Contacts of the helix formed by residues 225 - 246 (chain W) in PDB entry 3FKS
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 PRO 225 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134S LYS* 5.6 0.7 - - - +
302S TYR* 3.4 24.0 - - + +
19W ALA* 6.1 2.2 - - + -
63W ALA* 4.9 7.9 - - + +
64W MET* 3.4 10.3 - - - +
65W ASP* 3.3 48.0 - - - +
224W GLU* 1.3 94.2 - - + +
226W PRO* 1.3 76.5 - - + +
227W GLY 4.3 4.3 - - - +
228W ALA* 3.0 17.0 + - + +
229W ARG* 3.1 9.7 + - - -
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Residues in contact with PRO 226 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299S ASP* 4.4 8.7 - - + -
302S TYR* 3.8 24.5 - - + -
19W ALA* 5.8 4.9 - - + -
225W PRO* 1.3 88.4 - - + +
227W GLY* 1.3 62.4 + - - +
228W ALA 3.0 0.5 + - - -
229W ARG* 3.2 16.2 + - - +
230W ALA* 2.9 26.7 + - - +
264W ALA* 4.0 3.5 - - + +
267W GLU* 3.5 35.7 - - + +
268W VAL* 3.8 18.7 - - + +
271W LEU* 4.6 12.6 - - + -
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Residues in contact with GLY 227 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62W ILE* 4.3 12.4 - - - +
63W ALA 3.4 18.0 + - - -
64W MET* 3.2 19.1 - - - +
225W PRO* 3.3 2.2 - - - +
226W PRO* 1.3 80.5 - - - +
228W ALA* 1.3 59.3 + - - +
230W ALA* 3.9 2.5 + - - +
231W ARG* 3.3 19.2 - - - +
268W VAL* 3.9 13.3 - - - +
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Residues in contact with ALA 228 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63W ALA 4.2 1.2 + - - -
64W MET* 3.9 13.8 - - - +
98W VAL* 3.8 18.1 - - + +
224W GLU* 3.7 22.9 - - + +
225W PRO* 3.0 26.6 + - + +
227W GLY* 1.3 74.7 - - - +
229W ARG* 1.3 66.9 + - - +
230W ALA 3.1 1.3 - - - -
231W ARG* 3.0 13.7 + - - +
232W VAL* 3.1 18.6 + - - +
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Residues in contact with ARG 229 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301S PHE* 3.8 19.7 - - - -
302S TYR* 3.6 24.7 - - - +
187W VAL* 3.3 17.9 - - + +
188W GLY* 4.4 8.1 - - - +
220W GLY* 3.6 23.1 - - - +
221W GLN 3.9 8.5 - - - +
222W MET* 3.9 9.9 + - - +
224W GLU* 3.1 29.3 + - + +
225W PRO 3.1 4.9 + - - +
226W PRO* 3.2 16.1 + - - +
228W ALA* 1.3 78.9 - - - +
230W ALA* 1.3 58.3 + - - +
231W ARG 3.1 1.8 + - - -
232W VAL* 3.1 24.6 + - - +
260W ARG* 5.1 7.6 + - - +
261W PHE* 4.5 3.8 - - - -
263W GLN* 4.8 3.8 - - - +
264W ALA* 3.8 23.2 - - + +
267W GLU* 2.8 32.9 + - - -
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Residues in contact with ALA 230 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226W PRO 2.9 15.9 + - - +
227W GLY* 4.2 5.2 - - - +
228W ALA 3.1 0.4 - - - -
229W ARG* 1.3 77.0 - - - +
231W ARG* 1.3 76.9 + - + +
234W LEU* 4.4 2.3 - - - +
261W PHE* 3.9 25.9 - - + -
264W ALA* 4.1 10.7 - - + +
265W GLY* 4.5 10.3 - - - +
268W VAL* 3.9 19.3 - - + -
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Residues in contact with ARG 231 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W LEU* 4.4 5.9 - - - +
49W GLU* 2.8 35.1 + - - +
62W ILE* 5.1 4.2 - - - +
64W MET* 3.9 13.2 - - + +
98W VAL* 4.2 12.3 - - + -
117W ILE* 4.4 11.5 - - + +
118W HIS* 3.0 25.2 - - - -
227W GLY 3.3 18.5 + - - +
228W ALA 3.0 5.7 + - - +
230W ALA* 1.3 94.2 + - - +
232W VAL* 1.3 60.2 - - - +
233W ALA 3.1 2.7 - - - -
234W LEU* 2.8 39.9 + - - +
235W THR* 3.1 11.2 + - - +
268W VAL* 5.8 6.1 - - - +
