Contacts of the helix formed by residues 1049 - 1070 (chain A) in PDB entry 5DSG
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 ASP1049 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048A LEU* 1.3 74.1 - - - +
1050A ALA* 1.3 57.6 + - - +
1051A VAL* 3.3 10.0 + - - +
1052A ARG* 3.0 60.8 + - - +
1053A ARG* 2.7 36.0 + - - +
1081A LYS* 5.3 6.5 - - - +
1083A TRP* 4.2 6.8 - - - -
1113A GLY* 4.5 3.1 - - - +
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Residues in contact with ALA1050 (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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224A SER* 4.5 17.6 - - - +
1049A ASP* 1.3 73.0 - - - +
1051A VAL* 1.3 61.7 + - + +
1053A ARG* 3.1 17.5 - - - +
1054A ALA* 2.9 29.1 + - - +
1115A TRP* 5.6 0.2 - - - -
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Residues in contact with VAL1051 (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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1006A MET* 5.5 0.2 - - - +
1049A ASP* 3.3 7.5 + - - +
1050A ALA* 1.3 79.3 - - + +
1052A ARG* 1.3 59.3 + - - +
1054A ALA* 3.1 6.1 + - - +
1055A ALA* 2.9 24.1 + - - +
1109A THR* 3.6 25.0 - - + +
1113A GLY* 3.4 32.5 - - - +
1114A THR* 4.0 4.3 - - - +
1115A TRP* 3.9 43.6 - - + +
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Residues in contact with ARG1052 (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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1048A LEU* 3.4 13.2 - - + +
1049A ASP* 3.0 44.5 + - - +
1051A VAL* 1.3 72.8 - - - +
1053A ARG* 1.3 62.0 + - - +
1055A ALA* 3.1 8.2 + - - -
1056A LEU 2.9 22.3 + - - -
1083A TRP* 3.4 43.7 - - - +
1109A THR 3.9 11.4 - - - +
1110A PHE* 2.4 46.5 + - + +
1111A ARG 3.0 23.6 + - - -
1112A THR 3.2 17.4 + - - -
1113A GLY* 3.4 8.7 - - - -
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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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224A SER* 6.2 0.4 - - - -
1045A TYR* 3.5 61.6 + - + -
1046A ASP* 3.9 11.9 + - - +
1048A LEU* 3.1 40.6 + - + +
1049A ASP 2.7 18.8 + - - +
1050A ALA* 3.1 24.8 - - - +
1052A ARG* 1.3 73.1 - - - +
1054A ALA* 1.3 58.9 + - + +
1056A LEU* 3.3 5.8 + - - +
1057A ILE* 2.9 33.1 + - + +
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Residues in contact with ALA1054 (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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224A SER 5.5 1.3 - - - +
1003A ILE* 3.9 28.3 - - + -
1006A MET* 3.3 14.4 - - + +
1050A ALA 2.9 15.7 + - - +
1051A VAL* 3.2 12.6 - - - +
1053A ARG* 1.3 78.6 - - + +
1055A ALA* 1.3 56.3 + - - +
1057A ILE* 3.3 13.8 + - - +
1058A ASN 2.9 21.1 + - - -
1115A TRP* 4.1 15.5 - - + -
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Residues in contact with ALA1055 (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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1006A MET* 4.6 5.6 - - - -
1051A VAL 2.9 12.4 + - - +
1052A ARG* 3.1 13.2 + - - +
1054A ALA* 1.3 75.4 - - - +
1056A LEU* 1.3 58.5 + - - +
1058A ASN* 3.0 11.4 + - - +
1059A MET* 2.9 28.9 + - - +
1106A VAL* 4.1 9.7 - - + +
1109A THR* 4.3 15.0 - - + -
1110A PHE* 3.5 26.5 - - + -
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Residues in contact with LEU1056 (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 ILE* 4.5 9.9 - - + -
1041A LEU* 4.2 10.1 - - + +
