Contacts of the helix formed by residues 1033 - 1056 (chain A) in PDB entry 6S1M
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 GLU1033 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A VAL* 4.6 19.8 - - + +
1030A GLN* 3.3 15.2 + - - +
1031A PRO 3.7 2.4 + - - -
1032A ARG* 1.3 75.3 - - - +
1034A SER* 1.3 62.9 + - - +
1035A GLU 3.3 1.3 - - - -
1036A LEU* 3.6 7.4 - - + +
1037A TYR* 2.8 28.6 + - - +
1099A PHE* 3.5 31.2 - - + -
312B HIS* 5.8 0.2 - - - -
314B CYS* 4.7 16.5 - - - +
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Residues in contact with SER1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033A GLU* 1.3 77.2 + - - +
1035A GLU* 1.3 57.4 + - - +
1037A TYR* 3.5 6.0 + - - +
1038A GLN* 2.9 40.1 + - - +
276B VAL* 5.2 1.2 - - - +
314B CYS* 3.4 23.6 + - - +
315B MET* 3.4 25.2 + - - +
317B PRO* 6.2 2.5 - - - -
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Residues in contact with GLU1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A ARG* 3.8 30.0 - - + +
1033A GLU 3.3 1.4 - - - +
1034A SER* 1.3 81.0 - - - +
1036A LEU* 1.3 57.5 + - + +
1038A GLN* 3.3 9.1 + - - +
1039A LYS* 2.9 39.8 + - - +
273B VAL* 3.8 37.1 - - + +
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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
----------------------------------------------------------
1013A ILE* 4.6 18.9 - - + +
1014A GLY* 4.0 31.0 - - - +
1025A VAL* 5.5 7.6 - - + -
1029A CYS* 4.8 8.5 - - + +
1032A ARG* 3.4 47.6 - - + +
1033A GLU* 3.2 12.4 + - + +
1035A GLU* 1.3 77.0 - - + +
1037A TYR* 1.3 56.9 + - - +
1039A LYS* 2.7 31.4 - - + +
1040A GLU* 3.8 10.6 - - - +
1099A PHE* 4.4 7.3 - - + -
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Residues in contact with TYR1037 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033A GLU 2.8 16.0 + - - +
1034A SER 3.9 3.8 - - - +
1036A LEU* 1.3 73.0 - - - +
1038A GLN* 1.3 69.9 + - - +
1039A LYS 3.1 6.1 - - - +
1040A GLU* 4.3 2.5 - - - +
1041A VAL* 3.7 30.2 + - + +
1096A LEU* 3.9 24.2 - - + +
1099A PHE* 3.7 41.7 - + + -
1102A PRO* 5.6 3.6 - - - +
301B PRO 5.0 6.3 + - - -
312B HIS* 3.5 41.6 + + + +
314B CYS* 3.9 19.7 - - - -
315B MET* 4.4 17.7 - - - -
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Residues in contact with GLN1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034A SER* 2.9 32.9 + - - +
1035A GLU* 3.5 8.2 - - - +
1037A TYR* 1.3 78.9 - - - +
1039A LYS* 1.3 71.6 + - + +
1040A GLU 3.5 1.6 + - - -
1041A VAL* 3.4 19.7 + - - +
1042A SER* 4.0 8.0 + - - -
272B SER* 2.8 42.7 + - - +
273B VAL* 3.2 26.6 - - - +
276B VAL* 3.9 7.4 - - - +
301B PRO* 4.9 6.7 - - + -
315B MET* 3.7 29.0 - - + +
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Residues in contact with LYS1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A GLU* 2.9 41.4 + - - +
1036A LEU* 2.7 27.0 - - + +
1037A TYR 3.5 0.5 - - - +
1038A GLN* 1.3 84.0 - - - +
1040A GLU* 1.3 77.7 + - - +
1042A SER* 6.0 0.9 - - - -
272B SER* 5.5 5.9 + - - -
273B VAL* 3.6 21.9 - - - +
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Residues in contact with GLU1040 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A ILE* 3.9 15.2 - - - +
1036A LEU 3.8 6.9 - - - +
1037A TYR* 4.3 1.7 - - - +
1038A GLN 3.5 1.0 + - - -
1039A LYS* 1.3 78.4 - - - +
1041A VAL* 1.3 59.9 + - - +
1042A SER* 3.3 4.4 - - - +
1043A HIS* 3.3 14.9 + - + +
1044A LEU* 3.1 22.2 + - - +
1092A GLN* 3.2 19.3 - - - +
1095A LEU* 3.3 29.2 - - + +
1096A LEU* 3.5 19.8 - - + +
1099A PHE* 3.2 30.9 - - - -
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Residues in contact with VAL1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A TYR* 3.7 29.8 - - + +
