Contacts of the helix formed by residues 1023 - 1048 (chain A) in PDB entry 2NZ6
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 VAL1023 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021A ILE 3.7 0.6 + - - -
1022A ARG* 1.3 70.8 - - - +
1024A GLU* 1.3 62.2 + - + +
1026A PHE* 3.1 27.8 + - - +
1027A GLU* 4.4 1.7 + - - +
1259A ILE* 4.2 20.4 - - + -
1263A ASN* 2.9 59.0 + - - +
1264A THR 3.7 3.4 - - - +
1265A VAL* 4.0 16.2 - - + -
1299A VAL* 3.8 26.8 - - + +
1302A GLN* 4.0 20.0 - - - +
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Residues in contact with GLU1024 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A ARG* 3.6 33.9 - - + -
1023A VAL* 1.3 84.2 - - + +
1025A ASN* 1.3 77.3 + - - +
1027A GLU* 5.3 1.0 + - - +
1263A ASN* 5.3 6.1 - - - +
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Residues in contact with ASN1025 (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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1021A ILE* 4.2 8.5 - - + -
1022A ARG* 2.9 24.9 + - - +
1024A GLU* 1.3 96.2 + - - +
1026A PHE* 1.3 57.6 + - - +
1027A GLU 3.5 2.2 - - - -
1028A ALA* 3.5 11.2 + - + +
1029A TYR* 3.1 26.8 + - + +
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Residues in contact with PHE1026 (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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1021A ILE* 4.0 13.7 - - + -
1022A ARG 3.2 7.9 + - - +
1023A VAL* 3.1 20.7 + - - +
1025A ASN* 1.3 75.4 - - - +
1027A GLU* 1.3 63.0 + - - +
1029A TYR* 3.7 25.1 - + - -
1030A PHE* 2.8 39.8 + + - +
1265A VAL* 3.9 23.8 - - + -
1267A VAL* 5.2 0.7 - - + -
1292A ASN* 3.6 35.2 - - - -
1295A VAL* 3.4 35.9 - - + -
1296A LEU* 3.8 17.9 - - + -
1299A VAL* 4.4 7.4 - - + -
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Residues in contact with GLU1027 (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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1023A VAL 4.4 1.0 + - - +
1024A GLU 5.3 1.0 + - - +
1026A PHE* 1.3 76.6 - - - +
1028A ALA* 1.3 62.4 + - - +
1030A PHE* 3.9 1.4 - - - +
1031A LYS* 3.1 24.3 + - - +
1296A LEU* 3.7 26.4 - - + +
1299A VAL* 4.1 21.8 - - + +
1300A ARG* 3.6 35.8 + - + +
1303A LYS* 5.4 5.9 - - - +
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Residues in contact with ALA1028 (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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1024A GLU 5.8 0.4 + - - +
1025A ASN* 3.5 12.8 + - + +
1026A PHE 3.3 0.4 - - - -
1027A GLU* 1.3 79.0 - - - +
1029A TYR* 1.3 60.9 + - - +
1031A LYS* 3.6 9.3 + - - +
1032A LYS* 3.3 20.1 + - - +
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Residues in contact with TYR1029 (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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1019A LYS* 4.1 12.7 - - - +
1021A ILE* 3.6 38.3 - - + +
1025A ASN* 3.1 17.7 + - + +
1026A PHE* 3.9 32.5 - + - +
1027A GLU 3.3 0.2 - - - -
1028A ALA* 1.3 74.1 - - - +
1030A PHE* 1.3 67.1 + - - +
1032A LYS* 3.3 11.1 + - + +
1033A GLN* 3.0 44.5 + - + +
1041A PHE* 3.7 20.3 - + - -
1044A GLU* 2.5 36.4 + - - -
1292A ASN* 4.2 3.3 + - - -
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Residues in contact with PHE1030 (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 PHE* 2.8 32.3 + + + +
1027A GLU 3.9 4.0 - - - +
1029A TYR* 1.3 74.3 - - - +
1031A LYS* 1.3 67.8 + - - +
1033A GLN* 3.2 0.9 + - - +
1034A GLN* 2.9 57.3 + - + +
1041A PHE* 3.6 27.1 - + - -
1289A VAL* 5.5 1.6 - - + -
1292A ASN* 3.7 34.3 - - + -
1293A GLN* 3.7 24.2 - - + -
1296A LEU* 3.6 34.5 - - + -
