Contacts of the helix formed by residues 1029 - 1052 (chain A) in PDB entry 5V6Y
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 GLU1029 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A THR* 3.9 27.4 + - - +
1026A ALA* 3.8 10.8 + - - +
1027A CYS 3.6 0.6 - - - -
1028A GLN* 1.3 86.1 - - + +
1030A ALA* 1.3 66.1 + - - +
1031A ASN* 3.2 11.5 + - + +
1032A TYR* 3.6 10.6 + - - +
1033A GLY 4.0 5.7 + - - -
1088A GLU* 4.7 9.0 - - - +
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Residues in contact with ALA1030 (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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1029A GLU* 1.3 73.1 - - - +
1031A ASN* 1.3 63.2 + - - +
1032A TYR 3.4 0.2 - - - -
1033A GLY* 3.6 2.3 + - - +
1034A ALA* 3.3 22.2 + - - +
1037A ARG* 5.2 2.1 + - - -
1091A ARG* 6.3 0.9 - - - +
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Residues in contact with ASN1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A ALA 5.5 1.8 - - - +
1029A GLU* 3.2 9.3 - - + +
1030A ALA* 1.3 78.7 - - - +
1032A TYR* 1.3 61.4 + - - +
1034A ALA* 3.4 7.2 + - - +
1035A LEU* 3.0 40.3 + - - +
1080A LEU* 5.8 5.9 - - + +
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Residues in contact with TYR1032 (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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1026A ALA 3.6 20.9 + - - +
1027A CYS* 3.6 33.7 - - + -
1029A GLU 3.6 5.2 + - - +
1030A ALA 3.4 0.6 - - - -
1031A ASN* 1.3 78.8 - - - +
1033A GLY* 1.3 62.9 + - - +
1035A LEU* 3.1 4.4 + - + +
1036A LEU* 3.0 59.5 + - + +
1073A THR* 3.1 21.7 + - - -
1076A MET* 4.0 15.0 - - + -
1077A ALA* 3.8 11.0 - - + +
1080A LEU* 3.6 23.5 - - + +
1088A GLU* 3.7 25.8 - - + -
1089A VAL* 3.6 20.7 - - + +
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Residues in contact with GLY1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029A GLU 4.0 5.0 + - - -
1030A ALA* 3.6 5.2 + - - -
1031A ASN 3.4 0.4 - - - -
1032A TYR* 1.3 80.1 - - - +
1034A ALA* 1.3 62.1 + - - +
1036A LEU* 3.4 11.5 + - - +
1037A ARG* 3.3 45.7 + - - +
1088A GLU* 4.2 15.1 + - - -
1091A ARG* 5.6 1.3 - - - -
1092A PHE* 6.1 0.9 - - - -
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Residues in contact with ALA1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A ALA 3.3 16.9 + - - +
1031A ASN* 3.6 9.9 - - - +
1032A TYR 3.2 0.6 - - - -
1033A GLY* 1.3 77.3 - - - +
1035A LEU* 1.3 56.6 + - + +
1037A ARG* 3.4 14.8 + - - +
1038A GLU* 2.9 39.2 + - - +
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Residues in contact with LEU1035 (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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1031A ASN* 3.0 35.1 + - - +
1032A TYR* 3.1 6.7 + - - +
1034A ALA* 1.3 75.7 - - + +
1036A LEU* 1.3 59.3 + - - +
1038A GLU* 4.5 12.3 - - - +
1039A LEU* 2.9 51.3 + - + +
1040A CYS* 3.8 0.9 + - - -
1076A MET* 4.4 23.1 - - + +
1080A LEU* 4.1 34.5 - - + -
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Residues in contact with LEU1036 (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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1032A TYR* 3.0 64.1 + - + +
1033A GLY* 3.7 8.7 - - - +
1034A ALA 3.2 0.2 - - - -
1035A LEU* 1.3 77.3 - - - +
1037A ARG* 1.3 57.2 + - - +
1040A CYS* 2.9 16.1 + - - +
1041A LEU* 2.9 25.1 + - - +
1073A THR* 3.7 29.2 - - + -
1076A MET* 4.0 10.8 - - + -
1088A GLU 4.5 4.0 - - - +
1089A VAL* 4.6 3.4 - - - -
1092A PHE* 3.7 41.8 - - + -
