Contacts of the helix formed by residues 1006 - 1020 (chain A) in PDB entry 5XJY
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 LYS1006 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A SER 4.7 0.2 - - - +
1005A GLU* 1.3 80.9 - - + +
1007A HIS* 1.3 66.2 + - - +
1008A VAL 3.5 0.7 - - - -
1009A LYS* 3.6 15.1 + - - +
1010A ALA* 3.7 6.8 + - - +
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Residues in contact with HIS1007 (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 LEU* 3.6 25.3 + - + +
1006A LYS* 1.3 80.6 - - + +
1008A VAL* 1.3 59.4 + - - +
1010A ALA* 3.1 8.8 + - - +
1011A GLU* 2.9 26.8 + - - +
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Residues in contact with VAL1008 (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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995A TRP* 6.4 0.2 - - - -
998A ALA* 4.2 25.3 - - + +
999A ARG* 5.0 3.4 - - + +
1002A GLY 5.0 0.9 - - - +
1003A LEU 3.1 17.2 + - - +
1004A SER* 3.3 21.2 + - - +
1006A LYS 3.5 0.2 - - - -
1007A HIS* 1.3 72.6 - - - +
1009A LYS* 1.3 59.6 + - - +
1011A GLU* 3.6 9.7 - - + -
1012A MET* 2.9 28.4 + - - +
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Residues in contact with LYS1009 (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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1004A SER 3.7 5.1 + - - +
1005A GLU 4.3 12.3 - - - +
1006A LYS* 3.6 10.7 + - - +
1007A HIS 3.2 0.4 - - - -
1008A VAL* 1.3 80.5 - - - +
1010A ALA* 1.3 59.7 + - - +
1012A MET* 3.5 15.2 + - - +
1013A GLU* 4.1 3.5 + - - +
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Residues in contact with ALA1010 (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 LYS 3.7 7.6 + - - +
1007A HIS* 3.1 10.5 + - - +
1009A LYS* 1.3 78.1 - - - +
1011A GLU* 1.3 60.8 - - - +
1013A GLU* 3.3 17.4 + - - +
1014A GLN* 3.6 8.8 + - - +
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Residues in contact with GLU1011 (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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998A ALA* 6.4 1.6 - - + -
1007A HIS 2.9 16.2 + - - +
1008A VAL* 3.6 10.5 - - - +
1009A LYS 3.3 0.2 - - - -
1010A ALA* 1.3 73.0 - - - +
1012A MET* 1.3 60.8 + - - +
1013A GLU 3.2 0.2 - - - -
1014A GLN* 3.9 9.5 - - + +
1015A MET* 2.9 29.5 + - - +
1048A VAL* 6.5 0.4 - - + -
1049A GLY* 5.2 14.8 - - - +
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Residues in contact with MET1012 (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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994A ILE* 6.0 5.6 - - + -
1008A VAL 2.9 16.5 + - - +
1009A LYS* 3.6 10.8 - - - +
1010A ALA 3.2 0.4 - - - -
1011A GLU* 1.3 78.7 - - - +
1013A GLU* 1.3 57.0 + - - +
1015A MET* 3.6 7.0 + - - +
1016A ALA* 2.9 26.5 + - - +
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Residues in contact with GLU1013 (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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1009A LYS 4.1 2.4 + - - +
1010A ALA* 3.3 12.1 + - - +
1011A GLU 3.2 0.4 - - - -
1012A MET* 1.3 76.8 - - - +
1014A GLN* 1.3 61.1 + - - +
1016A ALA* 3.1 11.3 + - - +
1017A LEU* 2.9 24.6 + - - +
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Residues in contact with GLN1014 (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 ALA 3.6 8.6 + - - +
1011A GLU* 3.6 10.0 + - + +
1012A MET 3.5 0.2 - - - -
1013A GLU* 1.3 75.4 - - - +
1015A MET* 1.3 64.5 + - - +
1017A LEU* 3.1 25.3 + - + +
1018A ASP* 3.7 3.5 + - - +
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Residues in contact with MET1015 (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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994A ILE* 5.3 12.8 - - + -
1011A GLU 2.9 20.3 + - - +
1012A MET* 3.7 7.6 - - - +
1014A GLN* 1.3 75.7 - - - +
1016A ALA* 1.3 61.3 + - - +
1018A ASP* 3.1 21.3 + - - +
1019A VAL* 3.7 7.1 + - - +
1044A ALA* 5.6 7.5 - - + +
1048A VAL* 5.3 14.8 - - + -
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Residues in contact with ALA1016 (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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1012A MET 2.9 16.0 + - - +
1013A GLU* 3.1 14.8 + - - +
1015A MET* 1.3 74.9 - - - +
1017A LEU* 1.3 55.5 + - - +
1018A ASP 3.1 6.4 + - - -
1019A VAL* 4.9 3.3 - - - +
1020A GLY* 3.8 18.9 + - - -
1021A LEU 5.1 1.2 + - - -
1022A PRO* 4.9 21.0 - - + +
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Residues in contact with LEU1017 (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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1013A GLU 2.9 11.1 + - - +
1014A GLN* 3.1 16.9 + - - +
1016A ALA* 1.3 76.3 - - - +
1018A ASP* 1.3 56.2 + - - +
1020A GLY* 5.2 1.8 - - - -
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Residues in contact with ASP1018 (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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1014A GLN 3.7 4.2 + - - +
1015A MET* 3.4 14.8 - - - +
1016A ALA 3.1 0.8 - - - -
1017A LEU* 1.3 80.3 - - - +
1019A VAL* 1.3 66.0 + - - +
1020A GLY* 4.9 0.2 - - - -
1040A LYS* 6.0 1.6 - - - +
1044A ALA* 5.1 15.0 - - + -
1074A LEU* 6.0 8.2 - - + +
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Residues in contact with VAL1019 (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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1015A MET 3.7 8.4 + - - +
1016A ALA* 3.9 3.7 + - - +
1018A ASP* 1.3 82.1 - - - +
1020A GLY* 1.3 60.7 + - - +
1021A LEU* 4.7 5.4 - - + +
1040A LYS* 6.0 8.7 - - + -
1041A LEU* 6.4 1.6 - - + -
1044A ALA* 5.9 6.5 - - + +
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Residues in contact with GLY1020 (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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1016A ALA 3.8 11.7 + - - -
1017A LEU* 5.8 1.3 - - - -
1018A ASP 3.8 0.6 - - - -
1019A VAL* 1.3 80.3 - - - +
1021A LEU* 1.3 63.9 + - - +
1022A PRO 4.1 0.4 - - - -
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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