Contacts of the helix formed by residues 1066 - 1088 (chain D) in PDB entry 1ZYR
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C ASN* 4.9 13.9 - - - +
516C ARG* 5.3 1.7 + - - -
906C PHE* 4.5 6.1 - - - -
1059D SER* 3.7 8.1 - - - +
1064D GLY 2.3 15.9 + - - +
1065D LEU* 1.3 79.0 - - - +
1067D VAL* 1.3 55.3 + - - +
1068D LEU* 3.9 2.5 + - - +
1069D GLU* 2.8 46.3 + - + +
1070D TYR* 2.7 29.0 + - - +
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Residues in contact with VAL1067 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C TYR* 4.2 1.3 - - + +
498C GLN* 3.7 13.2 - - + +
499C ALA* 6.3 0.4 - - + -
500C ASN* 3.5 27.8 - - - +
536C PRO* 4.4 10.5 - - + -
539C VAL* 3.6 35.0 - - + -
540C PHE* 4.7 0.9 - - + -
906C PHE* 2.9 48.1 - - + -
1066D THR* 1.3 69.1 - - - +
1068D LEU* 1.3 64.2 + - - +
1069D GLU 3.0 0.7 - - - -
1070D TYR* 2.8 20.8 + - - +
1071D PHE* 2.8 12.9 + - - +
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Residues in contact with LEU1068 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C TYR* 4.5 15.9 - - + -
498C GLN* 3.7 15.2 + - + +
516C ARG* 2.6 76.7 - - + +
521C PRO* 3.7 10.8 - - + -
1066D THR* 3.9 1.6 + - - -
1067D VAL* 1.3 82.6 - - - +
1069D GLU* 1.3 57.6 + - - +
1071D PHE* 3.7 13.2 - - + -
1072D ILE* 2.8 55.8 + - + +
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Residues in contact with GLU1069 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C ARG* 4.7 2.4 - - - +
1056D PRO 4.2 3.5 - - - +
1057D VAL* 2.9 49.3 - - + +
1058D ARG* 3.1 7.3 + - - +
1059D SER* 2.6 33.4 + - - -
1065D LEU* 3.2 13.5 - - + +
1066D THR* 2.8 34.3 + - + +
1067D VAL 3.0 0.8 - - - -
1068D LEU* 1.3 75.9 - - - +
1070D TYR* 1.3 66.2 + - - +
1072D ILE* 3.3 9.6 + - - +
1073D SER* 3.1 22.2 + - - -
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Residues in contact with TYR1070 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C VAL* 4.4 4.5 - - + -
540C PHE* 3.7 25.4 - + + -
550C LEU* 2.9 51.5 - - + +
551C GLU* 4.0 15.7 - - - -
553C ASP 3.0 22.0 + - - -
555C ALA* 3.2 25.5 - - + -
558C ALA* 3.2 14.2 - - - +
906C PHE* 4.0 11.9 - + + -
1065D LEU* 3.7 18.8 - - + +
1066D THR 2.7 17.6 + - - +
1067D VAL 2.8 6.0 + - - +
1069D GLU* 1.3 76.3 - - - +
1071D PHE* 1.3 63.4 + - - +
1073D SER* 2.7 24.6 + - - -
1074D SER* 3.1 8.5 + - - -
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Residues in contact with PHE1071 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C VAL* 4.1 15.7 - - + -
431C HIS 3.5 23.6 - - - -
432C ARG* 4.7 7.0 - - - -
434C HIS 4.3 0.7 - - - -
435C TYR* 3.7 50.0 - + + -
440C PRO* 3.4 31.0 - - + -
539C VAL* 4.5 7.4 - - + -
540C PHE* 5.1 1.7 - - - -
1067D VAL 2.8 13.8 + - - +
1068D LEU* 3.9 14.4 - - + +
1070D TYR* 1.3 78.8 - - - +
1072D ILE* 1.3 74.8 + - + +
1074D SER* 3.1 22.9 + - - -
1075D HIS* 3.8 20.2 + + - -
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Residues in contact with ILE1072 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C PRO* 3.9 6.1 - - + -
1045D MET* 3.8 22.7 - - + +
1053D PHE* 3.4 49.4 - - + -
1055D VAL 5.3 3.1 - - - +
1057D VAL* 4.4 10.8 - - + -
1068D LEU* 2.8 48.6 + - + +
1069D GLU* 3.4 9.0 - - - +
1071D PHE* 1.3 87.5 - - + +
1073D SER* 1.3 59.9 + - - +
1075D HIS* 3.1 26.0 + - - +
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Residues in contact with SER1073 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C ALA* 4.8 5.9 - - - +
1042D ARG* 3.7 29.8 + - - -
