Contacts of the helix formed by residues 217 - 239 (chain J) in PDB entry 4DVQ
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 SER 217 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211J LEU* 4.0 16.0 - - - +
215J SER 3.6 1.0 + - - -
216J PRO* 1.3 75.3 - - - +
218J SER* 1.3 62.1 + - - +
219J ALA* 3.5 10.2 + - - +
220J SER* 2.9 40.9 + - - -
221J LEU* 3.2 13.1 + - - +
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Residues in contact with SER 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217J SER* 1.3 70.9 - - - +
219J ALA* 1.3 62.3 + - - +
221J LEU* 3.9 10.4 - - - +
222J ASN* 2.9 44.4 + - - +
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Residues in contact with ALA 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217J SER* 3.2 9.3 + - - +
218J SER* 1.3 82.4 + - - +
220J SER* 1.3 56.4 + - - +
222J ASN* 3.5 7.9 + - - +
223J PHE* 3.0 27.4 + - - +
266J TYR* 4.2 19.8 - - + -
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Residues in contact with SER 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194J HIS* 2.8 35.9 + - - -
197J ILE* 4.3 9.6 - - - -
211J LEU* 4.1 13.9 - - - -
217J SER* 2.9 35.8 + - - -
219J ALA* 1.3 75.0 - - - +
221J LEU* 1.3 59.7 + - - +
223J PHE* 3.0 8.0 + - - +
224J LEU* 2.8 35.4 + - - +
266J TYR* 4.9 4.9 - - - -
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Residues in contact with LEU 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194J HIS* 4.5 7.4 - - + -
216J PRO* 3.6 32.3 - - + +
217J SER 3.2 20.1 + - - +
218J SER* 3.5 8.5 + - - +
220J SER* 1.3 79.7 + - - +
222J ASN* 1.3 63.7 + - - +
224J LEU* 3.6 10.8 + - + +
225J HIS* 3.1 23.7 + - - +
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Residues in contact with ASN 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J SER* 2.9 29.4 + - - +
219J ALA* 3.6 7.3 - - - +
221J LEU* 1.3 76.0 - - - +
223J PHE* 1.3 56.4 + - - +
225J HIS* 3.2 6.5 + - - +
226J ALA* 2.7 36.4 + - - +
262J CYS* 3.9 18.3 - - - -
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Residues in contact with PHE 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J ILE* 4.3 17.5 - - + -
219J ALA 3.0 15.7 + - - +
220J SER* 3.0 9.1 + - - +
222J ASN* 1.3 72.5 - - - +
224J LEU* 1.3 65.8 + - - +
226J ALA* 3.3 4.7 + - - +
227J LEU* 2.9 44.6 + - + +
262J CYS* 4.7 3.6 - - - -
263J ILE* 4.2 32.8 - - + -
266J TYR* 3.6 57.0 - + + -
309J MET* 5.8 0.2 - - + -
312J THR* 3.9 21.8 - - + -
313J ALA* 4.3 5.4 - - - -
316J VAL* 3.6 24.5 - - + -
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Residues in contact with LEU 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190J PRO* 6.1 0.7 - - + -
193J PHE* 3.7 25.1 - - + -
194J HIS* 3.6 33.4 - - + +
197J ILE* 3.5 15.3 - - + -
220J SER 2.8 20.1 + - - +
221J LEU* 4.0 10.3 - - + +
223J PHE* 1.3 76.4 - - - +
225J HIS* 1.3 57.1 + - - +
227J LEU* 3.5 8.6 + - + +
228J GLU* 3.0 27.4 + - - +
316J VAL* 3.5 32.3 - - + -
317J ASP* 5.0 4.7 - - - +
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Residues in contact with HIS 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J LEU 3.1 18.8 + - - +