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Residues in contact with ARG1037 (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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1030A ALA 5.2 1.6 + - - -
1033A GLY* 3.3 38.4 + - - +
1034A ALA* 3.8 12.2 - - - +
1036A LEU* 1.3 77.2 - - - +
1038A GLU* 1.3 60.3 + - - +
1041A LEU* 3.4 34.4 - - + +
1042A THR* 3.6 7.4 + - - -
1088A GLU* 5.5 0.2 + - - -
1091A ARG* 4.7 19.2 - - - +
1092A PHE* 3.8 24.4 - - + +
1095A ALA* 6.1 5.2 - - - -
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Residues in contact with GLU1038 (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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1034A ALA* 2.9 24.8 + - - +
1035A LEU* 4.1 12.5 - - - +
1037A ARG* 1.3 79.8 - - - +
1039A LEU* 1.3 68.7 + - + +
1042A THR* 2.6 22.2 + - - +
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Residues in contact with LEU1039 (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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1035A LEU* 2.9 31.8 + - + +
1038A GLU* 1.3 92.8 - - + +
1040A CYS* 1.3 63.5 + - - +
1041A LEU 3.4 0.4 - - - -
1042A THR* 3.9 7.6 + - - -
1043A GLN* 4.1 11.1 + - - +
1072A CYS* 4.6 2.8 - - - -
1076A MET* 3.7 35.2 - - + -
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Residues in contact with CYS1040 (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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1036A LEU* 2.9 32.8 + - - +
1039A LEU* 1.3 76.9 - - - +
1041A LEU* 1.3 59.9 + - - +
1043A GLN* 4.1 3.8 + - - +
1044A PHE* 3.6 11.6 + - - +
1069A LEU* 3.3 25.7 - - + +
1072A CYS* 2.0 67.0 - - + +
1073A THR* 3.6 6.7 - - + -
1076A MET* 4.2 9.4 - - - -
1092A PHE* 4.7 0.2 - - + -
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Residues in contact with LEU1041 (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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1036A LEU 2.9 6.1 + - - +
1037A ARG* 3.4 44.4 + - + +
1039A LEU 3.4 0.2 - - - -
1040A CYS* 1.3 76.1 - - - +
1042A THR* 1.3 61.0 + - - +
1043A GLN 3.4 0.2 - - - -
1044A PHE* 3.8 23.6 - - + -
1045A GLN* 3.0 32.1 + - + +
1069A LEU* 4.4 1.8 - - + +
1092A PHE* 4.1 8.3 - - + -
1096A VAL* 4.2 21.3 - - + -
1099A ARG* 6.0 5.8 - - - -
1100A TYR* 4.7 12.8 - - + +
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Residues in contact with THR1042 (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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1037A ARG 3.6 5.1 + - - -
1038A GLU* 2.6 30.3 + - - -
1039A LEU* 3.9 3.7 + - - -
1040A CYS 3.5 1.0 - - - -
1041A LEU* 1.3 79.4 - - - +
1043A GLN* 1.3 61.2 + - - +
1045A GLN* 3.5 9.8 + - - +
1046A VAL* 3.2 31.2 + - + +
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Residues in contact with GLN1043 (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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1039A LEU 4.1 8.5 + - - +
1040A CYS* 4.1 6.1 + - - +
1041A LEU 3.4 0.4 - - - -
1042A THR* 1.3 76.7 - - - +
1044A PHE* 1.3 65.7 + - - +
1046A VAL* 3.2 16.2 + - - +
1047A ASP* 3.0 48.6 + - - +
1068A GLU* 5.8 7.9 - - + -
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Residues in contact with PHE1044 (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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1040A CYS 3.6 16.7 + - - +
1041A LEU* 3.4 11.9 + - + +
1042A THR 3.4 0.4 - - - -
1043A GLN* 1.3 79.2 - - - +
1045A GLN* 1.3 56.7 + - - +
1047A ASP* 3.3 5.8 + - - +
1048A MET* 2.9 63.1 + - + +
1062A THR 5.4 0.2 - - - -
1065A SER* 3.6 33.0 - - - +
1066A TYR* 4.1 9.9 - + + -
1069A LEU* 3.7 32.1 - - + -
1096A VAL* 4.0 11.0 - - + -
