Contacts of the helix formed by residues 1197 - 1210 (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 PRO1197 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340M LEU* 3.8 9.4 - - + -
343M LYS* 3.3 30.3 - - - +
1428M VAL 4.8 0.9 - - - +
1429M ILE 3.0 23.8 - - - +
1430M LEU 2.9 29.4 - - - +
1431M GLY 3.6 0.7 - - - +
1152N MET* 3.2 12.5 - - - -
1156N ASP* 3.5 14.8 - - + +
1157N ALA 3.9 0.4 - - - +
1196N ILE* 1.3 76.7 - - + +
1198N TYR* 1.3 57.6 + - - +
1199N ALA 3.0 0.2 - - - -
1200N ALA* 2.5 37.0 + - + +
1201N LYS 3.1 4.0 + - - -
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Residues in contact with TYR1198 (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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245M PRO* 3.5 21.0 + - - +
1113N VAL 5.2 1.7 + - - -
1114N LEU 3.7 18.6 + - - -
1115N THR 3.5 14.8 - - - +
1116N ARG* 3.1 56.1 + - + +
1156N ASP* 3.4 21.4 - - + +
1158N PHE* 3.7 33.5 - + + +
1196N ILE 3.2 3.4 + - - -
1197N PRO* 1.3 70.0 - - - +
1199N ALA* 1.3 62.6 + - - +
1201N LYS* 3.0 41.8 + - + +
1202N LEU* 2.9 29.9 + - + +
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Residues in contact with ALA1199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335M ARG* 3.8 7.7 - - - +
339M ASN* 3.9 14.6 - - + +
340M LEU* 3.4 17.7 - - + -
1115N THR* 4.6 4.5 - - + -
1117N GLN* 3.6 27.6 - - - +
1156N ASP* 3.2 7.0 + - - +
1197N PRO 2.9 1.0 + - - -
1198N TYR* 1.3 80.9 - - - +
1200N ALA* 1.3 52.2 + - - +
1202N LEU* 3.3 10.5 - - + +
1203N LEU* 2.7 33.3 + - - +
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Residues in contact with ALA1200 (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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340M LEU* 3.0 13.3 - - + +
1429M ILE 3.2 13.5 - - - +
1430M LEU* 5.0 0.4 - - - -
1196N ILE* 3.8 11.4 - - + -
1197N PRO* 2.5 39.8 + - + +
1199N ALA* 1.3 68.7 - - - +
1201N LYS* 1.3 67.8 + - - +
1203N LEU* 3.0 8.6 + - - +
1204N PHE* 2.9 36.0 + - + -
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Residues in contact with LYS1201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77M CYS 4.8 0.2 + - - -
78M PRO* 3.2 33.0 - - + +
79M GLY 3.5 4.4 - - - +
245M PRO* 3.9 8.5 - - - +
1116N ARG* 5.4 1.2 - - - +
1158N PHE* 3.8 24.1 - - + -
1160N VAL* 4.9 0.4 - - + -
1169N MET* 3.3 32.5 - - + +
1196N ILE* 3.4 11.0 - - + +
1197N PRO 3.1 4.6 + - - -
1198N TYR* 3.0 50.6 + - + +
1200N ALA* 1.3 79.9 - - - +
1202N LEU* 1.3 52.6 + - - +
1204N PHE* 2.8 5.5 + - - +
1205N GLN* 2.6 61.7 + - - +
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Residues in contact with LEU1202 (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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245M PRO 4.5 4.0 - - - +
246M VAL* 4.3 21.8 - - + -
335M ARG* 2.8 21.5 - - - +
1114N LEU* 3.1 37.0 - - + +
1115N THR* 4.4 4.0 - - - -
1198N TYR* 2.9 21.0 + - + +
1199N ALA* 3.3 11.7 - - - +
1201N LYS* 1.3 81.1 - - - +
1203N LEU* 1.3 55.6 + - - +
1205N GLN* 4.2 8.3 - - - +
1206N GLU* 2.6 79.6 + - + +
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Residues in contact with LEU1203 (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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329M LEU* 3.8 28.7 - - + -
335M ARG* 3.9 4.0 - - + -
336M ILE* 3.4 37.2 - - + -
340M LEU* 3.9 12.6 - - + -
1397M LEU* 4.5 10.8 - - + -
1409M LEU* 4.7 1.3 - - + -
1429M ILE* 4.6 2.0 - - + -
1199N ALA 2.7 19.3 + - - +
1200N ALA* 3.1 11.4 - - - +
1202N LEU* 1.3 71.8 - - - +
1204N PHE* 1.3 80.8 + - + +
1206N GLU* 3.4 11.6 + - - +
1207N LEU* 3.0 36.3 + - + +
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Residues in contact with PHE1204 (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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17M VAL* 5.7 3.8 - - + -
