Contacts of the helix formed by residues 1051 - 1061 (chain N) in PDB entry 2JA7
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 THR1051 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806M ARG* 5.8 4.5 - - - +
726N ALA* 3.8 13.5 - - + +
727N LYS* 3.8 38.1 - - + +
1027N ILE* 6.2 1.1 - - - -
1049N ASP 5.1 1.1 + - - +
1050N ILE* 1.3 88.8 - - - +
1052N VAL* 1.3 62.8 + - - +
1053N GLU* 3.8 6.5 - - - +
1054N GLY* 3.0 23.4 + - - -
1055N ILE* 2.9 32.8 + - - +
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Residues in contact with VAL1052 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666M ILE* 4.3 16.6 - - + -
670M ILE* 4.6 6.5 - - + -
805M LEU* 3.3 37.9 - - + +
761N HIS* 5.7 0.2 - - + -
1027N ILE* 3.8 28.7 - - + -
1030N LEU* 3.9 23.3 - - + -
1051N THR* 1.3 72.4 - - - +
1053N GLU* 1.3 57.9 + - + +
1055N ILE* 3.1 5.4 + - - +
1056N SER* 2.7 43.2 + - - +
1067N ARG* 4.6 8.7 - - - +
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Residues in contact with GLU1053 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670M ILE* 4.6 13.5 - - + +
726N ALA* 3.8 33.0 - - + -
1051N THR* 3.8 0.2 - - - -
1052N VAL* 1.3 81.6 - - + +
1054N GLY* 1.3 61.2 + - - +
1056N SER* 3.5 6.3 + - - -
1057N LYS* 3.4 39.7 + - - +
1067N ARG* 3.3 28.3 + - - +
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Residues in contact with GLY1054 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050N ILE* 5.9 0.9 - - - -
1051N THR* 3.0 24.7 + - - -
1053N GLU* 1.3 77.1 - - - +
1055N ILE* 1.3 62.8 + - - +
1057N LYS* 3.7 13.9 + - - +
1058N LEU* 3.6 23.6 + - - +
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Residues in contact with ILE1055 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758N PHE* 5.2 0.9 - - + -
1027N ILE* 4.9 10.3 - - + -
1030N LEU* 4.0 24.0 - - + -
1031N LEU* 3.5 46.4 - - + +
1034N VAL* 3.9 23.1 - - + -
1050N ILE* 4.3 16.8 - - + -
1051N THR 2.9 19.2 + - - +
1052N VAL* 3.1 5.6 + - - +
1054N GLY* 1.3 74.2 - - - +
1056N SER* 1.3 70.1 + - - +
1057N LYS 3.1 0.2 - - - -
1058N LEU* 2.8 18.4 + - + +
1059N LEU* 2.8 21.5 + - + -
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Residues in contact with SER1056 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030N LEU* 4.1 7.2 - - - +
1052N VAL 2.7 20.7 + - - -
1053N GLU* 3.7 5.4 - - - -
1055N ILE* 1.3 77.0 - - - +
1057N LYS* 1.3 57.1 + - - +
1059N LEU* 3.2 4.3 + - - +
1060N ARG* 2.8 30.0 + - - +
1066N SER* 2.7 38.0 + - - -
1067N ARG* 2.8 29.4 + - - -
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Residues in contact with LYS1057 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053N GLU* 3.4 26.8 + - - +
1054N GLY* 3.8 13.0 - - - +
1055N ILE 3.1 0.8 - - - -
1056N SER* 1.3 76.0 - - - +
1058N LEU* 1.3 64.7 + - + +
1060N ARG* 3.1 9.6 + - - +
1061N GLU* 3.0 28.9 + - - +
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Residues in contact with LEU1058 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034N VAL* 4.7 18.8 - - + -
1054N GLY 3.6 16.8 - - - +
1055N ILE* 2.8 18.9 + - + +
1057N LYS* 1.3 78.8 - - + +
1059N LEU* 1.3 64.0 + - - +
1061N GLU* 3.1 38.5 + - - +
1062N HIS* 3.4 15.5 - - + -
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Residues in contact with LEU1059 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030N LEU* 3.8 17.7 - - + -
1033N LYS* 3.8 32.8 - - + +
1034N VAL* 3.6 26.9 - - + +
1037N LEU* 4.4 10.5 - - + -
1055N ILE* 2.8 14.7 + - + +
1056N SER* 3.7 9.2 - - - +
1058N LEU* 1.3 73.5 - - - +
1060N ARG* 1.3 62.6 + - - +
1062N HIS* 3.1 18.4 + - - +
1063N GLY 3.7 0.5 + - - -
1064N TYR* 3.5 14.7 + - + +
1065N GLN 3.0 25.4 - - - +
1066N SER* 4.2 2.9 - - - -
1068N GLY* 3.7 20.9 - - - +
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Residues in contact with ARG1060 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056N SER 2.8 15.2 + - - +
1057N LYS* 3.2 13.0 - - - +
1058N LEU 3.1 0.2 - - - -
1059N LEU* 1.3 72.2 - - - +
1061N GLU* 1.3 52.5 + - + +
1062N HIS 2.7 16.4 + - - -
1063N GLY* 2.9 15.1 + - - -
1064N TYR 4.1 13.9 - - - -
1066N SER* 4.4 17.6 - - - +
199O LYS 3.7 23.3 + - - -
200O GLU* 4.5 6.6 + - - +
202O PRO* 3.7 34.5 - - - +
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Residues in contact with GLU1061 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057N LYS* 3.0 18.8 + - - +
1058N LEU* 3.1 31.0 + - + +
1060N ARG* 1.3 73.8 - - + +
1062N HIS* 1.3 64.0 + - + +
1063N GLY 3.7 0.2 - - - -
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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