Contacts of the helix formed by residues 225 - 245 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302L TYR* 3.3 24.0 - - + +
19M ALA* 5.1 5.4 - - + -
63M ALA 5.0 2.7 - - - +
64M MET 3.7 13.2 - - - +
65M ASP* 3.7 34.1 - - - +
66M GLY* 4.3 4.0 - - - +
223M ASN 4.3 0.2 - - - +
224M GLU* 1.3 96.0 - - + +
226M PRO* 1.3 79.0 - - + +
227M GLY 3.4 3.1 - - - +
228M ALA* 3.0 14.7 + - - +
229M ARG* 3.2 3.7 - - - -
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Residues in contact with PRO 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299L ASP* 4.8 7.4 - - + -
302L TYR* 4.4 11.7 - - + -
19M ALA* 4.5 11.2 - - + -
225M PRO* 1.3 88.3 - - + +
227M GLY* 1.3 64.7 + - - +
228M ALA 3.0 1.2 + - - -
229M ARG* 3.1 19.8 + - - +
230M ALA* 3.2 10.8 + - - +
264M ALA* 3.5 12.6 - - + +
267M GLU* 3.2 37.2 - - + +
268M VAL* 3.6 29.2 - - + -
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Residues in contact with GLY 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA* 4.8 1.8 - - - +
62M ILE* 3.6 22.4 - - - +
63M ALA 3.5 20.3 + - - -
64M MET* 3.5 18.6 - - - +
225M PRO 3.4 0.8 - - - -
226M PRO* 1.3 79.4 - - - +
228M ALA* 1.3 62.8 + - - +
230M ALA* 3.6 7.3 + - - +
231M ARG* 3.5 15.2 + - - +
268M VAL* 4.9 0.6 - - - +
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Residues in contact with ALA 228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M ALA 4.4 0.2 + - - -
64M MET* 3.6 26.6 + - - +
98M VAL* 3.8 11.4 - - + +
220M GLY 5.3 0.9 - - - +
224M GLU* 3.5 35.7 - - + +
225M PRO 3.0 13.0 + - - +
226M PRO 3.0 0.2 + - - -
227M GLY* 1.3 76.7 - - - +
229M ARG* 1.3 59.1 + - + +
231M ARG 3.3 2.3 + - - -
232M VAL* 2.9 32.6 + - - +
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Residues in contact with ARG 229 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301L PHE* 3.7 24.3 - - - -
302L TYR* 3.3 19.4 - - - +
187M VAL* 3.6 15.6 - - + +
188M GLY* 4.1 12.8 - - - -
220M GLY 3.5 20.0 - - - +
221M GLN 3.7 9.0 - - - +
222M MET* 4.5 8.1 - - - +
224M GLU 2.7 38.2 + - - -
225M PRO 3.2 21.9 - - - -
226M PRO* 3.1 8.3 + - - +
228M ALA* 1.3 80.3 - - + +
230M ALA* 1.3 63.8 + - - +
232M VAL* 3.2 21.4 + - - +
233M ALA* 3.9 2.3 + - - +
260M ARG* 4.1 17.5 + - - +
261M PHE* 4.4 3.6 - - - -
263M GLN* 4.4 4.6 + - - -
264M ALA* 4.1 6.6 - - + +
267M GLU* 2.8 36.4 + - - -
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Residues in contact with ALA 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M ILE* 6.2 1.1 - - + -
226M PRO 3.2 15.2 + - - +
227M GLY* 3.8 9.2 - - - +
228M ALA 3.2 0.4 - - - -
229M ARG* 1.3 77.8 - - - +
231M ARG* 1.3 79.6 + - + +
233M ALA* 4.5 1.9 + - - +
234M LEU* 4.3 2.4 - - - +
261M PHE* 3.1 37.0 - - + +
264M ALA* 3.7 20.6 - - + +
265M GLY* 5.0 2.0 - - - +
268M VAL* 6.4 1.1 - - + -
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Residues in contact with ARG 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M LEU* 5.2 3.2 - - - +
49M GLU* 3.2 30.3 + - - -
62M ILE* 5.9 5.6 - - + +
64M MET* 3.5 32.1 - - + -
83M ILE* 6.1 1.1 - - + -
98M VAL* 3.7 10.5 - - + -
117M ILE* 5.1 7.1 - - + +
118M HIS* 3.9 13.3 - - - -
227M GLY 3.5 6.9 + - - +
228M ALA 3.3 2.2 + - - -
230M ALA* 1.3 104.4 + - + +
232M VAL* 1.3 60.7 + - - +
233M ALA 3.1 2.5 - - - -
234M LEU* 3.2 29.6 + - + +
235M THR* 3.0 28.5 + - - +
261M PHE* 4.2 9.9 - - - -
