Contacts of the helix formed by residues 1059 - 1087 (chain A) in PDB entry 5KHR
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 ASP1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1058A SER* 3.8 25.1 - - - +
1060A HIS* 3.8 28.3 - - - +
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Residues in contact with HIS1060 (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 ASP* 3.8 25.4 - - - +
1061A GLU* 3.8 28.5 - - - +
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Residues in contact with GLU1061 (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 SER* 4.6 15.5 - - - +
1060A HIS* 3.8 28.7 - - - +
1062A PHE* 3.8 25.6 - - - +
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Residues in contact with PHE1062 (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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1061A GLU* 3.8 28.0 - - - +
1063A ILE* 3.9 26.0 - - - +
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Residues in contact with ILE1063 (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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1062A PHE* 3.9 25.6 - - - +
1064A GLU* 3.9 28.5 - - - +
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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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1063A ILE* 3.9 25.4 - - - +
1065A GLU* 3.8 29.2 - - - +
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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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1064A GLU* 3.8 26.5 - - - +
1066A LYS* 3.8 28.7 - - - +
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Residues in contact with LYS1066 (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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1065A GLU* 3.8 28.3 - - - +
1067A GLU* 3.8 26.0 - - - +
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Residues in contact with GLU1067 (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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1066A LYS* 3.8 28.9 - - - +
1068A ASN* 3.9 25.4 - - - +
1070A LEU* 4.7 15.5 - - - +
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Residues in contact with ASN1068 (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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1067A GLU* 3.9 25.8 - - - +
1069A ARG* 3.8 28.9 - - - +
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Residues in contact with ARG1069 (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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1068A ASN* 3.8 28.7 - - - +
1070A LEU* 3.8 24.9 - - - +
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Residues in contact with LEU1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A GLU* 4.7 16.2 - - - +
1069A ARG* 3.8 28.5 - - - +
1071A LEU* 3.9 26.5 - - - +
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Residues in contact with LEU1071 (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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1070A LEU* 3.9 24.7 - - - +
1072A GLN* 3.8 28.3 - - - +
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Residues in contact with GLN1072 (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 LEU* 3.8 28.7 - - - +
1073A LEU* 3.9 25.8 - - - +
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Residues in contact with LEU1073 (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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1072A GLN* 3.9 26.0 - - - +
1074A CYS* 3.8 28.3 - - - +
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Residues in contact with CYS1074 (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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1073A LEU* 3.8 26.5 - - - +
1075A GLN* 3.8 28.7 - - - +
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Residues in contact with GLN1075 (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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1074A CYS* 3.8 24.9 - - - +
1076A ARG* 3.8 28.7 - - - +
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Residues in contact with ARG1076 (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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1075A GLN* 3.8 28.0 - - - +
1077A THR* 3.9 26.2 - - - +
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Residues in contact with THR1077 (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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1076A ARG* 3.9 27.6 - - - +
1078A MET* 3.9 26.5 - - - +
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Residues in contact with MET1078 (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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1077A THR* 3.9 25.1 - - - +
1079A ALA* 3.8 29.6 - - - +
1135A ALA* 4.5 21.1 - - - +
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Residues in contact with ALA1079 (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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1078A MET* 3.8 29.2 - - - +
1080A LEU* 3.8 26.9 - - - +
1556A LEU* 4.3 23.6 - - - +
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Residues in contact with LEU1080 (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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1079A ALA* 3.8 28.5 - - - +
1081A PRO* 3.9 26.5 - - - -
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Residues in contact with PRO1081 (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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1080A LEU* 3.9 25.8 - - - -
1082A VAL* 3.9 28.3 - - - -
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Residues in contact with VAL1082 (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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1081A PRO* 3.9 26.5 - - - -
1083A GLY* 3.8 28.7 - - - +
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Residues in contact with GLY1083 (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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1082A VAL* 3.8 28.7 - - - +
1084A ARG* 3.8 26.5 - - - +
1560A MET* 4.3 22.7 - - - +
1563A GLY* 4.7 16.6 - - - +
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Residues in contact with ARG1084 (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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1083A GLY* 3.8 27.8 - - - +
1085A GLY* 3.8 26.2 - - - +
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Residues in contact with GLY1085 (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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1084A ARG* 3.8 26.2 - - - +
1086A MET* 3.8 28.7 - - - +
1142A ALA* 4.0 26.2 - - - +
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Residues in contact with MET1086 (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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1085A GLY* 3.8 25.6 - - - +
1087A PHE* 3.8 29.8 - - - +
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Residues in contact with PHE1087 (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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1086A MET* 3.8 28.5 - - - +
1088A THR* 3.7 29.8 - - - +
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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