Contacts of the helix formed by residues 1055 - 1079 (chain A) in PDB entry 6MZL
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 VAL1055 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970A ASN 4.3 11.7 - - - +
971A LYS* 4.2 18.6 - - + +
1054A SER* 1.3 80.6 - - - +
1056A ALA* 1.3 65.3 + - + +
1057A GLU 3.4 0.4 - - - -
1058A HIS* 3.7 5.0 + - + +
1059A GLN* 3.5 30.4 + - - +
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Residues in contact with ALA1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A SER 3.5 3.2 - - - +
1055A VAL* 1.3 83.0 - - + +
1057A GLU* 1.3 58.6 + - - +
1059A GLN* 3.9 5.2 + - - +
1060A GLU* 3.2 28.8 + - - +
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Residues in contact with GLU1057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A SER* 3.8 20.6 + - - +
1055A VAL 3.4 0.4 - - - -
1056A ALA* 1.3 77.6 - - - +
1058A HIS* 1.3 58.5 + - - +
1060A GLU* 3.8 11.8 - - + +
1061A ARG* 2.9 57.1 + - + +
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Residues in contact with HIS1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A LEU* 3.7 26.9 - - + +
968A ILE* 4.6 13.0 - - + +
969A PRO 3.7 10.6 + - - -
970A ASN 3.9 3.6 + - - -
971A LYS* 3.2 39.9 + - + +
1054A SER 3.3 18.8 + - - +
1055A VAL* 3.9 7.0 - - + +
1056A ALA 3.4 0.4 - - - -
1057A GLU* 1.3 77.3 - - - +
1059A GLN* 1.3 60.9 + - - +
1061A ARG* 3.7 5.0 + - - +
1062A TYR* 3.3 18.9 + - + +
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Residues in contact with GLN1059 (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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947A LEU* 4.4 18.5 - - + +
970A ASN* 4.6 21.8 + - - +
1055A VAL* 3.5 21.1 + - - +
1056A ALA* 4.5 4.4 - - - +
1057A GLU 3.4 0.2 - - - -
1058A HIS* 1.3 79.5 - - - +
1060A GLU* 1.3 61.3 + - - +
1062A TYR* 3.5 10.7 + - + +
1063A LYS* 3.1 25.5 + - - +
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Residues in contact with GLU1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A ALA 3.2 21.4 + - - +
1057A GLU* 3.4 12.0 + - + +
1059A GLN* 1.3 74.8 - - - +
1061A ARG* 1.3 59.5 + - - +
1063A LYS* 3.1 9.1 + - + +
1064A GLU* 2.8 53.5 + - + +
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Residues in contact with ARG1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A GLU* 2.9 44.6 + - + +
1058A HIS* 4.1 5.8 - - - +
1060A GLU* 1.3 72.6 - - - +
1062A TYR* 1.3 61.1 + - - +
1064A GLU* 3.8 15.5 - - + +
1065A GLU* 3.0 30.7 + - + +
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Residues in contact with TYR1062 (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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731A LEU* 4.2 3.3 - - - +
941A ALA* 4.8 3.3 - - - +
947A LEU* 3.7 32.5 - - + -
948A LEU* 3.3 68.8 + - + +
950A VAL* 3.7 12.1 - - + -
968A ILE* 5.1 3.6 - - + -
1058A HIS* 3.3 13.0 + - + +
1059A GLN* 3.5 13.0 - - + +
1060A GLU 3.2 0.2 - - - -
1061A ARG* 1.3 80.0 - - - +
1063A LYS* 1.3 60.3 + - + +
1065A GLU* 3.5 4.3 + - + +
1066A CYS* 2.9 52.1 + - - -
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Residues in contact with LYS1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A LEU 4.5 14.8 - - - +
732A GLY* 4.4 1.8 - - - -
733A SER* 3.3 27.3 + - - +
1059A GLN 3.1 14.2 + - - +
1060A GLU* 3.1 11.4 + - + +
1062A TYR* 1.3 81.2 - - + +
1064A GLU* 1.3 58.3 + - + +
1066A CYS* 3.5 4.2 + - + +
1067A GLN* 2.9 62.7 + - + +
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Residues in contact with GLU1064 (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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1060A GLU* 2.8 42.7 + - + +