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Residues in contact with VAL 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M VAL* 3.6 19.5 - - + +
185M THR* 3.5 8.2 - - + +
186M GLY 4.3 2.9 - - - +
187M VAL* 3.8 16.8 - - + -
218M VAL* 4.2 11.6 - - + +
219M PHE 3.6 9.0 - - - +
220M GLY* 3.6 37.7 - - - +
228M ALA 2.9 11.3 + - - +
229M ARG* 3.2 28.5 - - - +
231M ARG* 1.3 75.6 - - - +
233M ALA* 1.3 66.8 + - - +
235M THR* 3.3 9.5 + - - -
236M GLY 3.4 9.9 + - - -
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Residues in contact with ALA 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M THR* 4.3 5.0 + - - +
187M VAL* 3.9 27.6 - - + -
229M ARG 3.9 1.3 + - - +
230M ALA 4.6 0.2 - - - +
231M ARG 3.1 0.2 - - - -
232M VAL* 1.3 83.5 - - - +
234M LEU* 1.3 61.2 + - - +
236M GLY* 3.7 1.0 + - - -
237M LEU* 3.4 23.2 + - - +
255M ILE* 5.3 9.2 - - + +
258M ILE* 6.2 1.8 - - + -
261M PHE* 4.3 27.4 - - + -
292M LEU* 4.4 12.9 - - + +
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Residues in contact with LEU 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ILE* 4.0 15.8 - - + +
118M HIS* 3.8 20.0 - - + +
230M ALA 4.3 6.1 - - - +
231M ARG* 3.2 45.4 + - - +
233M ALA* 1.3 76.9 - - - +
235M THR* 1.3 65.4 + - - +
237M LEU* 3.3 12.3 + - - +
238M THR* 3.1 19.9 + - - -
261M PHE* 4.9 5.6 - - + -
291M LEU 5.2 1.6 - - - +
292M LEU* 3.4 29.6 - - + -
295M ARG* 3.5 28.6 + - - +
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Residues in contact with THR 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M VAL* 3.7 23.9 - - + +
96M ILE* 4.1 13.5 - - + -
97M ASN 3.6 22.2 - - - +
98M VAL* 3.0 21.9 + - - +
117M ILE* 4.2 14.8 - - - +
218M VAL* 4.1 4.3 - - + -
231M ARG* 3.0 14.7 + - - +
232M VAL* 3.5 11.2 - - - -
233M ALA 3.2 0.2 - - - -
234M LEU* 1.3 78.7 - - - +
236M GLY* 1.3 62.6 + - - +
237M LEU 3.1 0.9 + - - -
238M THR* 3.4 11.3 + - - -
239M ILE* 3.6 12.6 + - - +
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Residues in contact with GLY 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183M VAL* 3.5 14.9 - - - +
185M THR* 3.7 22.4 + - - -
218M VAL* 3.7 24.1 - - - +
232M VAL 3.4 7.7 + - - -
233M ALA 3.7 0.4 + - - -
234M LEU 3.5 0.2 - - - -
235M THR* 1.3 77.5 - - - +
237M LEU* 1.3 60.8 + - - +
238M THR 3.4 0.2 - - - -
239M ILE* 3.7 3.1 + - - +
240M ALA* 3.4 16.6 + - - +
253M LEU* 4.4 1.4 - - - +
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Residues in contact with LEU 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ALA 3.4 14.2 + - - +
234M LEU* 3.3 11.2 + - + +
235M THR 3.1 0.6 - - - -
236M GLY* 1.3 77.0 - - - +
238M THR* 1.3 59.7 + - - +
240M ALA* 3.2 6.0 + - + +
241M GLU* 2.9 36.7 + - + +
253M LEU* 3.8 18.2 - - + -
255M ILE* 4.5 4.3 - - + -
292M LEU* 3.5 27.6 - - + +
295M ARG* 3.4 45.3 - - + +
296M ILE* 3.4 32.5 - - + -
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Residues in contact with THR 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M VAL* 4.6 6.3 - - - -
87M VAL* 4.0 8.7 - - + -
115M LYS* 3.8 40.6 - - + +
116M PRO 3.9 9.0 - - - +
117M ILE* 3.4 19.1 - - - +
234M LEU 3.1 13.6 + - - -
235M THR 3.8 7.5 + - - -
236M GLY 3.4 0.2 - - - -
237M LEU* 1.3 75.6 - - - +
239M ILE* 1.3 66.6 + - - +
241M GLU* 3.1 15.4 + - + +
242M TYR* 3.1 23.0 + - - +
295M ARG* 3.8 5.9 + - - +
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Residues in contact with ILE 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M VAL* 4.0 14.6 - - + -
