Contacts of the helix formed by residues 1066 - 1088 (chain N) in PDB entry 2A69
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 THR1066 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500M ASN* 3.9 13.9 + - - -
516M ARG* 5.3 4.6 + - - +
906M PHE* 3.6 4.4 - - - -
1059N SER* 6.0 0.2 - - - -
1064N GLY 3.0 8.6 + - - -
1065N LEU* 1.3 80.8 - - - +
1067N VAL* 1.3 72.6 + - - +
1068N LEU* 3.7 3.5 + - + +
1069N GLU* 3.0 53.2 + - + +
1070N TYR* 3.3 22.0 + - - +
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Residues in contact with VAL1067 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435M TYR* 4.1 7.1 + - - +
498M GLN* 3.3 32.1 - - + +
500M ASN* 3.0 34.8 - - - +
516M ARG* 5.1 0.7 - - - +
536M PRO* 4.2 15.5 - - + -
539M VAL* 4.4 16.9 - - + +
540M PHE* 5.0 5.0 - - + -
906M PHE* 3.9 35.5 - - + -
1066N THR* 1.3 78.3 + - - +
1068N LEU* 1.3 58.4 + - - +
1070N TYR* 3.3 16.6 - - - +
1071N PHE* 3.7 5.9 + - - +
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Residues in contact with LEU1068 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435M TYR* 3.1 33.9 - - + +
516M ARG* 3.1 68.6 - - + +
521M PRO* 4.0 15.7 - - + -
1066N THR* 3.7 4.1 + - + +
1067N VAL* 1.3 77.0 - - + +
1069N GLU* 1.3 68.6 + - + +
1070N TYR 2.6 6.9 + - - -
1071N PHE* 2.9 17.5 + - + +
1072N ILE* 2.9 38.9 + - + +
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Residues in contact with GLU1069 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516M ARG* 6.2 0.4 - - - +
1056N PRO 3.4 7.2 - - - +
1057N VAL* 3.0 24.3 - - + +
1058N ARG* 2.6 36.1 + - - +
1059N SER* 2.8 22.8 + - - -
1065N LEU* 3.3 13.2 - - + -
1066N THR* 3.0 29.6 - - + +
1068N LEU* 1.3 80.0 - - + +
1070N TYR* 1.3 51.4 + - - +
1072N ILE* 3.4 10.6 - - - +
1073N SER* 2.7 35.9 + - - -
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Residues in contact with TYR1070 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440M PRO* 6.1 1.1 - - + -
441M VAL* 4.6 7.4 - - + -
540M PHE* 3.6 26.2 - + - -
550M LEU* 3.3 35.3 - - + +
551M GLU 4.9 1.1 - - - -
553M ASP 2.5 31.4 + - - -
554M ASP* 3.8 0.6 - - - -
555M ALA* 3.3 33.5 - - + -
558M ALA* 3.9 0.7 - - - +
906M PHE* 3.5 17.0 - + + -
1042N ARG* 5.3 1.3 - - - -
1065N LEU* 3.3 30.5 - - + +
1066N THR 3.3 11.4 + - - +
1067N VAL 3.3 13.2 - - - +
1068N LEU 2.6 0.4 + - - -
1069N GLU* 1.3 73.5 - - - +
1071N PHE* 1.3 67.0 + - - +
1072N ILE 2.9 1.6 - - - -
1073N SER* 2.8 18.2 + - - -
1074N SER* 2.9 13.4 + - - -
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Residues in contact with PHE1071 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430M VAL* 3.8 13.9 - - + -
431M HIS 3.7 11.2 - - - -
432M ARG* 3.6 26.9 - - + -
434M HIS* 4.3 4.3 - - + -
435M TYR* 3.4 52.3 - + + -
438M ILE 5.2 0.4 - - - -
440M PRO* 4.6 17.5 - - + -
539M VAL* 4.1 14.3 - - + +
540M PHE* 6.0 1.1 - - - -
1067N VAL 3.7 5.7 + - - +
1068N LEU* 2.9 16.7 + - + +
1070N TYR* 1.3 77.2 - - - +
1072N ILE* 1.3 63.0 + - + +
1074N SER* 2.5 27.5 + - - -
1075N HIS* 3.5 30.7 - + - -
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Residues in contact with ILE1072 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519M GLY 5.7 0.9 - - - +
521M PRO* 4.0 12.3 - - + -
1045N MET* 3.6 26.1 - - + +
1046N GLN 4.3 2.1 - - - +
1053N PHE* 3.4 49.8 - - + -
1055N VAL 5.5 3.1 - - - +
1057N VAL* 4.8 7.4 - - + -
1068N LEU* 2.9 31.9 + - + +
1069N GLU* 3.4 13.2 - - - +
1071N PHE* 1.3 80.9 - - + +
1073N SER* 1.3 64.4 + - - +
1074N SER 3.3 0.5 + - - -
1075N HIS* 3.5 25.6 + - + +
1076N GLY 4.6 0.3 + - - -