1044A VAL* 4.3 11.2 - - + -
1045A TYR* 4.0 42.0 - - + +
1048A LEU* 4.4 4.3 - - + -
1052A ARG 2.9 12.0 + - - +
1053A ARG* 3.3 10.1 + - - +
1055A ALA* 1.3 75.6 - - - +
1057A ILE* 1.3 57.5 + - - +
1059A MET* 3.1 13.8 + - - +
1060A VAL* 2.9 33.4 + - + +
1068A VAL* 3.8 19.1 - - + -
1075A LEU* 3.8 24.9 - - + -
1078A LEU* 5.0 2.2 - - + -
1110A PHE* 3.6 10.7 - - + -
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Residues in contact with ILE1057 (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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1003A ILE* 4.2 30.3 - - + -
1007A LEU* 5.9 0.4 - - + -
1028A VAL* 4.7 9.6 - - + -
1031A ALA* 4.4 15.3 - - + +
1032A VAL* 3.8 24.9 - - + -
1035A ILE* 3.8 23.8 - - + -
1045A TYR* 3.8 17.5 - - + +
1053A ARG* 2.9 21.2 + - + +
1054A ALA* 3.4 16.6 - - - +
1055A ALA 3.2 0.2 - - - -
1056A LEU* 1.3 76.2 - - - +
1058A ASN* 1.3 58.2 + - - +
1060A VAL* 3.4 2.8 + - - +
1061A PHE* 2.9 29.8 + - + +
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Residues in contact with ASN1058 (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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1006A MET* 3.5 27.1 - - + +
1007A LEU* 3.9 14.0 - - - +
1010A ASP* 2.8 27.0 + - - -
1054A ALA 2.9 13.6 + - - +
1055A ALA* 3.0 15.7 + - - +
1057A ILE* 1.3 75.5 - - - +
1059A MET* 1.3 56.8 + - - +
1061A PHE* 3.1 7.5 + - - +
1062A GLN* 2.9 25.1 + - - +
1102A ARG* 2.5 39.3 + - - -
1106A VAL* 4.1 12.8 - - + +
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Residues in contact with MET1059 (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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1055A ALA 2.9 14.0 + - - +
1056A LEU* 3.4 14.6 - - - +
1058A ASN* 1.3 76.8 - - - +
1060A VAL* 1.3 57.2 + - - +
1062A GLN* 3.2 4.1 + - - -
1063A MET* 2.9 59.4 + - + +
1068A VAL* 3.3 17.5 - - + +
1071A PHE* 3.9 31.4 - - + -
1075A LEU* 6.1 1.1 - - + -
1078A LEU* 5.7 2.2 - - - -
1090A LEU* 4.4 8.7 - - + -
1095A TRP* 4.2 23.6 - - + -
1106A VAL* 4.2 12.3 - - + -
1110A PHE* 4.1 25.1 - - - -
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Residues in contact with VAL1060 (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 ALA* 3.8 30.4 - - + +
1034A GLY* 5.5 0.4 - - - -
1035A ILE* 3.6 26.7 - - + -
1041A LEU* 4.3 7.2 - - + -
1056A LEU* 2.9 22.1 + - + +
1057A ILE 3.8 4.5 - - - +
1059A MET* 1.3 74.9 - - - +
1061A PHE* 1.3 59.0 + - - +
1064A GLY* 2.8 24.1 + - - +
1065A GLU* 3.8 23.3 - - + +
1068A VAL* 3.6 25.8 - - + -
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Residues in contact with PHE1061 (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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1007A LEU* 3.5 28.7 - - + -
1011A GLU* 3.5 27.0 - - - +
1024A PHE* 3.6 29.4 - + - -
1027A ASP* 3.4 46.0 - - + -
1028A VAL* 3.7 15.7 - - + -
1031A ALA* 4.5 7.6 - - + +
1057A ILE* 2.9 15.9 + - + +
1058A ASN* 3.1 14.6 + - - +
1060A VAL* 1.3 78.9 - - - +
1062A GLN* 1.3 60.0 + - - +
1064A GLY 4.9 0.2 + - - -
1102A ARG* 4.5 1.6 - - - +
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Residues in contact with GLN1062 (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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1011A GLU* 5.7 0.7 - - - -
1058A ASN* 2.9 10.4 + - - +
1059A MET* 3.2 5.0 + - - +
1061A PHE* 1.3 79.4 - - - +
1063A MET* 1.3 66.8 + - + +