86M PRO 3.1 28.5 - - - +
87M VAL* 3.8 15.9 - - + -
88M GLY 4.8 2.6 + - - +
91M THR* 3.3 31.0 - - + +
96M ILE* 5.1 7.2 - - + -
183M VAL* 4.4 10.3 - - + -
216M ALA* 4.5 5.4 - - + -
218M VAL* 4.6 10.8 - - + -
235M THR 3.6 13.2 - - - +
236M GLY* 3.9 10.3 - - - +
237M LEU 3.4 0.2 - - - -
238M THR* 1.3 77.0 - - - +
240M ALA* 1.3 60.0 + - - +
242M TYR* 3.6 8.8 + - - +
243M PHE* 3.0 35.2 + - + -
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Residues in contact with ALA 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183M VAL* 4.0 11.2 - - + +
236M GLY 3.4 11.0 + - - +
237M LEU* 3.2 11.2 + - + +
238M THR 3.1 0.8 - - - -
239M ILE* 1.3 77.4 - - - +
241M GLU* 1.3 65.4 + - + +
243M PHE* 3.3 10.3 + - - +
244M ARG* 3.4 9.0 + - - +
251M VAL* 3.6 29.1 - - + +
253M LEU* 4.1 23.8 - - + -
304M VAL* 5.2 5.5 - - + +
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Residues in contact with GLU 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M LYS* 5.7 1.9 + - - -
119M ALA* 4.7 8.3 - - - +
120M ASP 5.4 2.3 - - - +
122M PRO* 5.2 2.3 - - - +
237M LEU* 2.9 20.4 + - + +
238M THR* 3.1 10.0 + - + +
240M ALA* 1.3 76.4 - - + +
242M TYR* 1.3 57.4 + - - +
244M ARG* 3.5 31.8 + - - +
245M ASP* 2.8 38.6 + - - +
295M ARG* 2.9 64.5 + - - +
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Residues in contact with TYR 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M VAL* 4.0 27.4 - - + -
88M GLY* 3.5 34.8 - - - +
89M ARG 5.0 0.2 - - - -
113M LEU* 3.8 26.8 - - + +
115M LYS* 4.0 19.5 - - + +
238M THR 3.1 11.6 + - - +
239M ILE 3.8 9.9 - - - +
240M ALA 3.2 0.2 - - - -
241M GLU* 1.3 77.9 - - - +
243M PHE* 1.3 65.5 + + - +
244M ARG 3.2 0.5 + - - -
245M ASP* 5.2 0.9 - - - -
246M GLU* 3.2 35.2 + - + +
247M GLU* 3.0 41.8 + - - -
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Residues in contact with PHE 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M GLY 3.3 29.2 - - - -
89M ARG* 3.9 10.3 - - + -
91M THR* 3.9 6.7 - - - -
92M LEU* 3.9 17.9 - - + -
181M PHE* 3.3 50.5 - + + -
183M VAL* 4.0 18.2 - - + -
216M ALA* 5.0 0.2 - - + -
239M ILE* 3.0 39.7 + - + -
240M ALA* 3.3 3.0 + - - +
242M TYR* 1.3 79.4 - + + +
244M ARG* 1.3 56.4 + - - +
247M GLU* 3.3 13.0 - - + +
248M GLY 3.3 5.5 + - - -
249M GLN* 2.8 27.0 + - - +
251M VAL* 3.5 20.2 - - + -
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Residues in contact with ARG 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M PRO* 4.0 16.8 - - - +
240M ALA 3.4 9.7 + - - +
241M GLU* 3.1 32.4 + - - +
242M TYR 3.0 0.6 - - - -
243M PHE* 1.3 78.1 - - - +
245M ASP* 1.3 103.3 + - - +
248M GLY* 3.0 21.3 + - - -
249M GLN 4.0 4.9 + - - -
251M VAL* 4.1 11.4 - - + -
295M ARG 3.4 17.8 + - - -
297M THR 2.9 24.9 + - - +
299M THR* 3.9 18.2 - - - +
301M LYS* 4.1 0.3 - - - +
302M GLY* 3.7 33.6 + - - +
303M SER 4.1 1.8 - - - +
304M VAL* 3.6 18.5 - - + +
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Residues in contact with ASP 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M GLU* 2.8 23.0 + - - +
242M TYR* 5.2 0.4 - - - -
244M ARG* 1.3 119.6 + - - +
246M GLU* 1.3 74.7 + - + +
248M GLY* 3.9 2.9 + - - -
299M THR* 4.1 9.9 + - - +
301M LYS* 4.0 26.4 - - + +
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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