1061A ARG* 3.8 15.6 - - + +
1062A TYR 3.3 0.2 - - - -
1063A LYS* 1.3 78.6 - - + +
1065A GLU* 1.3 57.5 + - - +
1067A GLN* 3.9 4.6 - - - +
1068A ARG* 3.1 29.5 + - - +
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Residues in contact with GLU1065 (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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950A VAL* 4.2 19.1 - - + -
951A THR* 2.5 30.9 + - - +
1061A ARG* 3.0 20.0 + - + +
1062A TYR* 3.9 5.4 - - + +
1064A GLU* 1.3 73.1 - - - +
1066A CYS* 1.3 65.4 + - - +
1068A ARG* 2.6 37.1 + - - +
1069A ILE* 3.4 30.1 + - - +
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Residues in contact with CYS1066 (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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731A LEU* 3.9 35.7 - - + +
732A GLY* 4.7 1.3 - - - -
950A VAL* 3.7 17.5 - - - -
963A PHE* 3.9 11.3 - - - -
1062A TYR* 2.9 57.8 + - - +
1063A LYS* 3.7 7.0 - - + +
1065A GLU* 1.3 77.9 - - - +
1067A GLN* 1.3 61.6 + - - +
1069A ILE 3.7 0.2 + - - -
1070A PHE* 3.1 26.1 + - - +
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Residues in contact with GLN1067 (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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732A GLY* 4.5 2.4 - - - -
733A SER* 2.9 44.0 + - - +
735A HIS* 3.7 9.5 + - - +
1063A LYS* 2.9 35.0 + - + +
1064A GLU* 3.9 5.8 - - - +
1065A GLU 3.4 0.2 - - - -
1066A CYS* 1.3 77.0 - - - +
1068A ARG* 1.3 57.9 + - - +
1070A PHE* 4.3 4.4 - - - -
1071A ASP* 2.8 71.5 + - - +
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Residues in contact with ARG1068 (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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951A THR* 4.3 3.2 + - - +
960A GLY 5.2 3.6 + - - -
1064A GLU 3.1 16.6 + - - +
1065A GLU* 2.6 38.4 + - - +
1066A CYS 3.3 0.4 - - - -
1067A GLN* 1.3 78.8 - - - +
1069A ILE* 1.3 73.4 + - - +
1071A ASP* 3.8 4.3 - - - +
1072A LEU* 2.9 48.5 + - + +
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Residues in contact with ILE1069 (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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950A VAL* 3.8 21.8 - - + +
951A THR* 4.3 4.7 - - - +
960A GLY* 3.7 17.5 - - - +
961A GLU* 3.8 4.3 - - - +
962A GLY* 3.7 36.6 - - - +
963A PHE* 3.7 15.7 - - + -
1065A GLU* 3.4 33.0 + - - +
1067A GLN 3.4 0.4 - - - -
1068A ARG* 1.3 93.1 - - - +
1070A PHE* 1.3 55.6 + - - +
1072A LEU* 3.6 6.5 - - + -
1073A GLN* 2.7 34.5 + - + +
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Residues in contact with PHE1070 (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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730A PHE* 3.9 26.9 - + + -
732A GLY* 3.8 31.9 - - - -
733A SER 4.0 16.8 - - - -
734A LEU* 4.9 4.0 - - + -
738A GLN* 5.0 6.3 - - - -
740A LEU* 3.7 24.9 - - + -
751A PRO* 5.5 6.5 - - + -
963A PHE* 4.0 18.5 - + + -
1066A CYS 3.1 19.6 + - - +
1067A GLN* 3.8 6.1 - - - +
1069A ILE* 1.3 78.1 - - - +
1071A ASP* 1.3 66.1 + - - +
1073A GLN* 3.8 8.8 - - + +
1074A ASN* 2.8 57.7 + - - +
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Residues in contact with ASP1071 (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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735A HIS* 3.3 24.1 + - - -
738A GLN* 5.2 0.7 + - - +
1067A GLN* 2.8 51.5 + - - +
1068A ARG* 3.9 5.0 - - - +
1070A PHE* 1.3 81.7 - - - +
1072A LEU* 1.3 64.7 + - - +
1074A ASN* 3.5 11.0 + - - +
1075A LYS* 3.2 22.2 + - - +
