Contacts of the helix formed by residues 213 - 233 (chain B) in PDB entry 1UW9
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 ARG 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 5.4 0.4 - - - +
110A GLU* 2.8 42.8 + - - -
208B SER* 3.5 14.3 + - - +
209B GLN* 3.4 29.2 + - - +
210B PRO* 3.6 22.1 + - - +
212B MET* 1.3 75.4 - - - +
214B TRP* 1.3 68.5 + - + +
215B ARG* 3.4 3.1 - - + +
216B ASP* 3.4 24.5 + - - +
217B ARG* 3.2 18.8 + - - +
149E VAL 5.3 5.3 + - - -
152E PRO 5.6 0.4 - - - +
285E ARG* 3.7 46.7 - - - +
372E PRO* 6.0 6.9 - - - +
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Residues in contact with TRP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASN 3.4 18.4 - - - +
208B SER* 3.0 27.8 + - - -
212B MET 3.9 0.4 + - - -
213B ARG* 1.3 73.3 - - + +
215B ARG* 1.3 92.2 + - + +
217B ARG* 3.1 19.6 + - - +
218B PHE* 2.9 48.5 + + + -
249B GLU* 3.9 5.3 + - - -
252B LYS* 3.8 31.8 - - + +
253B ARG* 3.5 51.8 - - + +
256B SMC 3.5 39.0 - - + -
286E ASP* 5.3 10.4 + - - -
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ARG* 3.4 2.3 - - + +
214B TRP* 1.3 113.9 - - + +
216B ASP* 1.3 65.0 + - - +
218B PHE* 3.3 2.1 + - - +
219B LEU* 3.1 52.0 + - - +
256B SMC 3.8 20.9 - - - +
161E LYS* 5.0 2.5 - - - +
258E LYS* 4.6 2.8 - - - +
285E ARG* 3.8 15.5 - - - +
286E ASP* 3.1 32.3 + - - +
287E ASN* 3.5 21.0 + - - +
288E GLY* 3.6 19.2 - - - +
63F VAL* 3.8 37.0 + - - +
65F CYS* 4.9 2.6 + - - +
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Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.6 18.8 - - + -
213B ARG* 3.4 25.8 + - - +
215B ARG* 1.3 79.4 - - - +
217B ARG* 1.3 62.1 + - - +
219B LEU* 3.3 4.3 + - - +
220B PHE* 3.1 28.3 + - + -
152E PRO 5.0 3.3 - - - +
153E HIS* 3.5 12.7 + - - -
157E VAL* 3.4 32.8 - - + +
161E LYS* 3.0 32.6 + - - +
285E ARG* 6.0 1.7 - - - -
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.5 11.1 - - - +
185B TYR* 3.7 14.4 - - + -
202B ASP* 2.8 41.7 + - - -
206B VAL* 3.4 20.7 + - - +
207B ASN* 2.7 32.9 + - - +
209B GLN* 5.5 0.2 + - - -
212B MET* 3.6 37.9 + - - +
213B ARG 3.2 3.5 + - - +
214B TRP* 3.1 18.7 + - - +
216B ASP* 1.3 78.7 - - - +
218B PHE* 1.3 76.4 + - - +
220B PHE* 3.3 1.4 + - - +
221B VAL* 2.8 47.8 + - + +
240B LEU* 4.6 2.2 - - + +
241B ASN 4.1 4.4 + - - -
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TRP* 2.9 53.1 + + + -
215B ARG 3.3 8.7 + - - +
217B ARG* 1.3 97.0 - - - +
219B LEU* 1.3 53.9 + - - +
221B VAL* 4.0 1.2 - - - +
222B THR* 2.8 38.3 + - - -
240B LEU* 3.6 48.0 - - + +
241B ASN 3.4 21.3 - - - -
242B ALA* 4.9 0.4 - - - -
253B ARG* 3.3 29.4 - - + -
256B SMC 3.8 14.8 - - + -
257B ALA* 4.3 7.2 - - + -
260B LEU* 4.1 12.3 - - + -
265B ILE* 5.4 1.1 - - + -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG* 3.1 45.6 + - - +
216B ASP* 3.6 9.4 - - - +
217B ARG 3.1 0.2 - - - -
218B PHE* 1.3 75.7 - - - +
