Contacts of the helix formed by residues 178 - 204 (chain D) in PDB entry 1FP1
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 ASP 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D TYR* 2.7 28.4 + - - -
174D PHE* 4.1 17.4 - - + +
175D MET* 2.9 14.1 - - - +
176D GLY 2.7 6.1 + - - -
177D LYS* 1.3 95.4 - - - +
179D LYS* 1.3 60.1 + - - +
180D LYS* 3.0 8.8 - - - +
181D MET* 2.7 37.9 + - + +
182D ASN* 3.6 6.8 + - - +
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Residues in contact with LYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D MET* 3.9 34.1 - - - -
176D GLY* 3.8 18.1 + - - +
178D ASP* 1.3 72.9 - - - +
180D LYS* 1.3 58.2 + - - +
182D ASN* 3.9 7.4 - - + +
183D GLN* 3.1 27.7 + - - +
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Residues in contact with LYS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TYR* 3.2 30.0 + - + +
142D PRO* 5.7 5.3 - - - +
178D ASP* 3.0 11.8 - - - +
179D LYS* 1.3 77.1 - - - +
181D MET* 1.3 63.0 + - - +
183D GLN* 3.0 9.3 + - - +
184D ILE* 2.9 36.4 + - + +
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Residues in contact with MET 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE* 4.1 19.2 - - + -
141D TYR* 3.3 43.2 + - + -
143D ALA* 4.4 4.5 - - - -
144D LEU* 3.8 27.1 - - + -
174D PHE* 3.9 32.3 - - + +
178D ASP* 2.7 20.5 + - + +
180D LYS* 1.3 72.8 - - - +
182D ASN* 1.3 58.7 + - - +
184D ILE* 3.2 4.0 + - - +
185D PHE* 2.8 31.2 + - + +
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Residues in contact with ASN 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D MET* 3.0 49.2 - - + +
178D ASP 3.6 8.0 + - - +
179D LYS* 3.9 9.2 - - - +
180D LYS 3.2 0.2 - - - -
181D MET* 1.3 79.2 - - - +
183D GLN* 1.3 55.8 + - - +
185D PHE* 3.4 8.9 + - - +
186D ASN* 2.6 65.0 + - - +
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Residues in contact with GLN 183 (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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179D LYS 3.1 17.0 + - - +
180D LYS* 3.0 8.0 + - - +
182D ASN* 1.3 81.0 + - - +
184D ILE* 1.3 69.7 + - - +
186D ASN* 4.0 5.4 - - - +
187D LYS* 3.0 68.8 + - - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 4.6 2.4 - - - +
137D THR* 4.1 22.4 - - + -
138D PHE* 3.6 35.7 - - + +
141D TYR* 3.6 35.4 - - + -
180D LYS* 2.9 27.3 + - + +
181D MET* 3.7 7.2 - - - +
183D GLN* 1.3 84.8 - - - +
185D PHE* 1.3 66.1 + - - +
187D LYS* 3.5 4.6 + - - +
188D SER* 3.1 22.3 + - - -
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Residues in contact with PHE 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D PHE* 5.1 0.2 - + - -
138D PHE* 3.6 39.5 - + + -
181D MET* 2.8 23.9 + - + +
182D ASN* 3.7 9.4 - - - +
184D ILE* 1.3 73.0 - - - +
186D ASN* 1.3 77.8 + - - +
188D SER* 2.7 20.8 + - - -
189D MET* 3.1 54.9 + - + +
2000D HCC 3.7 32.5 - + - -
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Residues in contact with ASN 186 (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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182D ASN* 2.6 57.8 + - - +
183D GLN* 4.0 5.3 - - - +
185D PHE* 1.3 87.1 - - - +
187D LYS* 1.3 63.8 + - - +
189D MET* 3.2 7.5 + - - +
190D VAL* 3.1 29.6 + - + +
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Residues in contact with LYS 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 4.7 7.2 - - - -
183D GLN* 3.0 47.0 + - - +
184D ILE* 3.8 5.8 - - - +
186D ASN* 1.3 75.8 - - - +
188D SER* 1.3 63.7 + - - +
190D VAL* 3.2 10.3 + - + +
191D ASP* 3.1 41.4 + - - +
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Residues in contact with SER 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 3.4 35.6 + - - -
135D PHE* 3.4 31.1 - - - -
138D PHE* 4.0 4.2 - - - +
