Contacts of the helix formed by residues 228 - 249 (chain D) in PDB entry 1F1H
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 MET 228 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA* 3.3 38.8 - - + +
111D ALA* 4.1 7.9 - - + -
112D GLU* 3.8 20.5 + - + +
124D VAL* 3.0 15.5 + - + -
126D PHE* 3.5 41.5 - - + -
226D ASN 3.5 1.3 + - - -
227D THR* 1.3 73.4 - - - +
229D THR* 1.3 64.8 + - - +
231D LYS* 3.2 3.1 + - - +
232D ALA* 3.1 16.1 + - - +
371D PHE* 3.6 34.9 - - + +
372D ALA* 3.7 15.5 - - - +
375D LEU* 4.2 13.2 - - + -
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Residues in contact with THR 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ARG* 4.3 15.3 - - + +
108D ALA* 3.4 38.1 + - + +
109D LYS* 3.7 25.5 + - + -
112D GLU* 3.1 22.0 + - - +
228D MET* 1.3 75.5 - - - +
230D LYS* 1.3 63.5 + - - +
232D ALA* 3.1 7.6 + - - +
233D ASP* 3.1 22.6 + - - +
368D TYR* 4.3 11.7 - - + -
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Residues in contact with LYS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D SER* 5.7 7.2 + - - -
226D ASN* 3.4 28.9 - - - +
227D THR* 3.2 21.8 + - - +
229D THR* 1.3 77.2 - - - +
231D LYS* 1.3 58.0 + - - +
233D ASP* 3.1 18.1 - - + +
234D GLU* 2.9 36.1 + - + +
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 3.4 25.8 - - + +
128D PRO* 3.3 35.0 - - + -
204D LEU* 5.0 0.8 - - - +
223D THR* 3.1 26.4 + - - -
224D ARG 2.8 21.9 + - - -
226D ASN* 4.0 15.8 - - + +
227D THR 2.8 16.4 + - - +
228D MET 3.5 4.5 - - - +
230D LYS* 1.3 77.8 - - - +
232D ALA* 1.3 56.6 + - - +
234D GLU* 2.8 34.8 + - - +
235D ILE* 2.9 32.0 + - - +
371D PHE* 4.1 2.5 - - + -
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA* 5.8 0.4 - - + -
228D MET* 3.1 7.8 + - + +
229D THR* 3.1 4.9 + - - +
231D LYS* 1.3 72.7 - - - +
233D ASP* 1.3 65.2 + - - +
235D ILE* 3.3 4.4 + - - +
236D GLN* 3.2 25.5 + - - +
367D PRO* 3.7 20.9 - - + +
368D TYR* 3.3 37.9 - - + +
371D PHE* 3.8 18.5 - - + -
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Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 4.3 6.0 - - + +
88D ARG* 3.4 19.4 + - - +
105D ARG* 2.9 34.7 + - - -
229D THR* 3.1 15.3 + - - +
230D LYS* 3.1 20.0 + - + +
232D ALA* 1.3 76.3 - - - +
234D GLU* 1.3 63.7 + - + +
236D GLN* 3.0 15.9 + - - +
237D ILE* 3.0 21.1 + - + +
368D TYR* 2.6 34.0 + - - -
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D GLY 4.0 14.0 - - - +
204D LEU* 3.8 30.8 - - + +
205D VAL 5.3 1.0 + - - -
224D ARG* 3.9 5.5 + - - +
226D ASN* 3.0 27.8 + - - -
230D LYS* 2.9 23.1 + - + +
231D LYS* 2.8 42.3 + - + +
233D ASP* 1.3 78.4 - - + +
235D ILE* 1.3 51.0 + - - +
237D ILE* 3.2 12.5 + - + +
238D TYR* 2.6 36.8 + - - +
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D PRO* 3.9 31.4 - - + -
130D PRO* 3.8 29.6 - - + -
223D THR* 5.8 1.8 - - - +
231D LYS* 2.9 20.7 + - + +
232D ALA 3.5 8.3 - - - +
233D ASP 3.2 0.4 - - - -
234D GLU* 1.3 74.6 - - - +
236D GLN* 1.3 63.9 + - - +
238D TYR* 3.3 8.9 + - + +
239D LYS* 2.8 44.4 + - + +
268D MET* 4.2 11.7 - - + -
367D PRO* 3.8 23.3 - - + -
