 1.3 66.0 + - + +
903B LYS* 3.5 22.0 + - - +
904B SER* 3.1 25.3 + - - -
972B TYR* 4.8 0.4 + - - -
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Residues in contact with ILE 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897B ARG* 2.9 31.0 + - + +
898B GLU* 3.5 8.3 - - - +
900B GLU* 1.3 75.9 - - + +
902B LEU* 1.3 62.5 + - - +
904B SER* 2.6 25.0 + - - -
905B LEU* 3.3 21.4 - - + +
972B TYR* 3.9 31.2 - - + +
995B PHE* 4.4 7.9 - - + -
998B THR* 3.4 51.8 - - + +
999B LYS* 4.8 0.2 - - - -
1000B VAL* 4.3 15.9 - - + -
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Residues in contact with LEU 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B GLU* 3.0 17.0 + - + +
899B ILE* 3.8 4.0 - - - +
901B ILE* 1.3 76.9 - - + +
903B LYS* 1.3 62.9 + - - +
905B LEU* 3.0 26.3 + - - +
910B ILE* 4.2 5.8 - - + -
911B VAL* 3.4 25.1 - - + +
913B TYR* 3.9 20.4 - - + +
927B LEU* 3.9 19.7 - - + -
929B MET* 3.7 37.7 - - + -
995B PHE* 3.7 35.7 - - + -
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Residues in contact with LYS 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B THR* 5.7 7.0 - - - +
899B ILE* 2.9 19.1 + - + +
900B GLU* 3.8 25.3 + - - +
902B LEU* 1.3 76.6 - - - +
904B SER* 1.3 59.7 + - - +
905B LEU 3.4 4.5 + - - +
906B GLN* 4.8 10.0 + - - +
913B TYR* 3.7 48.4 + - + +
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Residues in contact with SER 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B GLU 3.1 13.2 + - - -
901B ILE 2.6 18.4 + - - -
902B LEU 3.2 0.2 - - - -
903B LYS* 1.3 76.5 - - - +
905B LEU* 1.3 59.1 + - - +
906B GLN* 3.8 3.0 + - - +
966B TYR* 3.8 1.6 + - - -
970B LYS* 3.0 32.5 + - - +
972B TYR* 2.6 29.3 + - - -
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Residues in contact with LEU 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B ILE* 3.3 21.5 - - + +
902B LEU* 3.0 19.3 + - - +
903B LYS 4.1 1.6 - - - +
904B SER* 1.3 78.2 - - - +
906B GLN* 1.3 67.1 + - - +
907B HIS 4.1 0.7 - - - -
910B ILE* 4.1 18.9 - - + +
911B VAL 5.3 2.4 - - - +
912B LYS* 6.0 0.7 - - - -
913B TYR* 5.5 3.6 + - - +
966B TYR* 3.6 23.8 - - + -
967B LEU* 3.6 34.3 - - + -
970B LYS* 4.1 8.3 - - + -
972B TYR* 3.7 16.6 - - + -
995B PHE* 3.7 30.3 - - + -
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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
------------------------------------------------------------
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