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Residues in contact with VAL 232 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98W VAL* 3.5 25.5 - - + +
185W THR* 3.6 11.5 - - + +
187W VAL* 3.5 20.6 - - + -
218W VAL* 4.0 3.5 - - + +
219W PHE 3.9 4.5 - - - +
220W GLY* 3.4 34.1 - - - +
224W GLU* 4.5 0.7 - - - +
228W ALA 3.1 16.0 + - - +
229W ARG* 3.1 28.0 - - - +
231W ARG* 1.3 76.7 - - - +
233W ALA* 1.3 64.1 + - - +
235W THR* 2.9 19.7 + - - -
236W GLY 3.1 11.1 + - - -
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Residues in contact with ALA 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185W THR* 4.2 4.9 - - - -
187W VAL* 3.8 17.9 - - + -
229W ARG 4.5 0.2 + - - -
231W ARG 3.1 0.4 - - - -
232W VAL* 1.3 82.3 - - - +
234W LEU* 1.3 61.0 + - - +
236W GLY* 3.9 0.7 + - - -
237W LEU* 3.3 23.2 + - - +
255W ILE* 4.7 16.1 - - + +
261W PHE* 3.7 33.4 - - + -
292W LEU* 4.1 18.9 - - + +
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Residues in contact with LEU 234 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117W ILE* 3.8 16.5 - - + +
118W HIS* 3.3 36.6 - - + +
230W ALA 4.4 3.8 - - - +
231W ARG* 2.8 35.3 + - + +
233W ALA* 1.3 76.7 - - + +
235W THR* 1.3 57.4 + - - +
237W LEU* 3.6 4.4 - - - +
238W THR* 2.7 34.7 + - - -
261W PHE* 5.4 4.9 - - + -
291W LEU* 5.3 2.7 - - + +
292W LEU* 3.8 30.5 - - + +
295W ARG* 3.5 23.1 - - - +
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Residues in contact with THR 235 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85W VAL* 3.6 26.3 - - + +
96W ILE* 5.3 2.7 - - + -
97W ASN 3.8 16.6 - - - +
98W VAL* 3.3 17.7 + - - +
117W ILE* 3.9 15.4 - - - +
218W VAL* 4.0 16.2 - - + -
231W ARG 3.1 11.3 + - - -
232W VAL* 2.9 17.5 + - - -
234W LEU* 1.3 76.1 - - - +
236W GLY* 1.3 64.4 + - - +
238W THR* 3.1 15.4 + - - -
239W ILE* 3.4 16.5 + - + +
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Residues in contact with GLY 236 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183W VAL* 3.2 14.8 - - - +
185W THR* 3.4 20.9 - - - -
218W VAL* 3.6 18.7 - - - +
232W VAL 3.1 7.7 + - - -
233W ALA 4.4 0.2 - - - -
235W THR* 1.3 80.2 - - - +
237W LEU* 1.3 60.7 + - - +
239W ILE* 3.5 2.5 + - - +
240W ALA 3.2 15.8 + - - -
253W LEU* 3.5 8.9 - - - +
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Residues in contact with LEU 237 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233W ALA 3.3 19.1 + - - +
234W LEU* 3.6 4.3 - - + +
235W THR 3.1 0.4 - - - -
236W GLY* 1.3 74.9 - - - +
238W THR* 1.3 65.3 + - - +
240W ALA* 3.1 3.0 + - + +
241W GLU* 2.9 41.9 + - + +
253W LEU* 3.4 28.4 - - + +
292W LEU* 3.6 33.9 - - + +
295W ARG* 3.6 39.3 - - + +
296W ILE* 4.2 12.6 - - + -
304W VAL* 4.7 9.4 - - + -
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Residues in contact with THR 238 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85W VAL* 4.0 10.5 - - + -
87W VAL* 4.2 5.6 - - + +
115W LYS* 3.9 27.9 - - + +
116W PRO 3.1 20.4 - - - +
117W ILE* 3.2 22.3 + - - +
234W LEU 2.7 21.9 + - - -
235W THR 3.1 7.1 + - - -
237W LEU* 1.3 76.5 - - - +
239W ILE* 1.3 63.0 + - - +
241W GLU* 2.9 34.0 + - - +
242W TYR* 3.3 6.4 + - - +
295W ARG* 3.8 1.0 + - - -
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Residues in contact with ILE 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85W VAL* 4.6 5.4 - - + -
86W PRO* 3.8 19.5 - - + +
87W VAL* 3.9 11.7 - - + -
91W THR* 3.6 30.1 - - + +
96W ILE* 4.6 15.7 - - + -
183W VAL* 4.0 13.9 - - + -