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Residues in contact with LEU1072 (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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960A GLY 4.8 5.8 - - - +
961A GLU* 3.7 35.7 - - + +
1068A ARG* 2.9 39.4 + - + +
1069A ILE* 3.2 7.8 + - - +
1071A ASP* 1.3 75.2 - - - +
1073A GLN* 1.3 63.7 + - - +
1075A LYS* 3.2 7.5 + - + +
1076A VAL* 3.1 43.3 + - + +
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Residues in contact with GLN1073 (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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684A SER* 5.3 0.2 + - - -
751A PRO* 4.9 9.8 - - + +
753A TYR* 4.1 4.1 - - + +
783A GLY* 3.6 10.9 - - - -
784A GLN* 3.1 44.4 + - - +
957A THR* 6.3 0.2 - - - +
961A GLU* 4.0 24.1 + - - +
962A GLY* 4.8 2.3 - - - -
963A PHE* 4.8 13.7 - - - -
1069A ILE 2.7 20.9 + - - +
1070A PHE* 3.8 9.0 - - + +
1072A LEU* 1.3 71.8 - - - +
1074A ASN* 1.3 65.2 + - - +
1076A VAL* 4.7 3.6 - - - +
1077A LEU* 3.3 39.3 + - + +
147J ARG* 4.7 5.8 - - - +
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Residues in contact with ASN1074 (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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738A GLN* 3.9 19.8 - - - +
740A LEU* 3.8 10.8 - - - +
751A PRO* 5.2 1.7 - - - +
753A TYR* 2.3 32.8 + - + +
1070A PHE* 2.8 58.8 + - - +
1071A ASP* 3.6 11.6 + - - +
1072A LEU 3.3 0.2 - - - -
1073A GLN* 1.3 80.1 - - - +
1075A LYS* 1.3 51.6 + - - +
1078A SER* 2.5 35.7 + - - -
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Residues in contact with LYS1075 (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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1071A ASP 3.2 16.5 + - - +
1072A LEU* 3.2 8.2 + - + +
1074A ASN* 1.3 77.2 - - - +
1076A VAL* 1.3 68.2 + - + +
1078A SER* 3.6 3.9 + - - -
1079A SER* 3.3 24.8 + - - -
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Residues in contact with VAL1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A GLU* 4.1 25.6 - - + +
1072A LEU* 3.1 35.4 + - + +
1073A GLN* 4.5 3.4 - - - +
1075A LYS* 1.3 80.3 - - + +
1077A LEU* 1.3 64.5 + - + +
1079A SER* 3.2 17.8 + - - -
139J PRO* 3.4 22.7 - - + +
146J ARG* 5.2 7.2 - - - +
147J ARG* 4.3 9.2 - - - +
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Residues in contact with LEU1077 (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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684A SER* 4.6 3.1 - - - +
753A TYR* 3.5 24.3 - - + +
755A HIS* 2.8 22.7 + - - -
781A VAL* 3.8 25.6 - - + +
783A GLY* 4.0 15.9 - - - -
1073A GLN* 3.3 36.1 + - + +
1076A VAL* 1.3 80.5 - - + +
1078A SER* 1.3 56.8 + - - +
139J PRO* 3.3 16.6 - - + +
140J LEU* 4.2 11.4 - - + -
147J ARG* 3.4 43.1 - - - +
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Residues in contact with SER1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A TYR* 4.1 20.6 - - - -
755A HIS* 3.7 14.5 - - - -
1074A ASN 2.5 25.4 + - - -
1075A LYS* 3.6 5.2 + - - -
1077A LEU* 1.3 77.5 - - - +
1079A SER* 1.3 64.7 + - - +
1080A THR* 3.6 6.8 + - - +
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Residues in contact with SER1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A HIS* 4.1 1.6 - - - -
1075A LYS* 3.3 20.1 + - - -
1076A VAL* 3.2 10.8 + - - -
1078A SER* 1.3 78.2 - - - +
1080A THR* 1.3 60.6 + - - +
1081A GLU* 3.2 29.6 + - - +
139J PRO* 3.3 27.5 - - - +
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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) + - + + + + + -
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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