Contacts of the helix formed by residues 991 - 1012 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A TRP* 3.3 13.9 - - - -
914A ARG* 4.0 19.0 + - - +
989A VAL* 3.5 1.5 - - - +
990A GLN* 1.3 83.0 + - - +
992A LYS* 1.3 57.8 + - - +
993A GLU* 2.9 39.3 - - + +
994A GLN* 3.2 23.7 + - + +
995A PHE 3.0 22.2 + - - -
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Residues in contact with LYS 992 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A LYS 5.5 0.7 - - - -
745A LEU* 4.1 26.7 - - + -
746A GLU* 3.8 37.5 - - - +
749A TRP* 3.2 45.3 - - + +
991A THR* 1.3 73.7 - - + +
993A GLU* 1.3 53.8 + - - +
995A PHE* 3.1 1.9 + - - +
996A GLU* 2.7 39.6 + - - +
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Residues in contact with GLU 993 (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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914A ARG 4.4 4.9 - - - +
915A GLY* 4.4 16.6 - - - -
916A VAL* 3.6 25.5 - - + +
991A THR* 2.9 12.0 - - + +
992A LYS* 1.3 79.3 - - - +
994A GLN* 1.3 56.1 + - - +
996A GLU* 3.6 16.1 - - - +
997A PHE* 2.9 26.5 + - - +
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Residues in contact with GLN 994 (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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911A TRP* 4.2 1.7 - - + +
914A ARG* 3.7 8.7 - - - +
915A GLY 3.0 40.4 + - - +
916A VAL* 3.7 11.2 - - + -
950A GLY* 3.5 16.0 - - - +
951A ARG* 3.9 19.2 - - - +
954A THR* 3.5 22.7 - - - +
989A VAL* 4.2 3.6 - - + -
990A GLN* 3.0 28.4 + - - +
991A THR* 3.2 24.2 + - + +
993A GLU* 1.3 73.0 - - - +
995A PHE* 1.3 61.3 + - - +
997A PHE* 3.2 3.0 + - - +
998A ALA* 2.9 24.4 + - - +
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Residues in contact with PHE 995 (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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734A TYR* 5.4 0.2 - - - -
745A LEU* 4.3 17.9 - - + -
748A GLU* 4.4 19.3 - - + -
749A TRP* 3.6 34.1 - + + -
752A LEU* 4.0 16.4 - - + -
957A LEU* 3.8 19.5 - - + -
974A ILE* 4.0 20.6 - - + -
975A ALA* 4.3 11.2 - - - -
978A LEU* 3.7 29.4 - - + -
989A VAL* 3.8 5.3 - - + +
991A THR 3.0 5.9 + - - -
992A LYS 3.1 6.9 + - - +
994A GLN* 1.3 73.6 - - - +
996A GLU* 1.3 67.1 + - - +
998A ALA* 3.1 6.6 + - - +
999A LEU* 3.0 39.7 + - + +
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Residues in contact with GLU 996 (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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739A LEU* 3.9 11.5 - - + +
745A LEU* 4.0 32.7 - - + +
992A LYS* 2.7 24.7 + - + +
993A GLU* 3.6 17.2 - - - +
995A PHE* 1.3 74.5 - - - +
997A PHE* 1.3 52.0 + - - +
999A LEU* 3.4 8.4 + - - +
1000A THR* 2.8 39.2 + - - +
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Residues in contact with PHE 997 (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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911A TRP* 4.3 1.6 - + - -
916A VAL* 3.6 22.9 - - + -
917A PRO* 3.7 26.9 - - + -
920A SER* 3.7 32.5 - - - -
923A LEU* 3.4 40.6 - - + -
954A THR* 3.8 15.3 - - + -
958A ILE* 3.7 11.7 - - + -
993A GLU 2.9 18.9 + - - +
994A GLN 3.4 3.8 - - - +
995A PHE 3.1 0.6 - - - -
996A GLU* 1.3 72.8 - - - +
998A ALA* 1.3 59.5 + - - +
1000A THR* 2.9 9.9 + - + -
1001A ALA* 2.8 41.3 + - + +
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Residues in contact with ALA 998 (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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954A THR* 3.6 9.4 - - + -
957A LEU* 4.0 26.0 - - + -
958A ILE* 3.4 29.8 - - + +
974A ILE* 5.9 0.4 - - + -
994A GLN 2.9 16.1 + - - +
995A PHE* 3.5 8.1 - - + +
997A PHE* 1.3 71.4 - - - +
999A LEU* 1.3 64.6 + - + +
1001A ALA* 3.3 1.7 + - - +
1002A VAL* 3.1 29.3 + - - +
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Residues in contact with LEU 999 (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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734A TYR* 4.5 3.4 - - + -
735A MET* 3.2 17.1 - - - +
738A HIS* 3.8 28.9 - - + +
739A LEU* 3.9 23.3 - - + -
745A LEU* 4.7 4.7 - - + -
748A GLU* 5.6 0.2 - - - +
974A ILE* 3.0 51.1 - - + -
995A PHE* 3.0 38.7 + - + +
996A GLU* 3.5 8.7 - - - +
998A ALA* 1.3 77.9 - - - +
1000A THR* 1.3 62.2 - - - +
1001A ALA 3.1 0.3 + - - -
1002A VAL* 4.7 0.2 - - - -
1003A ALA* 3.0 21.0 + - - +
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Residues in contact with THR1000 (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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739A LEU* 3.7 23.7 - - + +
920A SER* 5.4 4.0 - - - -
996A GLU* 2.8 23.5 + - - +
997A PHE* 2.9 14.9 + - + -
999A LEU* 1.3 75.1 - - - +
1001A ALA* 1.3 57.7 + - - +
1003A ALA* 3.6 2.7 + - + +
1004A GLU* 3.0 50.3 + - + +
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Residues in contact with ALA1001 (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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920A SER* 4.4 14.6 - - - +