1100A TYR* 3.6 36.3 - + - -
1101A PHE* 4.3 13.7 - + - -
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Residues in contact with GLN1045 (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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1041A LEU* 3.0 22.4 + - + +
1042A THR* 3.8 9.6 - - - +
1044A PHE* 1.3 77.1 - - - +
1046A VAL* 1.3 58.2 + - + +
1048A MET* 3.8 0.9 - - - +
1049A GLU* 2.8 48.0 + - + +
1100A TYR* 3.5 25.0 + - + +
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Residues in contact with VAL1046 (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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1042A THR* 3.2 20.6 + - + +
1043A GLN* 3.2 23.4 + - - +
1045A GLN* 1.3 80.3 - - + +
1047A ASP* 1.3 63.7 + - - +
1049A GLU* 3.4 11.5 + - - +
1050A ALA* 3.2 22.5 + - + +
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Residues in contact with ASP1047 (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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1043A GLN* 3.0 37.7 + - - +
1044A PHE* 3.8 6.3 - - - +
1046A VAL* 1.3 78.8 - - - +
1048A MET* 1.3 62.4 + - - +
1050A ALA* 3.2 15.9 + - - +
1051A VAL* 3.2 14.4 + - - +
1064A ARG* 3.7 25.0 + - - +
1065A SER* 3.2 31.9 + - - +
1068A GLU* 5.3 5.7 - - - +
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Residues in contact with MET1048 (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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1044A PHE* 2.9 52.6 + - + +
1045A GLN 4.1 1.1 - - - +
1047A ASP* 1.3 73.4 - - - +
1049A GLU* 1.3 65.7 + - - +
1051A VAL* 3.2 13.4 - - - +
1052A GLY* 3.2 3.6 + - - -
1056A TRP* 2.8 56.3 + - + +
1062A THR* 3.7 25.6 - - + -
1065A SER* 4.5 9.4 - - - -
1100A TYR* 3.7 20.9 - - + -
1101A PHE* 3.7 28.0 - - + -
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Residues in contact with GLU1049 (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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1045A GLN* 2.8 34.9 + - + +
1046A VAL* 3.8 10.1 - - - +
1047A ASP 3.3 0.2 - - - -
1048A MET* 1.3 77.6 - - - +
1050A ALA* 1.3 60.6 + - - +
1052A GLY* 3.8 9.3 + - - -
1053A GLU* 6.3 0.4 - - - -
1056A TRP* 4.8 6.2 - - + -
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Residues in contact with ALA1050 (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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1046A VAL* 3.2 13.6 + - + +
1047A ASP* 3.5 11.2 - - - +
1048A MET 3.1 0.4 - - - -
1049A GLU* 1.3 76.3 - - - +
1051A VAL* 1.3 63.2 + - - +
1052A GLY* 3.3 0.8 - - - -
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Residues in contact with VAL1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A ASP 3.2 7.2 + - - +
1048A MET* 3.2 33.2 - - - +
1050A ALA* 1.3 78.0 - - - +
1052A GLY* 1.3 59.1 + - - +
1054A THR* 5.1 0.9 + - - -
1055A LEU* 3.9 28.6 - - + +
1056A TRP* 3.7 17.9 - - + -
1061A ARG* 3.7 57.4 + - + +
1062A THR* 4.4 4.0 - - + -
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Residues in contact with GLY1052 (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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1048A MET 3.2 9.1 + - - -
1049A GLU* 3.8 7.4 + - - -
1050A ALA 3.3 3.0 - - - -
1051A VAL* 1.3 79.0 - - - +
1053A GLU* 1.3 65.5 + - - -
1054A THR* 3.1 7.6 - - - -
1055A LEU 3.0 11.1 + - - -
1056A TRP* 3.0 19.4 + - - -
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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
------------------------------------------------------------
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