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Residues in contact with SER1073 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555M ALA* 5.6 1.6 - - - -
1042N ARG* 3.8 30.5 + - - -
1045N MET* 3.3 32.9 - - - +
1057N VAL* 3.9 5.2 - - - +
1065N LEU* 4.8 2.0 - - - +
1069N GLU 2.7 18.8 + - - -
1070N TYR* 2.8 14.6 + - - -
1072N ILE* 1.3 72.7 - - - +
1074N SER* 1.3 64.6 + - - +
1075N HIS 3.3 1.0 + - - -
1076N GLY* 3.4 10.6 + - - -
1077N ALA* 3.5 8.9 + - - +
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Residues in contact with SER1074 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430M VAL* 3.6 22.2 - - - +
440M PRO* 4.2 25.2 - - - +
441M VAL* 6.1 0.9 - - - -
555M ALA* 4.8 12.9 - - - +
1070N TYR* 2.9 11.3 + - - -
1071N PHE* 2.5 27.3 + - - -
1073N SER* 1.3 77.6 - - - +
1075N HIS* 1.3 65.8 + - - +
1077N ALA* 2.8 25.6 + - - +
1078N ARG* 3.3 4.9 + - - +
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Residues in contact with HIS1075 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429M ASP* 4.5 4.3 - - - +
430M VAL* 2.9 40.2 + - + +
431M HIS 4.5 4.3 - - - -
432M ARG* 4.6 5.4 - - + +
1046N GLN 4.1 9.6 - - - +
1047N LYS 4.6 6.7 - - - +
1048N PRO* 4.2 27.6 - - + +
1053N PHE* 4.5 16.1 - + - -
1071N PHE* 3.5 38.2 - + - -
1072N ILE* 3.5 27.4 - - - +
1073N SER 3.3 0.4 + - - -
1074N SER* 1.3 81.9 + - - +
1076N GLY* 1.3 65.5 + - - +
1077N ALA 3.0 0.9 + - - -
1078N ARG* 3.1 13.7 + - - +
1079N LYS* 3.4 9.6 + - - +
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Residues in contact with GLY1076 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045N MET* 6.1 1.7 - - - +
1046N GLN* 4.8 7.9 + - - +
1072N ILE 4.6 0.8 + - - -
1073N SER 3.4 7.0 + - - -
1074N SER 3.3 1.0 - - - -
1075N HIS* 1.3 79.8 - - - +
1077N ALA* 1.3 62.9 + - - +
1079N LYS* 3.3 12.5 + - - +
1080N GLY* 3.1 17.3 + - - -
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Residues in contact with ALA1077 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555M ALA* 4.9 12.3 - - + -
556M ASN* 5.0 21.9 - - + +
1073N SER 3.5 8.0 + - - +
1074N SER* 2.8 22.6 + - - +
1076N GLY* 1.3 76.1 - - - +
1078N ARG* 1.3 61.0 + - + +
1080N GLY* 2.9 13.4 + - - -
1081N GLY* 3.0 10.7 + - - -
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Residues in contact with ARG1078 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428M ARG 2.5 34.6 + - - +
429M ASP* 3.7 17.8 - - - +
430M VAL* 3.5 33.1 - - + +
434M HIS* 5.5 3.4 + - - -
438M ILE* 5.8 0.4 - - - +
439M CYS 4.3 8.7 + - - -
440M PRO* 4.0 29.1 + - - +
443M THR* 3.4 42.4 - - - +
449M ILE* 4.5 11.2 - - - -
450M GLY* 3.9 7.7 + - - -
453M THR* 4.9 6.9 + - - +
559M LEU* 5.6 2.2 - - - +
1074N SER 4.3 2.5 - - - +
1075N HIS 3.1 9.0 + - - +
1077N ALA* 1.3 80.3 - - + +
1079N LYS* 1.3 53.0 + - - +
1081N GLY* 2.9 4.0 + - - +
1082N ALA* 2.7 37.3 + - + +
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Residues in contact with LYS1079 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425M PHE* 3.5 30.6 - - + -
429M ASP* 3.9 2.5 + - - +
1046N GLN* 4.5 14.2 + - - +
1075N HIS 3.4 6.6 + - - +
1076N GLY* 3.3 13.6 + - - +
1077N ALA 3.3 0.6 - - - -
1078N ARG* 1.3 77.9 - - - +
1080N GLY* 1.3 63.6 + - - +
1083N ASP* 3.1 33.9 + - - +
1237N THR* 5.9 4.9 - - - -
1239N ARG* 5.1 21.3 - - - +
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Residues in contact with GLY1080 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076N GLY 3.1 8.1 + - - -
1077N ALA* 2.9 9.2 + - - -
1079N LYS* 1.3 78.2 - - - +
1081N GLY* 1.3 51.2 + - - +