222J ASN* 3.5 6.5 + - - +
223J PHE 3.1 0.2 - - - -
224J LEU* 1.3 75.5 - - - +
226J ALA* 1.3 66.1 + - - +
228J GLU* 3.1 20.6 + - - +
229J VAL* 3.0 42.8 + - + +
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Residues in contact with ALA 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J ASN 2.7 18.0 + - - +
223J PHE* 3.8 4.0 - - - +
225J HIS* 1.3 74.6 + - - +
227J LEU* 1.3 57.2 + - - +
229J VAL* 3.2 3.7 + - - -
230J MET* 2.8 32.9 + - - +
259J ALA* 3.6 19.5 - - - +
262J CYS* 3.4 34.8 - - + -
263J ILE* 4.1 9.0 - - + -
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Residues in contact with LEU 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J PHE* 2.9 49.5 + - + +
224J LEU* 3.6 11.4 - - - +
226J ALA* 1.3 75.1 - - - +
228J GLU* 1.3 64.1 + - - +
230J MET* 3.2 6.6 + - + +
231J PHE* 2.9 38.5 + - + -
263J ILE* 3.8 25.6 - - + -
313J ALA* 3.6 30.3 - - + +
316J VAL* 4.0 13.2 - - + -
317J ASP* 3.5 27.6 - - - +
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Residues in contact with GLU 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J LEU 3.0 14.8 + - - +
225J HIS* 3.1 24.5 + - + +
227J LEU* 1.3 76.1 - - - +
229J VAL* 1.3 58.3 + - + +
231J PHE* 3.4 8.9 + - + +
232J LYS* 3.0 27.9 + - - +
317J ASP* 5.3 4.4 + - - +
486J SER* 5.0 0.7 + - - -
490J ARG* 4.4 24.9 + - - +
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Residues in contact with VAL 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J HIS* 3.0 43.7 + - + +
226J ALA* 3.8 4.5 - - - +
228J GLU* 1.3 73.7 - - + +
230J MET* 1.3 60.5 + - - +
232J LYS* 3.7 10.4 - - - +
233J SER* 2.8 30.5 + - - +
255J GLU* 3.7 35.0 - - + +
259J ALA* 3.8 15.3 - - + -
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Residues in contact with MET 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J TRP* 3.5 19.1 - - + -
226J ALA 2.8 18.2 + - - +
227J LEU* 3.2 8.3 + - + +
229J VAL* 1.3 76.0 - - - +
231J PHE* 1.3 96.9 + - + +
233J SER* 3.3 7.3 + - - -
234J THR* 2.7 42.3 + - - -
256J HIS* 3.5 1.7 + - + -
259J ALA* 3.7 11.2 - - + +
260J TRP* 3.4 54.5 - - + +
263J ILE* 3.9 16.2 - - + -
313J ALA* 6.3 0.7 - - + -
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Residues in contact with PHE 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J TRP* 4.3 1.3 - + - -
227J LEU* 2.9 31.2 + - + +
228J GLU* 3.7 7.2 - - + +
230J MET* 1.3 97.0 - - + +
232J LYS* 1.3 66.4 + - - +
234J THR* 3.0 18.6 + - - -
235J VAL* 3.4 10.7 + - - +
313J ALA 5.2 1.8 - - - -
317J ASP* 3.6 33.0 - - + -
318J THR* 5.6 0.9 - - + -
486J SER* 3.3 21.2 - - - +
487J PHE* 3.9 24.4 - + + +
488J ILE* 3.8 26.0 - - + -
602J 1CA 3.9 35.0 - - + -
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Residues in contact with LYS 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J GLN* 4.3 16.3 + - + +
60J GLY* 5.3 2.5 - - - -
228J GLU 3.0 17.4 + - - +
229J VAL* 3.7 13.2 - - - +
231J PHE* 1.3 73.5 - - - +
233J SER* 1.3 58.6 - - - +
235J VAL* 3.0 26.5 + - - +
236J GLN* 3.5 23.5 + - - +
255J GLU* 2.8 35.0 + - - -
486J SER* 3.6 16.0 + - - +
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Residues in contact with SER 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229J VAL 2.8 20.7 + - - -