1095A TRP* 2.9 32.5 + - - +
1099A THR* 3.0 39.2 + - - +
1102A ARG* 3.2 47.6 + - - +
1106A VAL* 5.6 0.3 - - - +
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Residues in contact with MET1063 (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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1059A MET* 2.9 59.8 + - + +
1062A GLN* 1.3 90.7 - - + +
1064A GLY* 1.3 65.6 + - - +
1067A GLY* 4.1 17.7 + - - +
1068A VAL* 3.8 6.7 - - + -
1071A PHE* 4.0 13.0 - - + -
1095A TRP* 3.7 39.0 - - + +
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Residues in contact with GLY1064 (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 VAL* 2.8 23.8 + - - -
1062A GLN 3.8 0.4 - - - -
1063A MET* 1.3 78.7 - - - +
1065A GLU* 1.3 65.6 + - - -
1066A THR 3.2 3.1 - - - -
1067A GLY 3.3 0.6 + - - -
1068A VAL* 3.1 24.9 + - - +
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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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1034A GLY* 2.9 37.6 - - - +
1037A ARG* 2.8 34.4 + - - +
1038A ASN* 4.1 15.8 + - - +
1041A LEU* 3.5 25.6 - - + +
1060A VAL* 3.8 11.9 - - + +
1064A GLY* 1.3 71.6 - - - +
1066A THR* 1.3 66.3 + - - +
1069A ALA* 2.9 30.7 + - - +
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Residues in contact with THR1066 (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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1038A ASN* 5.2 2.5 - - - +
1064A GLY* 3.2 0.8 - - - -
1065A GLU* 1.3 84.6 - - - +
1067A GLY* 1.3 65.4 + - - +
1069A ALA* 3.2 15.7 + - + +
1070A GLY* 3.3 9.9 + - - -
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Residues in contact with GLY1067 (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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1063A MET* 4.1 18.3 + - - -
1064A GLY 3.3 7.4 + - - -
1066A THR* 1.3 79.7 - - - +
1068A VAL* 1.3 61.6 + - - +
1070A GLY* 3.3 10.4 + - - -
1071A PHE* 3.3 18.4 - - - -
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Residues in contact with VAL1068 (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 LEU* 3.7 18.2 - - + -
1056A LEU* 3.8 23.3 - - + -
1059A MET* 3.3 47.1 - - + +
1060A VAL* 3.5 10.3 - - + +
1063A MET* 3.8 10.8 - - + -
1064A GLY 3.1 16.9 + - - +
1065A GLU 4.1 3.6 - - - +
1067A GLY* 1.3 72.1 - - - +
1069A ALA* 1.3 62.9 + - - +
1070A GLY 3.0 5.4 - - - -
1071A PHE* 3.1 19.9 + - - -
1075A LEU* 3.4 12.3 - - + +
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Residues in contact with ALA1069 (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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1038A ASN* 3.7 25.8 - - - +
1040A LYS* 3.1 38.1 + - + +
1041A LEU* 3.9 8.5 - - - +
1065A GLU 2.9 19.6 + - - +
1066A THR* 3.2 9.8 + - + +
1068A VAL* 1.3 77.0 - - - +
1070A GLY* 1.3 60.2 + - - +
1071A PHE 3.2 1.0 + - - -
1072A THR* 3.8 1.7 + - - -
1075A LEU* 4.3 2.9 - - - -
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Residues in contact with GLY1070 (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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1040A LYS* 5.2 0.4 - - - -
1066A THR 3.3 10.6 + - - -
1067A GLY 3.3 6.8 + - - -
1068A VAL 3.0 1.6 - - - -
1069A ALA* 1.3 75.5 - - - +
1071A PHE* 1.3 57.0 + - - +
1072A THR* 2.9 18.6 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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