1038A GLN* 3.4 16.2 - - - +
1039A LYS 3.5 1.2 - - - -
1040A GLU* 1.3 78.1 - - - +
1042A SER* 1.3 59.7 + - - +
1043A HIS 3.1 4.3 - - - -
1044A LEU* 3.8 16.8 - - + +
1045A ASN* 2.9 29.2 + - - +
1096A LEU* 4.7 10.3 - - + -
301B PRO* 4.2 38.1 - - + +
302B THR* 4.4 15.8 - - - +
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Residues in contact with SER1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A GLN 4.0 7.8 + - - -
1039A LYS* 6.0 0.7 - - - -
1040A GLU 3.3 2.6 - - - -
1041A VAL* 1.3 82.0 - - - +
1043A HIS* 1.3 57.0 + - - +
1045A ASN* 4.1 11.0 + - - +
1046A ALA* 3.8 16.5 + - - +
253B GLN* 5.8 3.8 - - - +
299B PHE* 6.1 1.7 - - - -
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Residues in contact with HIS1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ARG* 5.9 8.3 - - - -
1040A GLU* 3.3 19.3 + - - +
1041A VAL 3.1 1.0 - - - -
1042A SER* 1.3 76.1 - - - +
1044A LEU* 1.3 65.4 + - - +
1045A ASN 3.2 1.1 - - - -
1046A ALA* 3.2 6.6 + - - +
1047A LEU* 3.0 49.7 + - + +
1050A ARG* 5.3 2.0 - - - -
1092A GLN* 3.2 34.7 + - + -
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Residues in contact with LEU1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A GLU 3.1 13.7 + - - +
1041A VAL* 3.5 15.0 + - + +
1043A HIS* 1.3 75.3 - - - +
1045A ASN* 1.3 56.3 + - - +
1047A LEU* 3.2 4.3 + - - +
1048A GLU* 3.0 48.1 + - + +
1089A LEU* 4.0 21.5 - - + -
1092A GLN* 3.9 21.2 - - + +
1093A GLU* 4.3 22.4 - - + +
1096A LEU* 3.8 23.3 - - + -
44B ARG* 5.5 3.4 - - - +
303B ASN* 4.9 13.5 - - + +
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Residues in contact with ASN1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041A VAL 2.9 18.6 + - - +
1042A SER* 4.1 11.6 + - - +
1043A HIS 3.2 0.2 - - - -
1044A LEU* 1.3 76.6 - - - +
1046A ALA* 1.3 61.5 + - - +
1048A GLU* 4.6 5.2 - - - -
1049A GLU* 3.5 19.7 + - - +
300B ASP 5.4 0.9 - - - +
302B THR 3.2 21.6 - - - +
303B ASN* 3.4 16.1 - - - +
304B TYR* 3.6 23.6 + - - +
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Residues in contact with ALA1046 (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 SER 3.8 11.4 + - - +
1043A HIS* 3.2 12.1 + - - +
1045A ASN* 1.3 80.2 - - - +
1047A LEU* 1.3 65.5 + - + +
1049A GLU* 3.7 9.8 + - - +
1050A ARG* 3.6 23.6 + - - +
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Residues in contact with LEU1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A HIS* 3.0 38.3 + - + +
1044A LEU 3.2 4.7 + - - +
1046A ALA* 1.3 78.1 - - + +
1048A GLU* 1.3 63.2 + - - +
1049A GLU 3.2 0.4 - - - -
1050A ARG* 3.2 33.8 + - - +
1051A PHE* 3.1 23.2 + - - +
1085A VAL* 4.0 7.0 - - + +
1088A ASP* 3.6 45.5 - - + +
1089A LEU* 3.7 17.3 - - + +
1091A ASP* 4.9 0.2 - - - +
1092A GLN* 3.8 23.6 - - + -
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Residues in contact with GLU1048 (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 LEU* 3.0 32.0 + - + +
1045A ASN 3.9 6.3 - - - +
1046A ALA 3.4 0.2 - - - -
1047A LEU* 1.3 76.1 - - - +
1049A GLU* 1.3 61.9 + - - +
1050A ARG 3.4 0.3 + - - -
1051A PHE* 3.7 11.5 + - - +
1052A SER* 3.7 15.8 + - - -
1089A LEU* 4.1 11.2 - - + +
44B ARG* 2.8 29.3 + - - -
46B PHE* 3.1 29.5 - - - -
303B ASN* 4.0 8.1 - - + +
304B TYR* 3.9 23.6 - - + +
305B THR* 3.3 23.4 - - + +
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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 ASN* 3.5 14.4 + - - +
1046A ALA* 4.0 9.5 - - - +
1047A LEU 3.2 0.8 - - - -
1048A GLU* 1.3 79.1 - - - +
1050A ARG* 1.3 63.9 + - - +
1052A SER* 4.1 3.3 + - - -