230J MET* 3.3 0.7 + - - -
232J LYS* 1.3 71.5 - - - +
234J THR* 1.3 64.3 + - - +
236J GLN* 3.4 14.7 + - - +
237J LEU* 3.3 28.2 + - - +
252J VAL* 4.1 7.2 - - - -
255J GLU* 3.9 19.5 - - - -
256J HIS* 2.7 47.7 + - - +
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Residues in contact with THR 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU* 4.4 5.8 - - + -
115J PRO* 4.5 3.2 - - + +
116J TRP* 2.9 34.1 + - + +
230J MET* 2.7 23.5 + - - -
231J PHE* 3.0 13.2 + - - -
233J SER* 1.3 77.0 + - - +
235J VAL* 1.3 63.7 + - - +
237J LEU* 3.7 3.4 + - - +
238J MET* 3.1 25.2 + - - +
256J HIS* 3.2 10.9 - - - -
487J PHE* 3.5 35.2 - - + -
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Residues in contact with VAL 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J ILE* 4.1 3.7 - - + +
60J GLY* 4.2 7.0 - - - +
61J TYR* 3.5 37.9 - - + +
231J PHE 3.7 9.2 - - - +
232J LYS 3.0 8.1 + - - +
234J THR* 1.3 75.5 - - - +
236J GLN* 1.3 66.1 + - - +
238J MET* 3.0 22.3 + - - +
239J PHE* 3.9 15.8 - - + -
485J TYR* 4.0 17.5 - - + +
486J SER* 4.0 8.5 - - - +
487J PHE* 3.6 30.3 - - + +
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Residues in contact with GLN 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J ILE* 3.5 24.8 + - + +
56J TRP* 5.6 1.0 + - - +
59J GLN* 3.2 51.9 + - - +
60J GLY* 4.1 1.1 - - - +
232J LYS* 3.5 28.0 - - - +
233J SER* 3.4 19.1 - - - +
234J THR 3.3 0.2 - - - -
235J VAL* 1.3 79.8 - - - +
237J LEU* 1.3 61.5 + - - +
238J MET 3.3 0.3 + - - -
239J PHE 4.4 1.6 + - - -
240J MET* 3.9 16.5 - - - +
252J VAL* 3.2 37.9 - - + +
255J GLU* 3.5 6.7 + - - +
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Residues in contact with LEU 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J PRO* 3.8 21.0 - - + +
233J SER 3.3 13.4 + - - +
236J GLN* 1.3 79.0 - - - +
238J MET* 1.3 63.3 + - - +
239J PHE 3.6 0.4 - - - -
240J MET* 3.3 22.6 - - - +
245J SER* 4.6 7.2 + - - +
249J SER* 4.6 4.9 - - - +
252J VAL* 3.5 23.1 - - + -
253J TRP* 3.2 64.5 - - + +
256J HIS* 3.8 36.6 - - + -
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Residues in contact with MET 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU* 3.9 20.6 - - + -
115J PRO* 4.5 6.9 - - - +
234J THR* 3.1 19.3 + - - +
235J VAL* 3.0 18.8 + - - +
236J GLN 3.2 0.2 - - - -
237J LEU* 1.3 80.3 - - - +
239J PHE* 1.3 101.6 + - + +
240J MET 3.0 9.2 + - - +
381J PHE* 5.1 10.3 - - + -
485J TYR* 3.6 18.6 - - + +
487J PHE* 3.9 27.8 - - + -
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Residues in contact with PHE 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J ARG* 3.3 41.1 - - - +
52J LEU* 3.1 32.2 - - + +
55J ILE* 3.3 32.3 - - + -
61J TYR* 3.8 22.7 - + - -
64J LEU* 4.5 14.6 - - + -
83J LEU* 6.0 1.8 - - + -
88J MET* 6.4 0.7 - - + -
235J VAL* 3.9 9.1 + - + -
236J GLN 4.4 2.0 + - - +
237J LEU 3.6 0.2 - - - -
238J MET* 1.3 114.3 - - + +
240J MET* 1.3 57.9 + - + +
381J PHE* 6.0 2.0 - + - -
485J TYR* 5.4 0.7 - + - -
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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