1083N ASP* 3.3 6.5 + - - +
1084N THR* 2.5 37.8 + - - +
1087N ARG* 5.3 0.2 + - - -
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Residues in contact with GLY1081 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445M GLU* 5.0 8.3 - - - -
449M ILE* 3.8 23.4 - - - +
556M ASN* 5.9 2.6 + - - -
1077N ALA 3.0 8.5 + - - -
1078N ARG 2.9 5.8 + - - -
1080N GLY* 1.3 72.7 - - - +
1082N ALA* 1.3 63.4 + - - +
1084N THR* 2.6 21.9 + - - -
1085N ALA* 3.0 15.6 + - - +
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Residues in contact with ALA1082 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425M PHE* 3.4 38.4 - - + -
428M ARG* 5.1 13.7 - - + +
449M ILE* 3.9 18.5 - - + +
1078N ARG 2.7 18.8 + - - +
1081N GLY* 1.3 72.3 - - - +
1083N ASP* 1.3 61.4 + - - +
1085N ALA* 3.7 1.4 + - - +
1086N LEU* 3.2 31.9 + - + +
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Residues in contact with ASP1083 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425M PHE* 3.7 17.5 - - - -
1079N LYS* 3.1 31.2 + - - +
1080N GLY* 3.5 7.0 - - - +
1082N ALA* 1.3 75.6 - - - +
1084N THR* 1.3 65.8 + - - +
1086N LEU* 3.1 17.4 + - - +
1087N ARG* 3.1 30.2 + - - +
1237N THR* 4.3 6.9 - - - +
1238N MET* 2.8 43.6 + - - +
1239N ARG* 4.6 4.4 - - - +
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Residues in contact with THR1084 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445M GLU* 4.8 7.2 + - - +
1080N GLY 2.5 20.5 + - - +
1081N GLY* 2.6 17.9 + - - -
1083N ASP* 1.3 73.9 - - - +
1085N ALA* 1.3 61.0 + - - +
1087N ARG* 3.0 25.7 + - - +
1088N THR* 3.2 14.5 + - - -
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Residues in contact with ALA1085 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428M ARG* 4.6 2.5 - - - +
446M GLY* 4.0 5.6 - - - +
447M ALA* 3.4 49.7 - - - +
449M ILE* 4.0 5.8 - - + -
1081N GLY 3.0 15.2 + - - +
1082N ALA 3.9 5.2 - - - +
1084N THR* 1.3 75.9 - - - +
1086N LEU* 1.3 61.8 + - + +
1087N ARG 3.5 0.3 + - - -
1088N THR* 3.5 20.2 + - - -
1089N ALA* 4.5 3.5 + - - +
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Residues in contact with LEU1086 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425M PHE* 5.0 14.8 - - + -
428M ARG* 4.5 17.7 - - - +
447M ALA 5.5 0.4 - - - +
1082N ALA* 3.2 22.5 + - + +
1083N ASP* 3.1 14.3 + - - +
1084N THR 3.0 1.0 - - - -
1085N ALA* 1.3 83.1 - - + +
1087N ARG* 1.3 60.9 + - - +
1088N THR 3.4 0.2 - - - -
1089N ALA* 4.0 4.8 + - - +
1090N ASP* 3.4 26.0 + - - +
1238N MET* 5.0 22.2 - - + +
1239N ARG 5.7 2.2 - - - +
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Residues in contact with ARG1087 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083N ASP* 3.1 43.6 + - - +
1084N THR* 3.0 18.8 + - - +
1086N LEU* 1.3 76.0 - - - +
1088N THR* 1.3 58.0 + - - +
1089N ALA 2.8 10.9 + - - -
1090N ASP* 3.4 10.8 - - + +
1091N SER* 2.9 33.2 + - - +
1233N GLY 4.7 1.8 - - - +
1234N THR* 2.8 48.6 + - + +
1235N GLN 4.7 0.6 - - - -
1236N LEU 3.0 20.4 + - - -
1237N THR* 5.1 1.6 - - - +
1238N MET* 3.2 37.6 - - - +
1256N LEU* 3.9 12.8 - - + -
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Residues in contact with THR1088 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447M ALA* 5.7 4.8 + - + -
1084N THR 3.2 15.2 + - - -
1085N ALA* 3.6 15.7 + - - -
1086N LEU 3.4 1.0 - - - -
1087N ARG* 1.3 77.1 - - - +
1089N ALA* 1.3 55.6 + - - +
1091N SER* 4.5 8.1 + - - -
1234N THR* 6.3 0.2 - - - -
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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