371D PHE* 4.2 10.3 - - + -
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Residues in contact with GLN 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 2.8 30.4 + - - +
26D GLY 3.1 27.3 + - - +
28D GLU* 3.2 35.2 - - - +
88D ARG* 3.7 17.3 - - - +
232D ALA 3.2 13.7 + - - +
233D ASP 3.0 8.8 + - - +
235D ILE* 1.3 78.7 - - - +
237D ILE* 1.3 56.0 + - - +
239D LYS* 3.5 21.2 + - - +
240D TYR* 3.0 22.3 + - - +
367D PRO* 3.7 15.7 - - + +
368D TYR* 4.1 9.6 - - + +
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Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLU* 5.1 2.2 - - - +
73D THR 5.9 0.9 - - - +
75D VAL* 5.0 11.4 - - + -
88D ARG* 3.8 20.9 - - - +
199D MET* 5.2 0.7 - - - +
202D MET* 3.8 48.7 - - + +
204D LEU* 3.6 24.2 - - + -
233D ASP* 3.0 20.5 + - + +
234D GLU* 3.5 12.1 - - + +
236D GLN* 1.3 72.6 - - - +
238D TYR* 1.3 59.7 + - - +
240D TYR* 3.2 6.9 + - - +
241D VAL* 2.9 33.0 + - + +
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Residues in contact with TYR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PRO* 2.9 44.3 + - + -
132D PHE* 3.6 6.8 - + - -
199D MET* 3.5 32.1 - - + -
204D LEU* 4.2 7.2 - - + -
221D VAL* 2.9 45.9 + - + -
223D THR* 4.0 17.5 - - + -
234D GLU 2.6 21.5 + - - +
235D ILE* 3.3 13.0 - - + +
237D ILE* 1.3 74.8 - - - +
239D LYS* 1.3 66.4 + - + +
241D VAL* 3.2 2.4 + - - +
242D VAL* 2.9 36.0 + - + +
255D PHE* 3.8 23.3 - + - -
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLY 4.1 9.1 + - - +
27D LYS* 6.1 0.7 - - - +
130D PRO* 6.5 0.4 - - + -
235D ILE* 2.8 31.9 + - + +
236D GLN* 3.8 26.7 + - - +
238D TYR* 1.3 73.8 - - + +
240D TYR* 1.3 59.0 + - - +
242D VAL* 3.8 0.3 - - - +
243D HIS* 2.9 44.4 + - + +
255D PHE* 3.7 39.0 - - + -
268D MET* 6.4 0.4 - - - -
363D PRO* 3.2 27.5 + - - -
364D ALA 5.0 2.6 + - - -
365D ALA 4.0 11.5 + - - -
367D PRO* 4.5 1.4 - - - +
468J VAL* 3.3 28.3 + - - +
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Residues in contact with TYR 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 4.0 18.6 - - + -
183C PRO* 3.6 18.5 - - + +
20D ARG* 3.4 28.2 + - - +
28D GLU* 3.9 6.7 - - - +
77D ASP* 2.6 33.3 + - - -
79D PHE* 3.4 25.0 - + - +
80D PHE* 3.2 20.6 - - - -
202D MET* 4.3 17.9 - - + -
236D GLN 3.0 15.4 + - - +
237D ILE* 3.2 10.9 + - - +
239D LYS* 1.3 76.9 - - - +
241D VAL* 1.3 59.2 + - - +
243D HIS* 3.8 3.5 - - - +
244D ASN* 2.9 57.4 + - - +
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 4.1 8.1 - - + -
195D MET* 3.6 28.0 - - + +
198D VAL* 3.9 16.8 - - + -
199D MET* 3.8 19.1 - - + -
202D MET* 3.6 28.9 - - - -
237D ILE* 2.9 21.8 + - + +
238D TYR 3.8 3.1 - - - +
240D TYR* 1.3 75.3 - - + +
242D VAL* 1.3 59.1 + - - +
245D VAL* 2.8 53.0 + - + +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 3.8 32.8 - - + -
195D MET* 3.7 13.7 - - + +
199D MET* 3.6 20.6 - - + -
238D TYR* 2.9 37.1 + - + +
239D LYS 3.8 3.4 - - - +
241D VAL* 1.3 75.9 - - - +
243D HIS* 1.3 64.1 + - - +
246D ALA* 3.0 27.5 + - - +
253D ALA* 3.7 18.6 - - + -
255D PHE* 3.7 17.7 - - + -
