Contacts of the helix formed by residues 1143 - 1152 (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 ALA1143 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500M GLU* 2.4 34.2 - - + +
504M LEU* 5.4 1.8 - - - -
505M CYS* 4.4 8.1 - - - -
1436M ILE* 5.7 0.2 - - - -
1138N MET* 3.0 44.3 + - + +
1139N ILE* 6.0 0.2 - - - -
1141N HIS* 3.0 7.4 + - + -
1142N GLY* 1.3 72.1 - - - +
1144N ALA* 1.3 61.1 + - - +
1146N PHE* 4.2 5.8 - - + -
1147N LEU* 3.0 18.7 + - - +
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Residues in contact with ALA1144 (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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500M GLU* 2.8 1.8 + - - -
1433M MET* 4.1 16.9 - - + +
1434M ALA* 4.2 11.1 + - - +
1436M ILE* 3.6 19.7 - - - +
1438M THR* 3.3 26.9 - - + -
1439M GLY 3.7 4.5 - - - +
1142N GLY 2.6 9.8 + - - -
1143N ALA* 1.3 69.9 - - - +
1145N SER* 1.3 65.3 + - - +
1147N LEU* 3.0 19.6 + - - +
1148N LYS* 3.2 10.2 + - - +
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Residues in contact with SER1145 (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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496M GLU* 3.9 28.1 + - - -
497M THR* 4.5 7.9 - - - -
500M GLU* 2.5 24.8 + - - -
1433M MET* 3.7 28.1 - - - +
1438M THR* 3.9 6.6 - - - +
1144N ALA* 1.3 74.6 - - - +
1146N PHE* 1.3 49.1 + - - -
1148N LYS* 2.9 11.1 + - - +
1149N GLU* 2.8 34.5 + - - +
92R ARG* 5.4 2.1 + - - +
63S PRO 5.6 1.1 - - - -
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Residues in contact with PHE1146 (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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443M LEU* 3.9 39.3 - - + -
490M HIS* 4.6 4.5 - - + -
492M PRO* 4.7 7.6 - - + -
497M THR* 3.6 34.4 + - + +
500M GLU* 3.0 21.6 + - + +
501M LEU* 4.1 18.6 - - + -
1130N PHE* 4.5 1.6 - + - -
1138N MET* 3.8 35.0 - - + -
1143N ALA* 3.5 3.1 - - + +
1145N SER* 1.3 77.4 - - - +
1147N LEU* 1.3 63.6 + - - +
1149N GLU* 3.1 5.2 + - - +
1150N ARG* 3.0 58.6 + - + +
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Residues in contact with LEU1147 (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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1424M VAL* 5.4 1.3 - - + -
1428M VAL* 4.0 14.1 - - + -
1434M ALA* 5.8 4.0 - - + -
1436M ILE* 5.5 3.4 - - + -
1130N PHE* 5.2 1.8 - - + -
1135N ARG* 3.9 16.8 - - + -
1138N MET* 4.3 13.2 - - + -
1139N ILE* 3.5 40.2 - - + +
1143N ALA 3.0 12.4 + - - +
1144N ALA* 3.0 12.8 + - - +
1146N PHE* 1.3 79.6 - - - +
1148N LYS* 1.3 66.9 + - - +
1150N ARG* 3.1 6.4 + - - +
1151N LEU* 3.0 52.1 + - + +
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Residues in contact with LYS1148 (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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1431M GLY* 3.6 29.6 - - - +
1432M GLN* 4.4 11.4 - - - +
1433M MET* 4.4 19.7 - - + +
1144N ALA 3.2 4.9 + - - +
1145N SER* 2.9 14.1 + - - +
1147N LEU* 1.3 82.8 - - - +
1149N GLU* 1.3 54.9 + - - +
1151N LEU* 2.9 6.6 + - - +
1152N MET* 2.6 41.5 + - + -
1153N GLU* 3.6 26.2 + - - +
1195N HIS* 6.5 1.1 - - - -
63S PRO* 4.4 10.3 + - - +
64S THR* 2.8 28.8 + - - +
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Residues in contact with GLU1149 (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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492M PRO* 3.6 8.1 - - - +
493M GLN* 3.0 33.4 + - + +
494M SER* 2.8 30.7 + - - -
497M THR* 2.7 28.4 + - - +
1145N SER 2.8 15.2 + - - +
1146N PHE* 3.1 11.8 + - + +
1148N LYS* 1.3 75.1 - - - +
1150N ARG* 1.3 67.3 + - - +
1153N GLU* 3.5 27.2 + - + +
1154N ALA* 3.0 31.6 + - + +
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Residues in contact with ARG1150 (chain N).
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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345M VAL* 3.5 23.4 - - + +
346M ASP 3.6 15.7 + - - -
347M PHE* 3.6 5.5 + - - +
490M HIS* 3.0 36.9 + - - +
491M VAL 3.1 26.6 + - - -
493M GLN* 4.4 1.6 - - - +
1130N PHE* 3.7 37.5 - - + -
1146N PHE* 3.0 45.3 + - + +
1147N LEU* 3.1 6.5 + - - +
1149N GLU* 1.3 85.8 + - - +
1151N LEU* 1.3 73.1 + - + +
1152N MET 3.6 0.2 + - - -
1154N ALA* 3.8 22.7 - - - +
1155N SER* 3.7 16.5 - - - -
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Residues in contact with LEU1151 (chain N).
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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340M LEU 4.4 3.1 - - - +
341M MET 5.4 5.2 - - - +
342M GLY* 6.1 0.2 - - - -
343M LYS* 2.4 51.3 + - + +
1428M VAL* 3.3 47.3 - - + +
1431M GLY* 5.4 3.1 - - - -
1130N PHE* 4.4 17.9 - - + +
1135N ARG* 5.7 1.8 - - + -
1147N LEU* 3.2 35.9 - - + +
1148N LYS* 2.9 9.4 + - - +
1150N ARG* 1.3 87.5 - - + +
1152N MET* 1.3 64.5 + - + +
1155N SER* 3.7 4.0 - - - -
1156N ASP* 3.9 2.1 + - - +
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Residues in contact with MET1152 (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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2M VAL* 5.5 0.9 - - + -
343M LYS* 4.5 0.2 - - - -
1431M GLY* 3.2 30.1 - - - +
1148N LYS* 2.6 24.1 + - + +
1150N ARG 3.5 0.2 - - - -
1151N LEU* 1.3 72.2 - - - +
1153N GLU* 1.3 83.5 + - - +
1154N ALA 3.1 1.8 - - - -
1155N SER 2.9 19.1 + - - -
1157N ALA* 3.3 33.6 - - + +
1158N PHE 4.1 0.7 - - - +
1195N HIS* 3.5 17.7 - - + +
1196N ILE* 3.3 35.2 - - - +
1197N PRO* 3.2 35.2 - - - -
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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