Contacts of the helix formed by residues 1010 - 1022 (chain A) in PDB entry 2OJ9
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 SER1010 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A ALA* 1.3 76.2 - - - +
1011A MET* 1.3 66.3 + - - +
1012A ARG* 3.7 9.7 + - - +
1013A GLU* 3.3 22.9 + - - +
1014A ARG* 2.9 25.8 + - - +
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Residues in contact with MET1011 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955A ASP* 6.3 2.9 - - - +
956A VAL 5.7 0.7 - - - +
1010A SER* 1.3 73.3 - - - +
1012A ARG* 1.3 72.7 + - - +
1014A ARG* 3.4 14.6 + - - +
1015A ILE* 2.9 62.7 + - + +
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Residues in contact with ARG1012 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A SER* 3.1 8.9 + - - +
1011A MET* 1.3 91.4 - - - +
1013A GLU* 1.3 51.5 + - - +
1015A ILE* 3.0 8.8 + - - +
1016A GLU* 2.7 50.5 + - + +
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Residues in contact with GLU1013 (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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980A PHE* 4.0 23.2 - - + +
1005A VAL* 4.1 7.5 - - + +
1006A ASN* 5.1 3.3 - - - +
1008A ALA 4.0 4.9 - - - +
1009A ALA* 3.4 27.8 - - + +
1010A SER* 3.3 19.3 + - - +
1012A ARG* 1.3 79.8 - - - +
1014A ARG* 1.3 57.1 + - - +
1016A GLU* 3.2 15.1 - - - +
1017A PHE* 3.0 26.3 + - - +
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Residues in contact with ARG1014 (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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954A ALA 3.9 3.6 + - - -
955A ASP* 2.2 62.7 + - + +
1005A VAL* 3.8 23.1 - - + -
1006A ASN 5.9 0.4 - - - -
1009A ALA* 4.0 17.1 + - + -
1010A SER 2.9 18.2 + - - +
1011A MET* 3.8 12.6 - - - +
1013A GLU* 1.3 74.6 - - - +
1015A ILE* 1.3 65.0 + - + +
1017A PHE* 3.4 6.8 - - - +
1018A LEU* 3.1 31.0 + - - +
1043A GLN* 2.9 38.7 - - - +
1045A THR* 3.1 16.5 + - - +
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Residues in contact with ILE1015 (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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955A ASP 4.1 17.0 - - - +
956A VAL 4.1 15.3 - - - +
957A TYR* 4.3 11.9 - - + -
1011A MET* 2.9 62.9 + - + +
1012A ARG* 3.0 6.3 + - - +
1014A ARG* 1.3 74.0 - - + +
1016A GLU* 1.3 55.0 + - - +
1018A LEU* 3.2 8.1 + - - +
1019A ASN* 2.7 55.5 + - - +
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Residues in contact with GLU1016 (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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980A PHE* 4.0 18.6 - - + -
1012A ARG* 2.7 28.2 + - + +
1013A GLU* 3.2 21.2 - - - +
1015A ILE* 1.3 73.8 - - - +
1017A PHE* 1.3 57.5 + - - +
1019A ASN* 3.1 7.1 + - - +
1020A GLU* 2.7 57.7 + - - +
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Residues in contact with PHE1017 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980A PHE* 3.5 52.2 - + + -
1003A LYS* 3.6 45.3 - - + -
1004A THR 4.0 9.9 - - - -
1005A VAL* 4.3 8.5 - - + -
1013A GLU 3.0 10.1 + - - +
1014A ARG* 3.4 9.2 - - - +
1016A GLU* 1.3 79.3 - - - +
1018A LEU* 1.3 78.6 + - + +
1020A GLU* 3.6 3.7 + - - +
1021A ALA* 3.3 22.3 + - - +
1045A THR* 3.8 22.4 - - + -
1047A VAL* 3.3 31.2 - - + -
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Residues in contact with LEU1018 (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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955A ASP* 4.1 7.9 - - + +
957A TYR* 3.8 25.3 - - + -
1014A ARG 3.1 13.6 + - - +
1015A ILE* 3.4 8.5 - - - +
1016A GLU 3.1 0.2 - - - -
1017A PHE* 1.3 85.9 - - + +
1019A ASN* 1.3 60.0 + - - +
1021A ALA* 3.4 6.0 + - - +
1022A SER* 2.7 33.0 + - - -
1038A VAL* 4.3 14.8 - - + +
1040A SER* 2.8 40.6 - - - +
1045A THR* 2.9 33.9 - - + -
1046A LEU 4.8 2.2 - - - +
1047A VAL* 4.6 6.1 - - + -
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Residues in contact with ASN1019 (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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957A TYR* 3.9 17.5 - - - +
1015A ILE* 2.7 44.6 + - - +
1016A GLU* 3.7 6.6 - - - +
1018A LEU* 1.3 70.9 - - - +
1020A GLU* 1.3 72.0 + - - +
1022A SER* 3.1 20.3 + - - -
1023A VAL* 3.9 9.2 + - - +
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Residues in contact with GLU1020 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980A PHE* 4.5 16.7 - - + -
1016A GLU* 2.7 51.7 + - - +
1017A PHE* 3.7 8.5 - - - +
1019A ASN* 1.3 78.3 - - - +
1021A ALA* 1.3 60.7 + - - +
1023A VAL* 3.7 19.2 + - - +
1024A MET* 5.0 2.1 + - - +
1123A ASP* 4.8 6.3 - - - +
1124A PHE* 5.9 4.5 - - + +
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Residues in contact with ALA1021 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003A LYS* 4.9 9.4 - - - +
1017A PHE 3.3 13.8 + - - +
1018A LEU 3.8 4.7 - - - +
1019A ASN 3.2 0.4 - - - -
1020A GLU* 1.3 75.6 - - - +
1022A SER* 1.3 56.9 + - - +
1023A VAL 3.1 5.7 + - - -
1024A MET* 2.8 37.5 - - + +
1025A LYS* 5.4 0.2 - - - -
1035A LEU* 4.0 11.2 - - + +
1038A VAL* 5.1 3.6 - - + -
1047A VAL* 3.9 33.4 - - + -
1049A MET* 5.5 0.4 - - - -
1123A ASP* 4.8 3.4 - - - -
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Residues in contact with SER1022 (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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957A TYR* 3.6 10.9 + - - -
1018A LEU 2.7 21.7 + - - -
1019A ASN* 3.1 11.7 + - - -
1021A ALA* 1.3 73.8 - - - +
1023A VAL* 1.3 66.2 + - - +
1025A LYS* 3.1 54.2 + - - +
1026A GLU* 4.6 6.2 - - - +
1038A VAL* 5.3 1.4 - - - +
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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