216W ALA* 4.6 4.7 - - + -
218W VAL* 3.7 30.5 - - + -
235W THR* 3.5 15.0 - - + +
236W GLY* 3.7 5.2 - - - +
237W LEU 3.3 0.4 - - - -
238W THR* 1.3 76.4 - - - +
240W ALA* 1.3 61.4 + - - +
241W GLU 3.3 0.5 + - - -
242W TYR* 3.4 6.8 + - - +
243W PHE* 2.9 36.3 - - + -
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Residues in contact with ALA 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183W VAL* 3.9 11.6 - - + +
236W GLY 3.2 10.5 + - - +
237W LEU* 3.1 11.3 + - - +
239W ILE* 1.3 79.2 - - - +
241W GLU* 1.3 61.0 + - - +
243W PHE* 3.5 8.6 + - - -
244W ARG 3.7 0.5 + - - -
251W VAL* 3.5 40.8 - - + +
253W LEU* 4.2 20.2 - - + -
304W VAL* 3.9 13.1 - - + +
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Residues in contact with GLU 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115W LYS* 6.1 1.6 - - + -
119W ALA* 4.2 7.9 - - - +
237W LEU* 2.9 26.8 + - + +
238W THR* 2.9 17.2 + - - +
240W ALA* 1.3 76.0 - - - +
242W TYR* 1.3 53.9 + - - +
244W ARG* 2.8 28.9 + - - +
245W ASP* 2.7 47.0 + - - +
295W ARG* 2.8 58.4 + - - +
304W VAL* 4.6 3.4 - - + -
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Residues in contact with TYR 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87W VAL* 3.6 37.7 - - + -
88W GLY* 3.7 29.2 - - - +
112W LYS* 4.0 16.6 + - - +
113W LEU* 3.8 29.9 - - + +
115W LYS* 4.2 24.0 - - + +
238W THR 3.3 4.8 + - - +
239W ILE 3.4 7.3 + - - +
241W GLU* 1.3 78.8 - - - +
243W PHE* 1.3 61.6 + + + +
245W ASP* 4.5 3.6 - - - +
246W GLU* 3.0 67.6 + - + +
247W GLU* 3.8 11.2 + - + +
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Residues in contact with PHE 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88W GLY 3.1 37.7 - - - -
89W ARG* 4.5 4.9 - - + -
91W THR* 4.4 0.4 - - - -
92W LEU* 3.9 21.8 - - + -
181W PHE* 3.3 49.1 - + + -
183W VAL* 5.1 4.7 - - + -
239W ILE* 2.9 41.7 - - + -
240W ALA* 3.7 3.8 - - - +
241W GLU 3.1 0.6 - - - -
242W TYR* 1.3 78.8 - + + +
244W ARG* 1.3 57.7 + - - +
247W GLU* 3.4 19.9 - - - +
248W GLY 3.1 19.9 + - - -
249W GLN* 3.3 14.5 + - - +
251W VAL* 3.7 23.8 - - + -
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Residues in contact with ARG 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122W PRO* 4.2 14.3 - - - +
240W ALA 4.2 0.4 - - - +
241W GLU* 2.8 26.4 + - - +
243W PHE* 1.3 78.1 - - - +
245W ASP* 1.3 80.5 + - - +
246W GLU 3.2 5.3 + - - -
248W GLY* 3.4 14.7 + - - +
249W GLN 4.3 6.5 - - - +
251W VAL* 4.2 2.5 - - + -
295W ARG 3.0 26.0 + - - -
297W THR* 2.9 27.1 + - - +
299W THR* 3.4 25.3 + - - +
301W LYS* 3.4 14.6 - - - +
302W GLY* 3.5 4.7 - - - -
303W SER* 3.3 31.9 - - - +
304W VAL* 3.5 31.8 - - + +
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Residues in contact with ASP 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115W LYS* 4.6 17.0 + - - +
241W GLU* 2.7 29.4 + - - +
242W TYR* 4.9 0.9 - - - +
244W ARG* 1.3 98.3 + - - +
246W GLU* 1.3 66.9 + - - +
299W THR* 4.7 9.7 + - - +
301W LYS* 4.5 23.4 - - - +
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Residues in contact with GLU 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W LYS* 5.8 1.4 + - - +
113W LEU* 4.5 8.5 - - - +
115W LYS* 5.3 6.7 + - - +
242W TYR* 3.0 59.1 + - + +
245W ASP* 1.3 86.8 - - + +
247W GLU* 1.3 62.2 + - + +
248W GLY 3.9 0.2 - - - -
301W LYS* 6.2 1.8 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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