1053A ARG* 3.7 40.2 + - + +
304B TYR* 3.9 40.1 + - + +
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Residues in contact with ARG1050 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A HIS* 5.3 2.8 - - - -
1046A ALA* 3.6 13.8 + - - +
1047A LEU* 3.2 36.7 + - - +
1049A GLU* 1.3 82.2 - - - +
1051A PHE* 1.3 64.8 + - - +
1052A SER 3.3 0.6 + - - -
1053A ARG* 3.7 3.9 + - - +
1054A LEU* 3.5 32.1 + - + +
1081A MET* 6.0 5.6 - - + -
1084A LYS* 4.1 13.0 - - - +
1085A VAL* 3.7 30.3 - - + +
1088A ASP* 3.9 19.2 + - - -
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Residues in contact with PHE1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A LEU 3.1 14.7 + - - +
1048A GLU* 3.8 6.7 - - - +
1049A GLU 3.6 0.2 - - - -
1050A ARG* 1.3 77.8 - - - +
1052A SER* 1.3 59.9 + - - +
1054A LEU* 3.9 1.9 - - - +
1055A TRP* 3.1 52.8 + + + +
1085A VAL* 4.0 10.8 - - + +
1086A ARG* 3.8 35.4 - - + -
1089A LEU* 4.0 22.0 - - + -
46B PHE* 3.9 31.9 - + + -
47B SER 4.5 5.8 - - - -
48B ARG 4.0 19.3 - - - -
50B TYR* 4.3 21.5 - + - -
386B PRO* 4.5 10.3 - - + -
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Residues in contact with SER1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048A GLU 3.7 13.3 + - - -
1049A GLU* 4.6 3.6 - - - -
1050A ARG 3.3 0.6 - - - -
1051A PHE* 1.3 77.7 - - - +
1053A ARG* 1.3 66.3 + - - +
1054A LEU 3.4 0.5 + - - -
1056A THR* 3.3 27.4 + - - +
50B TYR* 2.7 34.7 + - - -
304B TYR* 6.0 3.1 - - - -
305B THR* 4.8 4.3 - - - +
383B GLY* 4.1 20.1 - - - -
384B CYS 4.0 5.4 + - - -
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Residues in contact with ARG1053 (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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1049A GLU* 3.7 37.2 + - - +
1050A ARG* 3.7 6.1 + - + +
1051A PHE 3.5 0.6 - - - -
1052A SER* 1.3 79.0 - - - +
1054A LEU* 1.3 59.9 + - + +
1056A THR* 4.1 5.8 - - - +
1057A GLN* 3.6 11.6 + - - +
1060A ARG* 4.4 3.0 + - - +
105B PRO* 4.1 19.2 + - - +
106B SER* 3.5 29.9 + - - +
107B ILE* 3.2 43.5 + - + +
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Residues in contact with LEU1054 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050A ARG* 3.5 26.2 - - + +
1051A PHE* 3.4 3.7 + - - +
1052A SER 3.2 0.6 - - - -
1053A ARG* 1.3 76.6 - - + +
1055A TRP* 1.3 67.0 + - + +
1056A THR 3.2 2.0 - - - -
1057A GLN* 3.2 17.2 + - - +
1058A CYS* 3.6 11.4 + - - -
1078A ILE* 4.0 19.6 - - + +
1081A MET* 3.5 48.9 - - + +
1082A ARG* 4.3 14.0 - - + +
1085A VAL* 4.0 15.3 - - + -
107B ILE* 3.7 28.7 - - + -
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Residues in contact with TRP1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A PHE* 3.1 48.1 + + + +
1054A LEU* 1.3 79.4 - - + +
1056A THR* 1.3 57.7 + - - +
1057A GLN 3.5 0.2 - - - -
1058A CYS* 4.4 13.6 + - + +
1059A GLN* 4.5 9.7 - - - +
1069A VAL* 5.1 13.3 - - + +
1082A ARG* 3.2 61.5 + - + +
1083A LYS* 5.9 0.4 - - - -
1085A VAL* 6.4 0.7 - - + -
1086A ARG* 3.4 35.1 - - - +
48B ARG 4.9 2.5 - - - +
49B GLN* 4.0 34.1 - - + -
50B TYR* 4.4 22.6 + - + +
107D LEU 3.3 25.1 - - - -
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Residues in contact with THR1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A SER 3.3 20.6 + - - +
1053A ARG* 4.1 5.4 - - - +
1055A TRP* 1.3 76.0 - - - +
1057A GLN* 1.3 64.8 + - - +
1058A CYS 3.3 1.6 - - - -
1059A GLN* 3.4 31.4 + - - +
1060A ARG* 3.4 30.1 + - - +
50B TYR* 4.2 13.2 - - - -
379B PRO* 3.8 16.4 + - - -
380B ASP* 4.0 22.2 + - - +
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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