220B PHE* 1.3 69.0 + - + +
222B THR* 3.2 7.5 + - - -
223B GLU* 3.1 17.8 + - - +
256B SMC 4.7 2.0 - - + -
260B LEU* 4.3 22.7 - - + -
161E LYS* 4.6 16.4 - - + +
63F VAL 4.7 3.6 - - - +
65F CYS 3.5 24.0 - - - +
66F LEU 3.7 19.1 - - - +
67F TYR* 4.0 23.7 - - + +
71F ARG* 5.1 2.8 + - - +
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.6 19.3 - - + +
183B LYS* 3.5 31.9 - - + -
186B GLY* 4.2 2.2 - - - -
216B ASP* 3.1 26.6 + - + +
217B ARG 4.0 1.1 - - - +
219B LEU* 1.3 77.0 - - + +
221B VAL* 1.3 62.9 + - - +
223B GLU* 3.2 8.1 + - - +
224B ALA* 3.0 17.7 + - - +
157E VAL* 5.2 3.6 - - + -
160E ASP* 3.6 44.9 - - + -
161E LYS* 3.7 23.1 - - + -
71F ARG* 4.2 25.1 - - + -
72F TYR* 3.4 36.7 - + - +
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 4.2 16.6 - - + -
186B GLY* 4.4 7.6 - - - +
189B VAL* 4.2 13.5 - - + -
217B ARG* 2.8 37.0 + - + +
218B PHE 4.0 2.0 - - - +
220B PHE* 1.3 75.8 - - - +
222B THR* 1.3 58.4 + - - +
224B ALA* 3.1 7.5 + - - +
225B ILE* 2.8 33.9 + - + +
238B HIS* 3.5 42.2 - - + +
240B LEU* 3.8 11.7 - - + -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PHE 2.8 24.6 + - - -
219B LEU* 3.4 7.0 - - - -
220B PHE 3.2 0.2 - - - -
221B VAL* 1.3 76.2 - - - +
223B GLU* 1.3 62.3 + - - +
225B ILE* 3.3 9.9 + - - +
226B TYR* 3.1 51.8 + - + -
240B LEU* 4.7 2.3 - - - +
260B LEU* 3.4 20.1 - - + +
262B VAL* 3.5 19.2 - - + +
60F PHE* 4.1 12.6 - - + -
67F TYR* 4.1 10.8 - - + -
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU 3.1 9.6 + - - +
220B PHE* 3.5 10.6 - - - +
222B THR* 1.3 78.0 - - - +
224B ALA* 1.3 56.6 + - - +
226B TYR* 3.9 1.2 - - - +
227B LYS* 3.0 32.7 + - + +
67F TYR* 3.4 26.0 + - + +
68F TYR 3.2 18.2 - - - +
69F ASP* 4.3 7.0 - - - +
70F ASN* 3.5 4.9 + - - +
71F ARG* 2.9 45.1 + - - +
72F TYR* 3.0 46.7 + - + +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLY 3.2 28.9 - - - +
189B VAL* 3.7 8.7 - - + -
190B TYR* 3.5 24.9 - - + +
193B LEU* 4.6 1.3 - - - -
220B PHE 3.0 11.9 + - - +
221B VAL 3.4 8.1 - - - +
223B GLU* 1.3 73.6 - - - +
225B ILE* 1.3 65.5 + - - +
227B LYS* 3.4 3.8 + - - +
228B ALA* 3.0 26.0 + - - +
72F TYR* 4.4 5.1 - - + -
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 4.9 0.2 - - + -
193B LEU* 3.9 15.7 - - + -
221B VAL* 2.8 30.0 + - + +
222B THR* 3.3 4.0 + - - +
224B ALA* 1.3 73.8 - - - +
226B TYR* 1.3 76.3 + - + +
228B ALA* 3.9 1.7 - - - +
229B GLN* 2.9 30.4 + - - +
236B LYS* 3.5 30.7 - - + +
237B GLY* 4.4 1.1 - - - -
238B HIS* 3.8 41.3 - - + +
240B LEU* 5.3 1.6 - - + -
262B VAL* 4.0 26.9 - - + -
263B PRO* 4.7 4.3 - - + -
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Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR* 3.1 37.1 + - + +
223B GLU 4.2 1.8 - - - +
225B ILE* 1.3 92.0 - - + +
227B LYS* 1.3 65.6 + - - +
229B GLN* 3.9 17.7 - - - +
230B ALA* 3.0 25.6 + - - +
260B LEU 2.7 24.0 + - - -