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Residues in contact with LYS1031 (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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1027A GLU 3.1 17.7 + - - +
1028A ALA* 3.6 8.7 - - - +
1029A TYR 3.3 0.2 - - - -
1030A PHE* 1.3 80.5 - - - +
1032A LYS* 1.3 62.6 + - - +
1034A GLN* 3.7 11.8 + - + +
1035A ALA* 3.5 19.8 + - - +
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Residues in contact with LYS1032 (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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1028A ALA 3.3 10.4 + - - +
1029A TYR* 3.3 15.2 + - + +
1030A PHE 3.2 0.2 - - - -
1031A LYS* 1.3 79.0 - - - +
1033A GLN* 1.3 78.2 + - - +
1034A GLN 3.6 0.5 + - - -
1035A ALA* 3.7 16.0 + - - +
1040A GLY 5.1 2.1 + - - -
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Residues in contact with GLN1033 (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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1019A LYS* 3.8 10.6 - - - +
1029A TYR* 3.0 39.9 + - + +
1030A PHE 3.2 0.4 + - - +
1032A LYS* 1.3 94.1 - - + +
1034A GLN* 1.3 58.8 + - - +
1035A ALA 3.4 0.4 + - - -
1038A ASN* 3.6 4.0 - - - -
1040A GLY* 3.2 38.9 + - - -
1041A PHE* 3.3 46.3 + - + -
1044A GLU* 2.7 26.1 + - - -
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Residues in contact with GLN1034 (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 PHE* 2.9 47.2 + - + +
1031A LYS* 3.7 11.8 + - - +
1033A GLN* 1.3 75.4 - - - +
1035A ALA* 1.3 71.4 + - - +
1036A ASP 3.7 0.5 + - - -
1037A SER* 4.0 1.9 + - - -
1038A ASN* 3.0 33.7 + - - +
1041A PHE* 3.8 5.1 - - + -
1293A GLN* 5.6 1.7 + - - -
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Residues in contact with ALA1035 (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 LYS 3.5 9.9 + - - +
1032A LYS* 3.7 14.7 - - - +
1033A GLN 3.4 2.0 - - - +
1034A GLN* 1.3 85.2 - - - +
1036A ASP* 1.3 74.3 + - - +
1039A CYS* 3.2 21.8 + - - +
1040A GLY 4.6 0.3 + - - -
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Residues in contact with ASP1036 (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 GLN 3.7 0.2 + - - -
1035A ALA* 1.3 76.0 - - - +
1037A SER* 1.3 74.4 + - - +
1039A CYS* 3.5 18.7 + - + +
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Residues in contact with SER1037 (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 GLN 4.0 2.3 + - - -
1035A ALA 3.5 0.4 - - - -
1036A ASP* 1.3 77.5 - - - +
1038A ASN* 1.3 74.8 + - - +
1039A CYS* 3.3 1.6 + - - -
1042A ALA* 5.3 1.2 - - - +
1285A GLU* 4.7 4.0 - - - +
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Residues in contact with ASN1038 (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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1033A GLN 3.6 9.6 - - - +
1034A GLN* 3.0 38.0 + - - +
1037A SER* 1.3 78.7 + - - +
1039A CYS* 1.3 59.2 + - - +
1040A GLY 3.4 2.7 - - - -
1041A PHE* 4.3 2.6 - - + -
1042A ALA* 2.9 28.8 + - - +
1285A GLU* 4.2 8.1 + - - +
1286A ASP* 5.4 4.4 + - - -
1289A VAL* 4.1 40.8 - - + +
1293A GLN* 5.8 0.3 + - - -
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Residues in contact with CYS1039 (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 ALA 3.2 14.5 + - - +
1036A ASP* 3.7 18.8 - - + +
1037A SER 3.3 2.5 + - - -
1038A ASN* 1.3 75.9 - - - +
1040A GLY* 1.3 62.8 + - - +
1042A ALA* 3.2 9.2 + - - +
1043A GLU* 3.1 22.6 + - - +
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Residues in contact with GLY1040 (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 LYS 5.1 1.9 + - - -
1033A GLN* 3.2 45.2 + - - -
1035A ALA 4.6 0.8 + - - -
1039A CYS* 1.3 79.2 - - - +