923A LEU* 6.3 0.7 - - + -
924A LEU* 3.5 25.9 - - + +
958A ILE* 4.0 20.4 - - + -
997A PHE* 2.8 28.2 + - + +
998A ALA 3.6 4.7 - - - +
1000A THR* 1.3 74.5 - - - +
1002A VAL* 1.3 67.3 + - - +
1004A GLU* 3.2 0.5 + - - -
1005A GLU* 3.0 21.3 + - - +
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Residues in contact with VAL1002 (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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731A ILE* 3.8 18.4 - - + -
735A MET* 3.5 18.4 - - + -
958A ILE* 4.1 28.5 - - + +
961A VAL* 4.1 26.9 - - + -
962A LEU* 4.1 23.6 - - + -
974A ILE* 5.0 2.2 - - + -
998A ALA* 3.1 14.3 + - + +
999A LEU* 3.6 6.5 - - - +
1001A ALA* 1.3 76.0 - - - +
1003A ALA* 1.3 64.3 + - - +
1005A GLU* 3.7 1.7 - - - +
1006A VAL* 2.9 27.9 + - + +
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Residues in contact with ALA1003 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731A ILE* 5.3 0.4 - - - -
732A LEU* 4.2 6.3 - - + +
735A MET* 3.8 26.4 - - + +
739A LEU* 4.3 10.3 - - + -
999A LEU 3.0 16.8 + - - +
1000A THR* 3.7 6.3 - - + +
1002A VAL* 1.3 78.4 - - - +
1004A GLU* 1.3 54.1 + - + +
1006A VAL* 3.3 6.8 + - - +
1007A ASN* 2.7 46.0 + - - +
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Residues in contact with GLU1004 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A SER* 2.4 33.1 + - - +
921A ARG* 4.6 2.8 + - - +
924A LEU* 4.7 3.8 - - + -
1000A THR* 3.0 38.8 + - + +
1001A ALA 3.2 3.6 + - - +
1003A ALA* 1.3 74.7 - - + +
1005A GLU* 1.3 66.2 + - - +
1007A ASN* 3.2 14.8 + - + +
1008A ALA* 3.0 21.8 + - - +
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Residues in contact with GLU1005 (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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924A LEU* 3.7 24.1 - - + +
927A ARG* 3.5 19.8 + - - -
928A ARG* 3.3 35.4 + - - +
962A LEU* 3.8 23.6 - - + -
1001A ALA 3.0 15.8 + - - +
1002A VAL 3.7 3.8 - - - +
1004A GLU* 1.3 76.8 - - - +
1006A VAL* 1.3 56.5 + - - +
1008A ALA* 3.0 12.8 + - - +
1009A ILE* 2.9 43.4 + - + +
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Residues in contact with VAL1006 (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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728A GLY* 3.6 37.5 - - - +
731A ILE* 4.3 10.3 - - + -
732A LEU* 4.1 16.3 - - + +
962A LEU* 3.9 13.9 - - + -
965A MET* 3.7 24.0 - - + -
1002A VAL* 2.9 30.8 + - + +
1003A ALA* 3.7 4.0 - - - +
1005A GLU* 1.3 76.1 - - + +
1007A ASN* 1.3 61.6 + - - +
1009A ILE* 4.1 6.2 - - - +
1010A LEU* 3.2 24.8 + - + +
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Residues in contact with ASN1007 (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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732A LEU* 3.6 27.0 - - - +
1003A ALA* 2.7 31.6 + - - +
1004A GLU* 3.4 14.7 - - - +
1006A VAL* 1.3 74.5 - - - +
1008A ALA* 1.3 55.9 + - - +
1010A LEU* 3.9 3.2 - - - +
1011A ALA* 3.0 29.5 + - - +
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Residues in contact with ALA1008 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A GLU 3.0 10.7 + - - +
1005A GLU* 3.0 18.0 + - - +
1007A ASN* 1.3 74.1 - - - +
1009A ILE* 1.3 68.6 + - + +
1011A ALA* 3.2 8.1 + - - +
1012A HIS* 3.2 18.9 + - - +
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Residues in contact with ILE1009 (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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724A ASP* 5.1 3.4 - - - +
725A ILE* 5.1 11.1 - - + +
962A LEU* 5.5 1.6 - - + -
965A MET* 3.9 39.7 - - + -
1005A GLU* 2.9 39.3 + - + +
1006A VAL 4.1 3.1 - - - +
1008A ALA* 1.3 75.6 - - + +
1010A LEU* 1.3 59.5 + - - +
1012A HIS* 3.0 31.2 + - - +
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Residues in contact with LEU1010 (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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725A ILE* 5.5 13.7 - - + -
728A GLY* 6.2 3.1 - - - -
729A HIS* 5.2 15.7 - - + +
732A LEU* 5.5 6.7 - - + -
965A MET* 6.5 0.4 - - + -
1006A VAL* 3.2 21.1 + - + +
1007A ASN* 4.3 3.1 - - - +
1009A ILE* 1.3 78.5 - - + +
1011A ALA* 1.3 66.1 + - - +
1012A HIS 3.4 7.0 + - - +
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Residues in contact with ALA1011 (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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1007A ASN 3.0 20.5 + - - +
1008A ALA* 3.4 9.9 - - - +
1010A LEU* 1.3 78.0 - - - +
1012A HIS* 1.3 60.0 + - - +
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Residues in contact with HIS1012 (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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1008A ALA 3.2 7.0 + - - +
1009A ILE* 3.0 21.6 + - - +
1010A LEU* 3.9 6.4 - - - +
1011A ALA* 1.3 81.4 - - - +
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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