261B GLY 3.2 11.7 + - - -
262B VAL* 3.6 8.9 + - + -
263B PRO* 5.7 0.9 - - + -
54C ASN* 5.8 2.0 - - - -
68C TYR* 5.4 3.6 - + - -
56F SER* 3.5 34.5 - - - +
59F ARG* 3.0 39.2 + - - -
60F PHE* 4.1 8.7 - + - -
67F TYR* 3.9 3.8 - - - +
69F ASP* 4.7 1.3 - - - +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.4 44.5 + - + -
223B GLU* 3.0 23.0 + - + +
224B ALA* 3.8 3.8 - - - +
226B TYR* 1.3 76.6 - - - +
228B ALA* 1.3 57.4 + - - +
230B ALA* 3.3 6.1 + - - +
231B GLU* 2.9 33.8 + - + +
45F ALA* 5.7 1.8 - - - +
49F LYS* 4.2 33.4 - - + +
69F ASP* 5.7 0.8 + - - -
70F ASN* 4.8 6.9 + - - +
72F TYR* 3.4 40.4 + - + +
73F TRP* 4.2 6.5 - - - +
74F THR* 4.5 3.0 + - - -
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 3.9 15.4 - - + +
193B LEU* 3.5 31.2 - - + -
194B ARG* 3.8 15.0 - - - +
224B ALA 3.0 16.8 + - - +
225B ILE 3.9 2.0 - - - +
227B LYS* 1.3 76.2 - - - +
229B GLN* 1.3 58.6 + - - +
231B GLU* 3.3 3.5 + - - -
232B THR* 2.8 36.4 + - - +
236B LYS* 4.1 3.6 - - + -
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 2.9 23.0 + - - +
226B TYR* 3.9 15.6 - - + +
227B LYS 3.3 0.2 - - - -
228B ALA* 1.3 76.7 - - - +
230B ALA* 1.3 57.2 + - - +
233B GLY* 2.8 30.0 + - - -
234B GLU 3.3 22.9 - - - +
235B VAL* 3.4 13.4 - - - +
236B LYS* 3.0 37.8 + - + +
52C VAL* 3.5 25.9 - - + +
54C ASN* 4.9 5.0 + - - +
68C TYR* 3.6 22.6 + - - -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR 3.0 17.9 + - - +
227B LYS* 3.7 4.7 - - - +
229B GLN* 1.3 77.4 - - - +
231B GLU* 1.3 62.1 + - - +
233B GLY* 4.0 1.4 + - - -
10C LYS* 3.2 23.9 + - - -
49F LYS* 4.3 22.4 - - - +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 2.6 28.8 + - - -
194B ARG* 2.9 44.6 + - - +
227B LYS* 2.9 21.7 + - + +
228B ALA* 3.6 5.6 - - - +
229B GLN 3.3 0.2 - - - -
230B ALA* 1.3 78.6 - - - +
232B THR* 1.3 62.2 + - + +
4C TRP* 5.2 0.5 - - - -
5C THR 4.4 1.3 - - - +
6C PRO* 3.4 38.6 - - + +
9C ASN* 4.2 6.0 + - + +
10C LYS* 4.0 23.3 + - - +
49F LYS* 6.3 1.1 - - - +
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 3.5 36.1 - - + +
228B ALA 2.8 20.8 + - - +
231B GLU* 1.3 82.9 - - + +
233B GLY* 1.3 64.2 + - - +
234B GLU* 3.2 17.0 + - - -
236B LYS* 3.3 22.2 - - - +
9C ASN 4.7 3.4 - - - +
10C LYS* 3.6 3.7 - - - +
11C MET* 2.8 42.1 + - + +
17C TYR* 4.8 5.6 - - - +
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLN* 2.8 14.3 + - - -
230B ALA* 4.0 2.9 + - - -
231B GLU 3.6 1.8 - - - -
232B THR* 1.3 77.3 - - - +
234B GLU* 1.3 62.0 + - - +
235B VAL 4.4 0.2 + - - -
10C LYS* 4.1 6.5 - - - +
11C MET 4.6 1.5 - - - +
12C PHE* 5.9 0.2 - - - -
13C GLU* 5.9 0.2 - - - +
51C TYR* 3.9 33.5 - - - -
52C VAL* 4.9 14.7 + - - +
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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
------------------------------------------------------------
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