1041A PHE* 1.3 59.1 + - - +
1043A GLU* 3.3 8.6 + - - +
1044A GLU* 3.2 17.8 + - - +
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Residues in contact with PHE1041 (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 TYR* 3.7 14.1 - + - -
1030A PHE* 3.6 42.4 - + - -
1033A GLN* 3.3 42.7 + - + -
1034A GLN* 3.8 11.0 - - + -
1038A ASN* 3.9 7.4 - - - +
1039A CYS 3.4 0.4 - - - -
1040A GLY* 1.3 74.0 - - - +
1042A ALA* 1.3 57.2 + - - +
1044A GLU* 3.4 17.1 + - - +
1045A TYR* 2.9 29.9 + - - +
1285A GLU* 5.1 1.1 - - - -
1288A TYR* 3.8 6.9 - + + -
1289A VAL* 3.9 32.8 - - + -
1292A ASN* 3.4 36.6 - - + -
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Residues in contact with ALA1042 (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 SER 5.3 1.3 - - - +
1038A ASN 2.9 19.2 + - - +
1039A CYS* 3.4 10.1 - - - +
1041A PHE* 1.3 76.4 - - - +
1043A GLU* 1.3 56.4 + - - +
1045A TYR* 3.6 1.6 + - - +
1046A GLU* 3.0 32.8 + - + +
1285A GLU* 3.8 31.7 + - - +
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Residues in contact with GLU1043 (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 CYS* 3.1 11.9 + - - +
1040A GLY* 3.6 11.2 - - - +
1042A ALA* 1.3 74.9 - - - +
1044A GLU* 1.3 66.1 + - + +
1046A GLU* 3.4 4.6 + - - +
1047A ASP* 3.0 40.3 + - - +
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Residues in contact with GLU1044 (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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1019A LYS* 3.1 29.3 + - + +
1029A TYR* 2.5 29.5 + - - -
1033A GLN* 2.7 20.2 + - - -
1040A GLY 3.2 8.6 + - - +
1041A PHE* 3.5 12.8 - - - +
1043A GLU* 1.3 81.1 - - + +
1045A TYR* 1.3 62.2 + - - +
1047A ASP* 3.4 3.4 + - - -
1048A LEU* 3.3 11.3 + - - +
1267A VAL* 5.7 0.7 - - - +
1268A TYR* 3.2 37.0 + - + +
1288A TYR* 2.6 37.8 + - - +
1292A ASN* 4.9 0.7 + - - -
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Residues in contact with TYR1045 (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 PHE 2.9 18.3 + - - +
1042A ALA 3.9 4.7 - - - +
1043A GLU 3.2 0.2 - - - -
1044A GLU* 1.3 77.2 - - - +
1046A GLU* 1.3 67.5 + - + +
1048A LEU* 3.2 22.6 + - + +
1049A LYS* 3.6 9.2 + - + +
1271A VAL* 5.4 0.2 - - + -
1275A ARG* 3.4 16.6 + - - -
1282A VAL* 2.7 31.7 + - + -
1283A GLN 2.9 21.2 + - - -
1284A THR* 3.5 15.3 - - - -
1285A GLU* 3.8 28.9 - - + -
1288A TYR* 3.5 35.2 - + + -
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Residues in contact with GLU1046 (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 ALA 3.0 20.1 + - - +
1043A GLU* 4.1 4.9 - - - +
1044A GLU 3.4 0.4 - - - -
1045A TYR* 1.3 81.7 - - + +
1047A ASP* 1.3 59.6 + - - +
1049A LYS* 3.0 33.8 - - + +
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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
----------------------------------------------------------
1043A GLU* 3.0 32.2 + - - +
1044A GLU* 3.6 8.5 - - - +
1045A TYR 3.3 0.2 - - - -
1046A GLU* 1.3 76.6 - - - +
1048A LEU* 1.3 58.4 + - - +
1049A LYS 3.4 0.8 + - - -
1050A LEU 4.9 1.4 + - - -
1051A VAL* 4.0 9.5 - - - +
1268A TYR* 3.7 23.7 + - + +
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Residues in contact with LEU1048 (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 GLU 3.3 8.3 + - - +
1045A TYR* 3.2 15.7 + - + +
1047A ASP* 1.3 76.9 - - - +
1049A LYS* 1.3 60.3 + - - +
1050A LEU 3.3 2.2 - - - -
1051A VAL* 3.2 21.2 + - + +
1268A TYR* 3.5 30.1 - - + +
1271A VAL* 3.8 17.9 - - + +
1272A TYR* 3.6 43.5 - - + +
1275A ARG* 3.0 25.3 + - + +
1288A TYR* 3.7 32.5 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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