Contacts of the helix formed by residues 1197 - 1210 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LEU* 3.7 4.9 - - + -
343A LYS* 3.3 29.8 - - - +
1428A VAL 4.7 0.4 - - - +
1429A ILE 3.0 23.3 - - - +
1430A LEU 3.0 31.0 - - - +
1431A GLY 3.5 0.9 - - - +
1152B MET* 3.1 12.0 - - - -
1156B ASP* 3.5 16.2 - - + +
1157B ALA 3.9 0.4 - - - +
1196B ILE* 1.3 76.5 - - + +
1198B TYR* 1.3 58.4 + - - +
1200B ALA* 2.6 41.5 + - + +
1201B LYS 3.1 8.7 + - - -
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Residues in contact with TYR1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 3.7 19.6 + - - +
1113B VAL 5.1 1.7 + - - -
1114B LEU 3.7 20.0 + - - -
1115B THR 3.3 13.9 - - - +
1116B ARG* 3.0 60.1 + - + +
1156B ASP* 3.4 20.9 + - + +
1158B PHE* 3.5 37.4 - + + +
1196B ILE 3.1 3.8 + - - -
1197B PRO* 1.3 69.9 - - - +
1199B ALA* 1.3 64.8 + - - +
1201B LYS* 3.0 38.7 + - + +
1202B LEU* 3.0 27.4 + - + +
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Residues in contact with ALA1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 3.8 6.8 - - - +
339A ASN* 3.8 12.6 - - + +
340A LEU* 3.4 17.9 - - + +
1115B THR* 4.5 5.4 - - + -
1117B GLN* 3.4 29.4 - - - +
1156B ASP* 3.0 11.5 + - - +
1197B PRO 3.0 0.6 + - - -
1198B TYR* 1.3 78.7 - - - +
1200B ALA* 1.3 58.6 + - - +
1202B LEU* 3.2 10.8 - - - +
1203B LEU* 2.8 25.1 + - - +
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Residues in contact with ALA1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LEU* 3.0 20.0 - - + +
1429A ILE* 3.2 15.0 - - + +
1430A LEU* 5.1 0.2 - - - -
1196B ILE* 3.9 10.8 - - + -
1197B PRO* 2.6 38.9 + - + +
1199B ALA* 1.3 69.4 - - - +
1201B LYS* 1.3 63.8 + - - +
1203B LEU* 2.8 13.8 + - - +
1204B PHE* 2.8 26.1 + - + -
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Residues in contact with LYS1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO* 3.1 37.6 - - + +
79A GLY 3.5 4.0 - - - +
245A PRO* 3.9 8.1 - - - +
1116B ARG* 5.3 1.6 - - - +
1158B PHE* 3.7 22.8 - - + -
1160B VAL* 5.0 1.1 - - + -
1169B MET* 3.3 30.4 - - + +
1196B ILE* 3.3 11.9 - - + +
1197B PRO 3.1 5.1 + - - -
1198B TYR* 3.0 48.3 + - + +
1200B ALA* 1.3 75.6 - - - +
1202B LEU* 1.3 53.4 + - - +
1204B PHE* 3.0 4.7 + - - +
1205B GLN* 2.6 60.9 + - - +
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Residues in contact with LEU1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO 4.5 4.5 - - - +
246A VAL* 4.3 23.1 - - + -
335A ARG* 3.1 20.6 - - - +
1114B LEU* 3.0 39.0 - - + +
1115B THR* 4.4 3.1 - - - -
1198B TYR* 3.0 21.4 + - + +
1199B ALA* 3.2 12.3 - - - +
1201B LYS* 1.3 79.2 - - - +
1203B LEU* 1.3 67.1 + - - +
1204B PHE 3.0 0.2 + - - -
1205B GLN* 3.0 7.6 + - - +
1206B GLU* 2.7 63.4 + - + +
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Residues in contact with LEU1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 3.7 29.4 - - + -
335A ARG* 4.0 4.0 - - + -
336A ILE* 3.5 35.9 - - + -
340A LEU* 3.9 14.4 - - + -
1397A LEU* 4.5 11.9 - - + -
1409A LEU* 4.7 1.3 - - + -
1429A ILE* 4.8 1.8 - - + -
1199B ALA 2.8 17.2 + - - +
1200B ALA 2.8 11.3 + - - +
1202B LEU* 1.3 70.4 - - - +
1204B PHE* 1.3 80.6 + - + +
1206B GLU* 3.4 11.5 + - - +
1207B LEU* 2.9 39.3 + - + +
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Residues in contact with PHE1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 5.8 3.1 - - + -
19A PHE* 6.1 0.9 - + - -
1397A LEU* 4.9 14.6 - - + -