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Residues in contact with HIS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C HIS* 3.7 20.3 - + - -
183C PRO 5.1 0.2 - - - +
184C PRO* 3.8 23.6 - - + +
27D LYS* 3.8 21.2 + - - -
239D LYS* 2.9 31.0 + - + +
240D TYR* 3.8 5.1 - - - +
242D VAL* 1.3 73.3 - - - +
244D ASN* 1.3 58.4 + - - +
246D ALA* 3.5 2.8 - - - +
247D HIS* 3.0 26.9 + - - +
252D THR* 5.8 0.5 - - - -
253D ALA* 3.2 35.9 + - + +
254D THR* 4.6 1.8 - - - -
255D PHE* 3.7 21.1 - + - -
467J SER 4.5 1.7 + - - -
468J VAL 3.7 22.3 + - - -
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Residues in contact with ASN 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C PRO* 3.0 31.4 - - - +
184C PRO* 3.6 21.2 - - - +
79D PHE* 3.5 35.0 - - + +
80D PHE* 6.0 0.2 - - - -
240D TYR* 2.9 40.7 + - - +
243D HIS* 1.3 73.3 - - - +
245D VAL* 1.3 59.5 + - - +
246D ALA 3.2 1.1 - - - -
247D HIS* 3.6 9.3 - - - +
248D ARG* 3.0 28.2 + - - +
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Residues in contact with VAL 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 3.8 16.8 - - + -
191D ILE* 4.1 4.5 - - + +
194D GLU* 4.1 11.2 - - + +
195D MET* 3.7 29.2 - - + +
198D VAL* 4.4 10.3 - - + -
241D VAL* 2.8 42.7 + - + +
244D ASN* 1.3 69.5 - - - +
246D ALA* 1.3 65.8 + - - +
248D ARG* 3.2 10.6 + - - +
249D PHE* 3.0 45.7 + - + -
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Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU* 3.8 26.2 - - + -
191D ILE* 5.0 2.0 - - - -
195D MET* 4.2 5.3 - - + +
242D VAL 3.0 19.0 + - - +
243D HIS 3.5 4.5 - - - +
245D VAL* 1.3 77.8 - - - +
247D HIS* 1.3 62.7 + - - +
249D PHE* 2.9 10.4 + - - -
250D GLY 3.3 0.2 + - - -
251D LYS* 2.9 34.2 + - + +
253D ALA* 3.9 16.6 - - + +
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Residues in contact with HIS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LYS* 4.6 21.4 - - + +
171C HIS* 5.9 2.2 - - - -
184C PRO* 4.1 28.1 - - + +
243D HIS 3.0 14.5 + - - +
244D ASN* 3.6 13.9 - - - +
246D ALA* 1.3 80.7 - - - +
248D ARG* 1.3 59.9 - - + +
250D GLY* 3.0 20.4 + - - -
251D LYS 3.4 12.1 + - - +
252D THR* 6.2 0.2 - - - -
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Residues in contact with ARG 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PRO* 4.2 10.5 + - - +
79D PHE* 3.8 34.0 - - + -
194D GLU* 2.9 31.1 + - - -
198D VAL* 4.5 8.1 - - - +
244D ASN 3.0 18.9 + - - +
245D VAL* 3.2 11.7 + - - +
247D HIS* 1.3 79.1 - - - +
249D PHE* 1.3 74.9 + - - +
250D GLY 3.4 0.6 + - - -
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Residues in contact with PHE 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ASP* 4.4 9.6 - - + -
191D ILE* 3.7 40.6 - - + -
194D GLU* 3.7 28.3 - - + -
245D VAL* 3.0 34.7 + - + +
246D ALA 2.9 10.0 + - - +
248D ARG* 1.3 94.9 - - + +
250D GLY* 1.3 61.3 + - - +
251D LYS* 3.3 15.8 + - + +
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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) + - + + + + + -
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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