19M PHE* 6.0 0.7 - + - -
1397M LEU* 5.0 14.6 - - + -
1429M ILE* 5.1 4.3 - - + -
1430M LEU* 4.0 20.6 - - + -
1169N MET* 4.0 19.1 - - + -
1196N ILE* 3.9 18.6 - - + -
1200N ALA* 2.9 26.7 + - + -
1201N LYS* 2.8 7.5 + - - +
1203N LEU* 1.3 95.0 - - + +
1205N GLN* 1.3 67.7 + - - +
1207N LEU* 2.7 23.1 + - + +
1208N MET* 2.8 17.8 + - - +
1214N PRO* 4.0 30.9 - - + +
1216N LEU* 4.2 26.0 - - + -
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Residues in contact with GLN1205 (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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78M PRO* 4.4 2.2 - - - +
79M GLY* 3.3 41.0 + - - +
81M PHE* 3.2 27.0 - - + -
242M PRO* 5.1 0.2 - - - +
243M PRO* 4.1 5.1 - - - +
245M PRO* 5.2 1.7 - - - +
246M VAL* 3.9 25.4 - - + +
1169N MET* 4.5 13.6 - - + +
1201N LYS* 2.6 50.5 + - + +
1202N LEU* 3.7 10.9 - - - +
1204N PHE* 1.3 71.2 - - - +
1206N GLU* 1.3 62.9 + - - +
1208N MET* 3.1 8.1 + - - -
1209N ALA* 3.0 20.6 + - - +
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Residues in contact with GLU1206 (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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246M VAL* 4.1 12.8 - - + -
325M ILE* 3.8 15.9 - - + +
328M ARG* 3.2 34.7 + - - +
329M LEU* 3.6 13.9 - - + +
335M ARG* 3.0 40.0 + - - +
1202N LEU* 2.6 53.3 + - + +
1203N LEU* 3.4 4.4 - - - +
1205N GLN* 1.3 73.6 - - - +
1207N LEU* 1.3 62.2 + - - +
1209N ALA* 3.3 14.9 + - - +
1210N MET* 3.4 15.3 + - - +
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Residues in contact with LEU1207 (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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19M PHE* 5.1 2.9 - - + -
329M LEU* 4.1 7.4 - - + -
1397M LEU* 6.1 0.7 - - + -
1406M VAL* 6.0 0.2 - - + -
1409M LEU* 3.3 45.3 - - + -
1410M PHE* 5.4 1.1 - - + -
1203N LEU* 3.0 31.2 + - + +
1204N PHE* 2.7 22.9 + - + +
1206N GLU* 1.3 69.3 - - - +
1208N MET* 1.3 56.7 + - - +
1210N MET* 2.7 46.8 + - + +
1212N ILE* 3.0 45.5 + - + +
1214N PRO* 4.9 8.3 - - + -
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Residues in contact with MET1208 (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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22M PHE* 3.9 29.4 - - + -
30M ILE* 5.2 6.5 - - + -
81M PHE* 3.3 47.1 - - + -
240M PRO* 3.6 6.9 - - - +
1168N LEU* 4.8 14.4 - - + -
1169N MET* 5.2 15.0 - - + +
1170N THR 6.3 0.4 - - - +
1204N PHE* 2.8 13.8 + - - +
1205N GLN* 3.1 18.1 + - - +
1207N LEU* 1.3 74.8 - - - +
1209N ALA* 1.3 55.1 + - - +
1211N ASN* 2.4 30.1 + - - -
1212N ILE 3.2 15.9 + - - +
1214N PRO* 3.9 15.3 - - + -
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Residues in contact with ALA1209 (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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81M PHE* 3.6 7.8 - - + -
239M LEU* 4.8 1.9 - - - +
240M PRO* 3.9 13.7 - - - +
242M PRO* 3.5 40.6 - - + -
246M VAL* 5.6 0.7 - - + -
303M TYR* 3.6 24.6 + - - +
304M MET* 4.0 2.3 - - - +
325M ILE* 3.7 9.9 - - + -
1205N GLN 3.0 9.6 + - - +
1206N GLU* 3.5 11.9 - - - +
1207N LEU 3.2 0.2 - - - -
1208N MET* 1.3 74.4 - - - +
1210N MET* 1.3 58.6 + - - +
1211N ASN 3.0 2.7 + - - -
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Residues in contact with MET1210 (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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92M HIS* 2.9 25.9 + - - -
304M MET* 3.5 22.4 - - + +
325M ILE* 3.2 46.4 - - + -
326M ARG* 4.1 9.2 - - - +
329M LEU* 3.8 25.1 - - + -
1406M VAL* 4.4 6.5 - - + -
1410M PHE* 3.3 35.2 - - + -
1206N GLU 3.4 3.1 + - - +
1207N LEU* 2.7 26.0 + - + +
1209N ALA* 1.3 76.1 - - - +
1211N ASN* 1.3 65.2 + - - +
1212N ILE* 3.2 4.6 + - + +
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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