184D ILE 3.1 11.8 + - - -
185D PHE* 2.7 22.2 + - - -
187D LYS* 1.3 76.0 - - - +
189D MET* 1.3 58.5 + - - +
191D ASP* 3.9 0.3 - - - +
192D VAL* 3.0 36.8 + - - +
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Residues in contact with MET 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D PHE* 4.9 5.4 - - - -
185D PHE* 3.1 51.9 + - + +
186D ASN* 3.2 9.4 + - - +
188D SER* 1.3 78.0 + - - +
190D VAL* 1.3 62.3 + - + +
192D VAL* 4.1 4.4 - - - +
193D CYS* 2.9 35.1 + - - +
275D ALA* 6.6 0.4 - - + -
1699D SAH 5.2 18.8 - - + +
2000D HCC 3.4 39.9 - - - +
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Residues in contact with VAL 190 (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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186D ASN* 3.1 18.0 + - + +
187D LYS* 3.2 11.2 + - + +
189D MET* 1.3 79.0 - - + +
191D ASP* 1.3 65.8 + - - +
193D CYS* 3.7 4.1 - - - +
194D ALA* 3.0 30.7 + - + +
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Residues in contact with ASP 191 (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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131D TYR* 3.3 36.7 + - + +
134D SER* 2.6 33.4 + - - +
187D LYS* 3.1 22.6 + - - +
188D SER 3.9 0.7 - - - +
190D VAL* 1.3 82.8 - - - +
192D VAL* 1.3 64.4 + - + +
194D ALA* 3.3 6.1 + - - +
195D THR* 2.9 27.9 + - - -
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Residues in contact with VAL 192 (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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131D TYR 4.9 1.6 - - - +
132D LEU* 4.3 17.9 - - + +
135D PHE* 4.1 15.9 - - + +
188D SER 3.0 21.5 + - - +
189D MET* 4.1 4.9 - - - +
191D ASP* 1.3 75.3 - - + +
193D CYS* 1.3 58.7 + - - +
195D THR* 3.1 7.7 + - - -
196D GLU* 2.9 45.2 + - + +
2000D HCC 3.7 59.0 - - + +
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Residues in contact with CYS 193 (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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189D MET 2.9 20.7 + - - +
190D VAL* 3.7 4.9 - - - +
192D VAL* 1.3 77.9 - - - +
194D ALA* 1.3 56.7 + - - +
196D GLU* 3.2 10.4 + - - +
197D MET* 2.8 35.1 + - - +
223D ASN* 3.1 42.2 - - - -
274D LYS* 3.6 19.1 - - - +
1699D SAH 3.8 10.3 - - - +
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Residues in contact with ALA 194 (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 GLY* 5.4 3.8 - - - -
190D VAL* 3.0 21.8 + - + +
191D ASP* 3.7 6.3 - - - +
192D VAL 3.3 0.2 - - - -
193D CYS* 1.3 75.3 - - - +
195D THR* 1.3 62.2 + - - +
197D MET* 4.0 5.7 - - - +
198D LYS* 3.0 26.0 + - - +
223D ASN* 5.8 0.2 - - - -
226D LEU* 5.1 8.9 - - + +
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Residues in contact with THR 195 (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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122D TYR* 4.4 11.9 - - + -
129D ARG 3.8 20.7 - - - +
130D GLY* 3.2 18.7 - - - -
131D TYR 3.3 9.5 + - - -
132D LEU* 3.9 25.4 - - + +
191D ASP 2.9 18.0 + - - -
192D VAL 3.1 8.9 + - - -
194D ALA* 1.3 79.3 - - - +
196D GLU* 1.3 62.9 + - + +
198D LYS* 3.6 2.6 + - - +
199D ARG* 3.6 13.7 + - - +
362D PHE* 3.7 19.1 - - + -
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Residues in contact with GLU 196 (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 LEU* 6.4 0.2 - - + -
192D VAL* 2.9 33.2 + - + +
193D CYS* 3.7 12.3 + - - +
195D THR* 1.3 78.9 - - - +
197D MET* 1.3 57.8 + - - +
199D ARG* 3.5 2.1 + - - +
200D MET* 3.0 30.9 + - - +
274D LYS* 2.8 36.3 + - - -
307D PHE* 3.4 30.3 - - + -
361D ALA* 5.2 0.2 - - - +
362D PHE* 3.9 16.6 - - + -
365D LEU* 3.7 25.7 - - + +
2000D HCC 4.1 4.2 - - + +
