Contacts of the helix formed by residues 1059 - 1069 (chain A) in PDB entry 5JQE
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 LEU1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003A PHE* 4.0 20.4 - - + -
1007A LEU* 6.2 0.2 - - + -
1054A LEU* 4.4 10.8 - - + -
1055A GLU 3.6 16.4 - - - +
1056A GLU 4.2 11.4 - - - +
1057A SER 4.0 1.1 - - - -
1058A ASN* 1.3 72.4 - - - +
1060A SER* 1.3 64.0 + - - +
1061A PHE 3.2 2.6 + - - -
1062A LEU* 3.2 9.0 + - + +
1063A LYS* 2.9 46.6 + - + +
1079A LEU* 4.0 26.0 - - + +
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Residues in contact with SER1060 (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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1058A ASN* 2.9 21.1 + - - -
1059A LEU* 1.3 77.6 - - - +
1061A PHE* 1.3 62.3 + - - +
1063A LYS* 3.6 10.8 + - - +
1064A GLU* 3.2 22.2 + - - +
1086A MET* 5.3 1.2 - - - +
1089A GLU* 5.7 4.9 - - - -
1095A ARG* 5.9 5.2 - - - -
1097A GLN* 3.3 17.5 + - - -
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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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1026A SER* 4.4 10.5 - - - -
1029A TYR* 3.5 40.2 - + - -
1048A LEU* 4.0 18.6 - - + -
1053A MET* 3.7 41.2 + - + +
1054A LEU* 5.7 0.7 - - + -
1059A LEU 3.3 0.6 - - - -
1060A SER* 1.3 79.8 + - - +
1062A LEU* 1.3 60.9 + - - +
1064A GLU* 3.1 7.2 + - - +
1065A LEU* 2.9 56.4 + - + +
1097A GLN* 3.5 33.9 - - + +
1098A ILE* 3.8 24.2 - - + -
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Residues in contact with LEU1062 (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* 3.8 28.7 - - + -
1010A ILE* 4.3 14.1 - - + -
1045A PHE* 3.5 38.8 - - + -
1048A LEU* 5.6 0.7 - - + -
1054A LEU* 3.9 29.0 - - + +
1059A LEU* 3.2 12.8 + - + +
1061A PHE* 1.3 78.2 - - - +
1063A LYS* 1.3 62.2 + - - +
1065A LEU* 3.2 12.9 + - + +
1066A LEU* 3.1 40.9 + - + +
1079A LEU* 4.5 12.3 - - + -
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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
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1059A LEU* 2.9 49.2 + - + +
1060A SER* 3.8 8.5 - - - +
1062A LEU* 1.3 75.5 - - - +
1064A GLU* 1.3 63.2 + - - +
1066A LEU 3.6 0.2 + - - -
1067A PHE* 3.1 23.7 + - - +
1075A LEU* 3.8 16.6 - - + +
1079A LEU* 4.0 28.6 + - + -
1081A THR* 3.4 24.7 + - - +
1085A GLU* 4.8 6.9 + - - -
1086A MET* 3.8 22.3 - - + +
1089A GLU* 6.0 1.8 - - - +
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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 SER 3.2 12.6 + - - +
1061A PHE* 3.1 10.4 + - - +
1063A LYS* 1.3 73.6 - - - +
1065A LEU* 1.3 60.7 + - - +
1067A PHE* 3.4 2.3 + - - +
1068A ARG* 2.9 43.5 + - + +
1086A MET* 3.9 12.9 - - + +
1090A LEU* 4.2 13.7 - - + -
1096A ALA* 3.5 16.6 - - - +
1097A GLN* 3.0 37.0 + - - +
1098A ILE* 3.3 41.2 + - + +
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Residues in contact with LEU1065 (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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1022A LEU* 3.6 25.4 - - + +
1025A LEU* 3.7 20.4 - - + -
1026A SER* 3.8 17.3 - - - +
1044A LEU* 5.5 1.8 - - + -
1045A PHE* 5.4 2.7 - - + -
1048A LEU* 4.3 15.0 - - + -
1061A PHE* 2.9 45.2 + - + +
1062A LEU* 3.2 16.8 + - + +
1064A GLU* 1.3 76.8 - - - +
1066A LEU* 1.3 63.6 + - + +
1068A ARG* 3.2 4.9 + - - +
1069A ILE* 3.2 26.0 + - - +
1098A ILE* 3.6 23.1 - - + -
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Residues in contact with LEU1066 (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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1010A ILE* 4.6 12.8 - - + -
1014A LEU* 4.3 32.5 - - + -
1022A LEU* 4.9 4.5 - - + -
1045A PHE* 5.0 0.2 - - + -
1062A LEU* 3.1 28.2 + - + +
1063A LYS 4.1 0.2 - - - +
1065A LEU* 1.3 77.4 - - - +
1067A PHE* 1.3 61.2 + - - +
1069A ILE* 3.3 12.2 + - + +
1070A ASN 3.1 4.9 + - - -
1071A ARG* 3.0 37.0 + - + +
1074A LEU* 4.5 17.3 - - + -
1075A LEU* 4.0 18.8 - - + -
1079A LEU* 3.7 29.4 - - + -
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Residues in contact with PHE1067 (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 LYS 3.1 18.8 + - - +
1064A GLU 3.7 3.1 - - - +
1066A LEU* 1.3 77.9 - - - +
1068A ARG* 1.3 77.5 + - - +
1070A ASN* 3.1 14.6 + - - +
1071A ARG 5.0 0.2 - - - +
1072A LEU* 3.8 27.3 - - + +
1075A LEU* 3.6 10.7 - - + +
1083A LYS* 4.1 16.4 - - + -
1086A MET* 3.6 27.1 - - + -
1087A GLU* 4.0 26.9 - - + -
1090A LEU* 3.7 31.0 - - + -
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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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1025A LEU* 3.6 19.3 - - + -
1064A GLU* 2.9 36.3 + - - +
1065A LEU 3.2 6.7 + - - +
1067A PHE* 1.3 95.3 - - - +
1069A ILE* 1.3 58.1 + - - +
1070A ASN* 3.4 5.0 + - - +
1090A LEU* 3.7 24.8 - - - +
1096A ALA* 4.5 9.3 - - - +
1098A ILE* 3.8 18.7 + - + -
1103A VAL* 3.7 44.0 - - + +
1106A TYR* 3.5 18.5 - - + -
1107A GLN* 5.2 4.9 - - - +
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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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1014A LEU* 4.5 4.5 - - + -
1018A ASP* 4.0 24.6 - - + +
1021A SER* 3.9 15.5 - - - -
1022A LEU* 4.0 28.5 - - + -
1025A LEU* 3.6 27.1 - - + -
1065A LEU 3.2 9.2 + - - +
1066A LEU* 3.4 16.2 - - + +
1068A ARG* 1.3 72.4 - - - +
1070A ASN* 1.3 68.2 + - - +
1071A ARG* 3.3 28.9 + - + +
1106A TYR* 3.5 24.2 + - - +
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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
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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