1045D MET* 3.2 33.2 - - - +
1057D VAL* 5.4 0.9 - - - -
1065D LEU* 4.6 0.7 - - - +
1069D GLU 3.1 7.3 + - - -
1070D TYR* 2.7 26.1 + - - -
1072D ILE* 1.3 77.0 - - - +
1074D SER* 1.3 68.0 + - - +
1075D HIS 3.1 0.9 + - - -
1076D GLY* 3.2 13.0 + - - -
1077D ALA* 3.7 4.0 + - - +
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Residues in contact with SER1074 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C VAL* 3.3 20.5 - - - +
440C PRO* 3.4 35.1 + - - +
441C VAL* 5.5 1.3 - - - -
555C ALA* 5.0 11.2 - - - -
1070D TYR* 3.1 9.8 + - - -
1071D PHE* 3.1 18.9 + - - -
1072D ILE 3.1 0.4 - - - -
1073D SER* 1.3 76.2 + - - +
1075D HIS* 1.3 55.6 + - - +
1077D ALA* 2.4 43.9 + - - +
1078D ARG* 3.8 0.9 + - - +
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Residues in contact with HIS1075 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ASP* 5.9 0.5 - - - +
430C VAL* 3.1 46.6 + - + +
431C HIS 4.6 0.7 - - - -
432C ARG* 4.3 12.0 - - - -
1046D GLN 3.3 16.4 - - - +
1047D LYS* 4.5 5.2 - - - -
1048D PRO* 3.9 20.3 - - + +
1053D PHE* 3.8 30.0 - + - -
1071D PHE* 3.8 28.9 - + - -
1072D ILE* 3.1 24.7 - - - +
1073D SER 3.1 0.2 + - - -
1074D SER* 1.3 78.9 + - - +
1076D GLY* 1.3 54.6 - - - +
1077D ALA 2.8 10.6 + - - -
1078D ARG* 3.3 4.7 + - - +
1079D LYS* 3.1 22.3 + - - +
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Residues in contact with GLY1076 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045D MET* 5.5 6.8 - - - +
1046D GLN 4.4 3.8 + - - -
1072D ILE 4.7 0.2 + - - -
1073D SER 3.2 11.3 + - - -
1074D SER 3.1 0.2 + - - -
1075D HIS* 1.3 76.9 - - - +
1077D ALA* 1.3 63.7 + - - +
1079D LYS* 3.1 42.4 + - - +
1080D GLY* 3.4 4.5 + - - -
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Residues in contact with ALA1077 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C PRO 4.9 7.6 - - - +
555C ALA* 5.5 8.1 - - + -
556C ASN* 5.8 11.8 - - + +
1073D SER 3.7 2.1 + - - +
1074D SER* 2.4 42.1 + - - +
1075D HIS 2.8 0.6 + - - -
1076D GLY* 1.3 66.2 - - - +
1078D ARG* 1.3 70.3 + - + +
1080D GLY* 3.0 5.7 + - - -
1081D GLY* 2.9 17.0 + - - -
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Residues in contact with ARG1078 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ARG* 2.8 41.0 + - + +
429C ASP* 4.4 10.9 + - - +
430C VAL* 4.3 24.7 - - + +
434C HIS* 5.0 5.7 + - - -
438C ILE* 5.2 0.4 - - - +
439C CYS 3.8 20.6 + - - -
440C PRO* 4.2 19.8 + - - +
441C VAL 4.7 2.6 + - - +
443C THR* 3.2 28.4 + - - +
444C PRO 5.9 0.2 - - - -
449C ILE* 3.9 22.2 - - + -
450C GLY* 3.4 18.6 + - - -
453C THR* 4.9 3.6 + - - -
1075D HIS 3.3 4.6 + - - +
1077D ALA* 1.3 78.5 - - + +
1079D LYS* 1.3 70.6 + - - +
1080D GLY 2.9 2.0 - - - -
1081D GLY* 2.7 4.8 + - - +
1082D ALA* 2.7 29.5 + - + +
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Residues in contact with LYS1079 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C PHE* 5.1 2.4 - - - -
429C ASP* 4.9 11.7 + - - +
1046D GLN* 4.0 31.8 + - + +
1047D LYS 5.8 4.0 - - - +
1048D PRO* 6.1 3.6 - - + +
1075D HIS 3.1 12.8 + - - +
1076D GLY* 3.1 30.2 + - - +
1078D ARG* 1.3 79.1 - - - +
1080D GLY* 1.3 63.7 + - - +
1082D ALA* 3.8 4.3 - - - +
1083D ASP* 2.6 39.4 + - - +
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Residues in contact with GLY1080 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076D GLY 3.4 3.3 + - - -
1077D ALA 3.0 7.9 + - - -
1078D ARG 2.9 0.4 - - - -
1079D LYS* 1.3 93.1 - - - +