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Residues in contact with MET 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D CYS* 2.8 21.7 + - - +
194D ALA 4.1 1.6 - - - +
196D GLU* 1.3 77.1 - - - +
198D LYS* 1.3 64.4 + - - +
200D MET* 4.1 21.1 - - + -
201D LEU* 3.0 35.3 + - + +
223D ASN* 3.3 39.9 - - + +
226D LEU* 3.7 21.8 - - + -
227D ILE* 3.4 34.5 - - + -
272D ILE* 5.6 2.9 - - + -
274D LYS* 3.9 26.9 - - - -
305D VAL* 6.0 0.4 - - - -
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Residues in contact with LYS 198 (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 SER* 3.4 31.9 + - - +
129D ARG* 3.2 49.4 - - - +
194D ALA 3.0 18.3 + - - +
195D THR 3.9 4.9 - - - +
196D GLU 3.3 0.4 - - - -
197D MET* 1.3 79.1 - - - +
199D ARG* 1.3 60.2 + - - +
201D LEU* 3.5 5.8 + - - +
202D GLU* 3.0 31.1 + - + +
226D LEU* 5.5 1.0 - - - +
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Residues in contact with ARG 199 (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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129D ARG* 4.2 13.5 - - - +
195D THR 3.6 3.4 + - - +
196D GLU 3.5 1.2 + - - +
197D MET 3.3 0.2 - - - -
198D LYS* 1.3 76.5 - - - +
200D MET* 1.3 66.9 + - - +
202D GLU* 2.8 58.3 + - - +
203D ILE* 3.3 34.0 + - + +
361D ALA* 3.4 29.4 - - + +
362D PHE* 3.5 36.3 - - + +
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Residues in contact with MET 200 (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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196D GLU 3.0 19.5 + - - +
197D MET* 3.8 29.6 - - + +
199D ARG* 1.3 77.6 - - - +
201D LEU* 1.3 61.2 + - - +
203D ILE* 3.3 9.2 + - - +
204D TYR* 2.9 43.8 + - + +
207D PHE* 3.8 37.2 - - + -
272D ILE* 4.2 4.5 - - + -
303D ILE* 5.8 0.2 - - + -
305D VAL* 4.0 29.6 - - + -
361D ALA* 4.7 5.6 - - + +
365D LEU* 5.3 4.5 - - + -
367D VAL* 3.7 25.8 - - + -
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Residues in contact with LEU 201 (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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197D MET* 3.0 25.3 + - + +
198D LYS* 3.9 5.2 - - - +
200D MET* 1.3 78.5 - - - +
202D GLU* 1.3 55.0 + - + +
203D ILE 3.3 0.2 - - - -
204D TYR 4.1 9.5 - - - +
207D PHE* 3.7 19.3 - - + -
226D LEU* 3.9 39.3 - - + +
227D ILE* 3.3 31.9 - - + -
230D LYS* 2.6 41.9 + - + +
231D TYR* 4.3 12.7 + - + +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ARG* 2.4 37.6 + - - -
198D LYS* 3.0 25.5 + - + +
199D ARG* 2.8 48.4 + - - +
201D LEU* 1.3 78.9 - - + +
203D ILE* 1.3 60.0 + - - +
204D TYR 5.3 0.2 - - - -
205D THR* 6.0 0.9 - - - +
230D LYS* 4.4 6.0 + - - +
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Residues in contact with ILE 203 (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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199D ARG* 3.5 43.5 - - + +
200D MET* 3.5 11.4 - - - +
202D GLU* 1.3 80.7 - - - +
204D TYR* 1.3 65.5 + - - +
205D THR* 3.6 11.2 + - - +
359D CYS* 3.9 26.7 - - + +
360D ARG 3.3 34.3 - - - +
361D ALA* 3.9 15.7 - - + +
367D VAL* 5.6 1.1 - - + -
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Residues in contact with TYR 204 (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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200D MET* 2.9 26.4 + - + +
201D LEU* 4.1 9.2 - - - +
202D GLU 5.3 0.2 - - - -
203D ILE* 1.3 76.7 - - - +
205D THR* 1.3 62.5 + - - +
206D GLY* 3.3 32.7 + - - -
207D PHE* 3.5 38.5 - + + -
230D LYS* 5.2 0.3 + - - -
231D TYR* 3.7 13.3 + - - -
301D LYS* 3.6 2.1 + - - -
303D ILE* 3.2 30.2 - - + +
358D ALA* 3.7 18.4 - - + -
359D CYS* 3.8 13.2 - - - -
367D VAL* 3.6 31.4 - - + -
369D GLU* 2.6 32.2 + - - +
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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