Contacts of the helix formed by residues 991 - 1012 (chain B) in PDB entry 2QEP
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 991 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749B TRP* 3.2 14.9 - - - -
914B ARG* 3.8 17.6 + - - +
989B VAL* 3.9 0.3 - - - +
990B GLN* 1.3 82.0 - - - +
992B LYS* 1.3 62.8 + - + +
993B GLU* 3.2 33.0 - - + +
994B GLN* 3.2 26.6 + - - +
995B PHE 3.1 21.0 + - - -
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Residues in contact with LYS 992 (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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742B LYS* 4.7 2.7 + - - +
745B LEU* 4.2 26.9 - - + +
746B GLU* 2.5 51.7 + - - +
749B TRP* 3.4 44.7 - - + +
991B THR* 1.3 75.3 - - + +
993B GLU* 1.3 55.1 + - - +
995B PHE* 3.1 2.8 + - - +
996B GLU* 2.8 37.8 + - + +
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Residues in contact with GLU 993 (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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914B ARG 4.0 6.6 - - - +
915B GLY* 3.9 15.2 - - - -
916B VAL* 3.2 37.1 + - + +
991B THR* 3.2 14.3 - - + +
992B LYS* 1.3 79.3 - - - +
994B GLN* 1.3 55.9 + - - +
996B GLU* 3.6 12.1 + - - +
997B PHE* 2.9 27.5 + - - +
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Residues in contact with GLN 994 (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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911B TRP* 4.2 2.2 - - - +
914B ARG* 3.8 7.3 - - - +
915B GLY 2.8 41.2 + - - +
916B VAL* 3.9 9.0 - - + -
950B GLY* 3.4 14.4 - - - +
951B ARG* 4.0 18.0 - - - +
954B THR* 3.5 18.9 - - + +
989B VAL* 3.9 5.2 - - + -
990B GLN* 2.9 30.2 + - - +
991B THR* 3.2 24.9 + - + +
992B LYS 3.1 0.4 - - - -
993B GLU* 1.3 73.8 - - - +
995B PHE* 1.3 67.5 + - - +
997B PHE* 3.0 4.6 + - - +
998B ALA* 2.9 22.3 + - - +
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Residues in contact with PHE 995 (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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734B TYR* 5.6 1.1 - - - -
738B HIS 5.7 0.2 - - - -
745B LEU* 3.7 35.4 - - + -
748B GLU* 4.4 12.1 - - + -
749B TRP* 3.6 35.2 - + + -
752B LEU* 3.9 22.0 - - + -
957B LEU* 4.3 14.1 - - + -
974B ILE* 4.6 8.5 - - + -
975B ALA* 4.3 22.4 - - + -
978B LEU* 4.0 20.4 - - + -
989B VAL* 3.6 6.7 - - + +
991B THR 3.1 5.9 + - - -
992B LYS 3.3 7.6 - - - +
994B GLN* 1.3 75.0 - - - +
996B GLU* 1.3 56.1 + - - +
998B ALA* 2.9 21.8 + - - +
999B LEU* 3.1 30.6 + - + +
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Residues in contact with GLU 996 (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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739B LEU* 3.9 12.9 - - + +
742B LYS* 2.5 38.5 + - - -
745B LEU* 3.7 19.8 - - + +
992B LYS* 2.8 24.8 + - + +
993B GLU* 3.7 12.7 - - - +
995B PHE* 1.3 73.8 - - - +
997B PHE* 1.3 61.7 + - - +
999B LEU* 3.6 10.9 + - - +
1000B THR* 3.1 31.6 + - - +
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Residues in contact with PHE 997 (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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911B TRP* 4.5 2.9 - + - -
916B VAL* 3.6 20.4 - - + -
917B PRO* 3.5 48.5 - - + -
918B SER 5.5 0.4 - - - -
920B SER* 3.8 36.3 - - - -
923B LEU* 3.8 24.0 - - + -
954B THR* 4.1 15.5 - - + -
958B ILE* 4.1 8.5 - - + -
993B GLU 2.9 19.1 + - - +
994B GLN 3.0 5.3 + - - +
996B GLU* 1.3 79.1 - - - +
998B ALA* 1.3 57.6 + - - +