1429A ILE* 5.2 4.5 - - + -
1430A LEU* 4.0 21.3 - - + -
1169B MET* 3.8 22.4 - - + -
1196B ILE* 4.0 12.3 - - + -
1200B ALA* 2.8 23.1 + - + -
1201B LYS* 3.1 5.8 - - - +
1203B LEU* 1.3 96.6 - - + +
1205B GLN* 1.3 67.0 + - - +
1207B LEU* 2.8 20.3 + - + +
1208B MET* 2.8 20.6 + - - +
1214B PRO* 4.0 29.3 - - + +
1216B LEU* 4.0 32.8 - - + -
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Residues in contact with GLN1205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PRO* 4.5 1.6 - - - +
79A GLY* 3.3 40.6 + - - +
81A PHE* 3.2 22.2 - - + -
243A PRO* 4.0 6.9 - - - +
245A PRO* 5.0 2.3 - - - +
246A VAL* 3.8 26.4 - - + +
1169B MET* 4.7 13.6 - - + +
1201B LYS* 2.6 49.8 + - + +
1202B LEU* 3.7 9.8 - - - +
1204B PHE* 1.3 71.4 - - - +
1206B GLU* 1.3 63.3 + - - +
1208B MET* 3.0 14.6 + - - -
1209B ALA* 3.0 19.6 + - - +
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Residues in contact with GLU1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL* 4.2 11.2 - - + -
325A ILE* 3.9 14.4 - - + +
328A ARG* 3.0 36.6 + - - +
329A LEU* 3.4 21.0 - - + +
335A ARG* 2.9 40.2 + - - +
1202B LEU* 2.7 46.2 + - + +
1203B LEU* 3.4 4.3 - - - +
1205B GLN* 1.3 71.7 - - - +
1207B LEU* 1.3 63.3 + - - +
1209B ALA* 3.1 18.3 + - - +
1210B MET* 3.3 15.1 + - - +
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Residues in contact with LEU1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 5.1 3.1 - - + -
329A LEU* 4.2 5.6 - - + -
1397A LEU* 6.0 0.4 - - + -
1406A VAL* 5.9 0.2 - - + -
1409A LEU* 3.3 47.1 - - + -
1410A PHE* 5.2 0.7 - - + -
1203B LEU* 2.9 31.1 + - + +
1204B PHE* 2.8 19.8 + - + +
1206B GLU* 1.3 71.8 - - - +
1208B MET* 1.3 58.7 + - - +
1210B MET* 2.9 42.9 + - + +
1212B ILE* 3.0 47.0 + - + +
1214B PRO* 5.0 8.5 - - + -
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Residues in contact with MET1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 4.0 28.8 - - + -
30A ILE* 5.3 6.3 - - + -
81A PHE* 3.3 45.3 - - + -
240A PRO* 3.4 8.3 - - - +
1168B LEU* 4.6 15.9 - - + -
1169B MET* 5.0 15.0 - - + +
1170B THR 6.2 0.4 - - - +
1204B PHE* 2.8 14.0 + - - +
1205B GLN* 3.0 19.9 + - - +
1207B LEU* 1.3 72.5 - - - +
1209B ALA* 1.3 54.1 + - - +
1210B MET 2.9 5.2 - - - -
1211B ASN* 2.6 27.7 + - - -
1212B ILE 3.3 15.9 + - - +
1214B PRO* 4.0 13.7 - - + -
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Residues in contact with ALA1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.5 7.8 - - + -
239A LEU* 4.8 1.9 - - - +
240A PRO* 3.9 13.4 - - - +
242A PRO* 3.4 40.2 - - + -
246A VAL* 5.7 0.4 - - + -
303A TYR* 3.4 26.9 + - - +
304A MET* 4.2 2.6 - - - +
325A ILE* 3.7 9.0 - - + -
1205B GLN 3.0 8.7 + - - +
1206B GLU* 3.1 11.4 + - - +
1208B MET* 1.3 74.6 - - - +
1210B MET* 1.3 58.0 + - - +
1211B ASN 3.1 3.3 + - - -
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Residues in contact with MET1210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS* 3.0 19.9 + - - -
304A MET* 3.5 22.9 - - + -
325A ILE* 3.2 47.1 - - + -
326A ARG* 4.2 8.5 - - - +
329A LEU* 3.7 25.8 - - + -
1406A VAL* 4.4 6.3 - - + -
1410A PHE* 3.3 35.2 - - + -
1206B GLU 3.3 1.3 + - - +
1207B LEU* 2.9 29.5 + - + +
1208B MET 2.9 1.2 - - - -
1209B ALA* 1.3 76.3 - - - +
1211B ASN* 1.3 69.2 + - - +
1212B 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
------------------------------------------------------------
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