1081D GLY* 1.3 59.9 + - - +
1082D ALA 3.2 1.3 - - - -
1083D ASP* 4.3 5.1 - - - +
1084D THR* 2.8 35.4 + - - +
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Residues in contact with GLY1081 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C GLU* 6.5 0.9 - - - -
449C ILE* 3.3 23.3 - - - +
1077D ALA 2.9 9.4 + - - -
1078D ARG* 2.7 10.7 + - - -
1080D GLY* 1.3 71.7 - - - +
1082D ALA* 1.3 71.0 + - - +
1084D THR* 2.7 15.2 + - - -
1085D ALA* 3.1 6.9 + - - +
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Residues in contact with ALA1082 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C PHE* 3.8 28.3 - - + +
428C ARG* 5.4 11.4 - - + +
449C ILE* 3.7 11.0 - - + +
1078D ARG* 2.7 16.0 + - + +
1079D LYS* 3.8 4.7 - - - +
1081D GLY* 1.3 84.3 - - - +
1083D ASP* 1.3 68.0 + - - +
1084D THR 2.7 0.3 + - - -
1085D ALA 2.7 9.0 + - - -
1525D STD 3.1 23.0 - - + -
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Residues in contact with ASP1083 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C PHE* 3.2 28.5 - - - -
1079D LYS* 2.6 26.5 + - - +
1080D GLY* 4.3 5.5 - - - +
1082D ALA* 1.3 78.1 - - - +
1084D THR* 1.3 53.8 + - - +
1086D LEU* 2.8 33.0 + - - +
1087D ARG* 3.0 28.4 + - - +
1237D THR* 5.7 8.5 - - + -
1241D PHE* 5.4 8.1 - - - -
1525D STD 4.4 0.2 - - - -
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Residues in contact with THR1084 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080D GLY* 2.8 21.1 + - - +
1081D GLY* 2.7 25.9 + - - -
1082D ALA 2.7 4.8 + - - -
1083D ASP* 1.3 69.3 - - + +
1085D ALA* 1.3 56.4 + - - +
1086D LEU 2.7 11.4 + - - -
1087D ARG* 3.1 41.9 + - - +
1088D THR* 2.8 22.2 + - - -
1234D THR* 5.2 0.2 - - - +
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Residues in contact with ALA1085 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C GLY* 4.1 30.5 - - - +
447C ALA* 4.7 1.3 - - - +
449C ILE* 4.8 0.7 - - + -
1081D GLY 3.7 9.9 - - - +
1082D ALA 2.7 7.1 + - - -
1084D THR* 1.3 76.6 + - - +
1086D LEU* 1.3 57.0 + - - +
1088D THR* 4.3 7.8 - - - -
1089D ALA* 4.0 8.8 + - - +
1525D STD 2.7 32.1 - - + +
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Residues in contact with LEU1086 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C PHE* 5.1 4.5 - - + -
1083D ASP* 2.8 20.4 + - - +
1084D THR 2.7 1.6 + - - -
1085D ALA* 1.3 78.2 - - - +
1087D ARG* 1.3 56.3 + - - +
1088D THR 2.9 4.3 - - - -
1089D ALA* 2.8 21.7 + - + +
1090D ASP* 3.0 40.0 + - - +
1525D STD 3.0 93.7 + - + +
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Residues in contact with ARG1087 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083D ASP* 3.0 20.5 + - - +
1084D THR* 3.1 49.0 - - - +
1086D LEU* 1.3 74.8 - - - +
1088D THR* 1.3 57.4 + - - +
1090D ASP* 4.7 1.8 - - - +
1091D SER* 2.8 27.6 + - - +
1233D GLY 4.8 0.4 - - - -
1234D THR* 2.7 39.7 + - + +
1235D GLN* 4.6 1.2 - - - +
1236D LEU* 3.9 21.8 + - - +
1237D THR* 4.0 26.6 + - - +
1256D LEU* 3.7 21.2 - - + +
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Residues in contact with THR1088 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D PRO* 6.4 2.2 - - + -
1084D THR* 2.8 22.6 + - - -
1085D ALA* 4.3 6.9 - - - -
1086D LEU 2.9 0.6 - - - -
1087D ARG* 1.3 75.3 - - - +
1089D ALA* 1.3 69.6 + - - +
1091D SER* 3.4 2.9 - - - -
1092D GLY* 3.2 14.2 + - - -
1234D THR* 3.4 26.7 + - + +
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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