1000B THR* 3.5 8.8 + - + -
1001B ALA* 2.9 24.8 + - + +
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Residues in contact with ALA 998 (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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954B THR* 4.2 7.9 - - + -
957B LEU* 4.1 25.6 - - + -
958B ILE* 3.6 28.1 - - + +
974B ILE* 5.7 2.7 - - + -
989B VAL* 6.0 0.2 - - + -
994B GLN 2.9 9.5 + - - +
995B PHE* 2.9 10.7 + - - +
997B PHE* 1.3 74.6 - - - +
999B LEU* 1.3 67.0 - - + +
1001B ALA* 3.4 2.6 + - - +
1002B VAL* 3.1 29.4 + - - +
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Residues in contact with LEU 999 (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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734B TYR* 4.0 12.3 - - + +
735B MET* 3.4 27.7 - - - +
738B HIS* 4.0 22.7 - - + +
739B LEU* 3.8 17.3 - - + -
745B LEU* 4.6 6.3 - - + -
974B ILE* 3.2 39.0 - - + -
995B PHE* 3.1 41.3 + - + +
996B GLU* 3.9 8.3 - - - +
998B ALA* 1.3 77.8 - - - +
1000B THR* 1.3 56.0 - - - +
1002B VAL* 3.3 1.9 + - - -
1003B ALA* 2.9 28.1 + - - +
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Residues in contact with THR1000 (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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739B LEU* 3.3 26.0 - - + +
920B SER* 4.9 6.5 - - - +
996B GLU* 3.1 20.6 + - - +
997B PHE* 3.7 11.9 - - + +
998B ALA 3.3 0.2 - - - -
999B LEU* 1.3 80.9 - - - +
1001B ALA* 1.3 56.9 + - - +
1003B ALA* 3.9 1.5 - - - +
1004B GLU* 3.1 49.0 + - + +
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Residues in contact with ALA1001 (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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920B SER* 4.3 16.4 - - - -
923B LEU* 5.5 0.7 - - + -
924B LEU* 3.4 26.6 - - + +
958B ILE* 3.6 27.1 - - + -
997B PHE* 2.9 26.9 + - + +
998B ALA 3.7 0.4 - - - +
999B LEU 3.2 0.2 - - - -
1000B THR* 1.3 76.1 - - - +
1002B VAL* 1.3 64.9 + - - +
1004B GLU 3.4 0.9 + - - -
1005B GLU* 3.3 17.7 + - - +
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Residues in contact with VAL1002 (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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731B ILE* 4.9 5.4 - - + -
735B MET* 3.4 21.3 - - + -
958B ILE* 4.3 13.0 - - + +
961B VAL* 4.1 32.3 - - + -
962B LEU* 4.1 31.4 - - + +
974B ILE* 4.7 4.5 - - + -
998B ALA 3.1 18.3 + - - +
999B LEU* 3.7 3.8 - - - +
1001B ALA* 1.3 73.4 - - - +
1003B ALA* 1.3 64.9 + - - +
1005B GLU* 3.2 4.5 + - - +
1006B VAL* 3.1 30.6 + - + +
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Residues in contact with ALA1003 (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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732B LEU* 4.2 14.3 - - + +
735B MET* 3.6 26.9 - - + +
739B LEU* 4.5 4.3 - - + -
999B LEU 2.9 17.0 + - - +
1000B THR* 3.9 7.4 - - - +
1002B VAL* 1.3 77.5 - - - +
1004B GLU* 1.3 59.3 + - + +
1006B VAL* 3.1 4.9 + - - +
1007B ASN* 2.9 37.1 + - - +
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Residues in contact with GLU1004 (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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920B SER* 2.6 32.5 + - - +
921B ARG 5.1 0.2 + - - -
924B LEU* 4.4 5.6 - - + +
1000B THR* 3.1 31.1 + - + +
1001B ALA 3.4 3.3 + - - +
1002B VAL 3.3 0.4 - - - -
1003B ALA* 1.3 80.4 - - + +
1005B GLU* 1.3 56.5 + - - +
1007B ASN* 4.2 17.1 - - - +
1008B ALA* 3.6 17.0 + - - +
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Residues in contact with GLU1005 (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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924B LEU* 3.8 31.7 - - + +
927B ARG* 3.9 16.6 + - - -
962B LEU* 3.8 22.7 - - + -
965B MET* 6.2 1.1 - - - -
1001B ALA 3.3 14.8 + - - +
1002B VAL 3.2 4.7 + - - +
1003B ALA 3.1 0.6 - - - -
1004B GLU* 1.3 77.1 - - - +
1006B VAL* 1.3 61.4 + - - +
1007B ASN 3.4 0.2 - - - -
1008B ALA* 3.3 8.7 + - - +
1009B ILE* 2.9 38.8 + - + +
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Residues in contact with VAL1006 (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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728B GLY* 3.1 37.5 - - - +
731B ILE* 4.2 15.7 - - + -
732B LEU* 3.8 16.4 - - + -
962B LEU* 4.7 4.0 - - + -
965B MET* 3.7 26.0 - - + -
1002B VAL* 3.1 21.7 + - + +
1003B ALA* 3.6 7.0 - - - +
1005B GLU* 1.3 73.6 - - - +
1007B ASN* 1.3 55.0 + - - +
1009B ILE* 3.3 5.1 + - - +
1010B LEU* 2.7 39.9 + - + +
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Residues in contact with ASN1007 (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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732B LEU* 3.3 29.6 - - - +
1003B ALA* 2.9 24.6 + - - +
1004B GLU* 4.3 16.1 - - - +
1006B VAL* 1.3 75.8 - - - +
1008B ALA* 1.3 52.6 + - - +
1010B LEU* 3.2 4.5 + - - +
1011B ALA* 2.6 41.7 + - + +
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Residues in contact with ALA1008 (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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1004B GLU 3.6 14.0 + - - +
1005B GLU* 3.3 14.9 + - - +
1006B VAL 3.3 0.6 - - - -
1007B ASN* 1.3 78.1 - - - +
1009B ILE* 1.3 62.3 + - + +
1011B ALA* 4.1 5.7 - - - +
1012B HIS* 3.4 19.9 + - - +
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Residues in contact with ILE1009 (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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724B ASP* 4.2 18.2 - - - +
725B ILE* 5.5 4.9 - - + +
965B MET* 4.5 15.0 - - + -
1005B GLU* 2.9 32.3 + - + +
1006B VAL* 3.8 5.8 - - - +
1008B ALA* 1.3 74.0 - - + +
1010B LEU* 1.3 73.5 + - + +
1012B HIS* 3.0 22.8 + - - +
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Residues in contact with LEU1010 (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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724B ASP 5.0 0.2 - - - +
725B ILE* 3.4 48.7 - - + +
728B GLY* 4.0 4.7 - - - -
729B HIS* 3.4 46.4 - - + +
732B LEU* 4.0 11.4 - - + -
965B MET* 5.4 0.2 - - + -
1006B VAL* 2.7 35.8 + - + +
1007B ASN* 3.8 4.5 - - - +
1009B ILE* 1.3 79.3 - - + +
1011B ALA* 1.3 59.9 + - - +
1012B HIS 3.6 4.2 + - - +
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Residues in contact with ALA1011 (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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1007B ASN* 2.6 24.1 + - + +
1008B ALA* 4.1 6.7 - - - +
1009B ILE 3.1 0.2 - - - -
1010B LEU* 1.3 72.1 - - - +
1012B HIS* 1.3 63.9 + - - +
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Residues in contact with HIS1012 (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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1008B ALA 3.4 11.5 + - - +
1009B ILE* 3.0 18.9 + - - +
1010B LEU 4.4 3.9 - - - +
1011B ALA* 1.3 83.1 - - - +
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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