Contacts of the helix formed by residues 203 - 227 (chain B) in PDB entry 1NLW
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 LYS 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B ARG* 1.3 71.4 + - + +
205B ALA* 3.2 5.6 - - - +
206B HIS* 3.0 36.5 + - + +
207B HIS* 2.9 27.3 + - - +
104F G 4.3 30.4 + - - +
105F T 4.3 25.6 + - - +
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 1.3 78.7 - - + +
205B ALA* 1.3 54.3 + - - +
207B HIS* 4.2 10.5 - - + +
208B ASN* 2.7 43.0 + - - +
312G T 3.8 34.4 + - + +
313G G 3.3 34.2 + - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS 3.2 4.2 - - - +
204B ARG* 1.3 77.4 - - - +
206B HIS* 1.3 56.2 + - - +
208B ASN* 3.5 10.4 - - - +
209B ALA* 3.1 24.9 + - - +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 3.0 33.2 + - + +
205B ALA* 1.3 76.6 - - - +
207B HIS* 1.3 66.3 + - - +
208B ASN 3.1 1.3 - - - -
209B ALA* 3.0 10.3 + - + +
210B LEU* 3.0 57.3 + - + +
213B LYS* 6.2 0.4 - - - -
105F T 2.6 32.3 + - - -
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 2.9 19.3 + - - +
204B ARG* 3.7 13.7 - - - +
206B HIS* 1.3 77.9 - - - +
208B ASN* 1.3 64.2 + - - +
210B LEU* 3.3 11.1 + - + +
211B GLU* 3.0 25.8 + - + +
105F T 6.2 7.0 - + + -
106F A 5.2 7.7 + - - -
107F G 3.8 10.5 + - - -
108F C 4.8 2.0 + - - -
312G T 4.0 18.1 - - + +
313G G 3.0 51.7 + + - -
314G C 4.0 6.4 + - - -
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Residues in contact with ASN 208 (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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204B ARG* 2.7 30.4 + - - +
205B ALA* 3.5 9.5 - - - +
207B HIS* 1.3 81.5 + - - +
209B ALA* 1.3 56.0 + - - +
211B GLU* 3.6 1.7 + - - +
212B ARG* 3.0 29.0 + - - +
215B ARG* 5.1 1.2 + - - -
311G G 3.5 47.5 + - - +
312G T 2.8 45.9 + - + +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA 3.1 13.8 + - - +
206B HIS* 3.0 16.2 + - - +
208B ASN* 1.3 78.2 - - - +
210B LEU* 1.3 56.7 + - - +
212B ARG* 3.4 11.1 + - - +
213B LYS* 2.9 43.2 + - - +
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Residues in contact with LEU 210 (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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206B HIS* 3.0 56.2 + - + +
207B HIS* 3.8 9.2 - - + +
209B ALA* 1.3 74.3 - - + +
211B GLU* 1.3 61.9 + - - +
213B LYS* 3.2 27.6 + - + +
214B ARG* 2.9 27.0 + - - +
105F T 3.4 34.1 - - + +
106F A 3.8 23.9 + - - +
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Residues in contact with GLU 211 (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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207B HIS* 3.0 22.2 + - + +
208B ASN 4.0 2.0 - - - +
210B LEU* 1.3 73.4 - - - +
212B ARG* 1.3 60.9 + - - +
214B ARG* 3.0 44.4 + - - +
215B ARG* 2.8 66.8 + - - +
107F G 4.1 2.6 - - - +
108F C 3.1 27.4 + - - +
109F A 3.7 8.7 + - - -
312G T 3.5 21.3 - - + +
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Residues in contact with ARG 212 (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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208B ASN 3.0 16.7 + - - +
209B ALA* 3.5 10.9 - - - +
210B LEU 3.2 0.2 - - - -
211B GLU* 1.3 77.7 - - - +
213B LYS* 1.3 60.9 + - - +
215B ARG* 3.3 14.1 + - - +
216B ASP* 3.0 33.9 + - - +
310G C 3.7 36.7 + - - +
311G G 3.5 22.6 + - - +
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Residues in contact with LYS 213 (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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206B HIS* 6.2 0.7 - - - -
209B ALA* 2.9 33.8 + - - +
210B LEU* 3.4 30.7 - - + +
212B ARG* 1.3 72.8 - - + +
214B ARG* 1.3 68.0 + - - +
216B ASP* 3.2 7.5 + - - +
217B HIS* 3.1 42.9 + - + +
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Residues in contact with ARG 214 (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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38A THR 4.8 0.4 + - - -
39A THR* 5.8 0.2 - - - -
210B LEU 2.9 13.9 + - - +
211B GLU* 3.0 45.0 + - - +
213B LYS* 1.3 77.9 - - - +
215B ARG* 1.3 69.8 + - - +
217B HIS* 3.3 12.4 + - - +
218B ILE* 3.3 45.1 + - + +
106F A 4.3 9.2 - - + +
107F G 3.2 64.7 + - - +
108F C 3.6 28.5 + - - +
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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
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208B ASN 5.1 1.0 + - - -
211B GLU* 2.8 44.5 + - - +
212B ARG* 3.4 26.8 - - - +
214B ARG* 1.3 80.3 - - - +
216B ASP* 1.3 58.7 + - - +
218B ILE* 3.2 11.4 + - + +
219B LYS* 2.9 29.0 + - - +
239B ARG* 4.7 4.1 + - - +
109F A 5.5 0.2 - - - +
110F C 5.9 0.2 - - - +
309G A 4.5 7.6 - - + -
310G C 3.3 59.1 + - - +
311G G 2.4 46.3 + - - -
312G T 4.4 0.2 - - - +
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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
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212B ARG* 3.0 30.8 + - - +
213B LYS* 3.2 12.3 + - - +
215B ARG* 1.3 77.8 - - - +
217B HIS* 1.3 62.2 + - + +
219B LYS* 3.3 14.6 + - - +
220B ASP* 2.9 34.9 + - - +
310G C 4.5 9.4 + - - -
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Residues in contact with HIS 217 (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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40A LEU* 4.7 16.4 - - + +
213B LYS* 3.1 29.8 + - + +
214B ARG* 3.7 10.7 - - - +
215B ARG 3.3 0.4 - - - -
216B ASP* 1.3 80.2 - - + +
218B ILE* 1.3 58.4 + - + +
220B ASP* 3.3 13.2 + - - +
221B SER* 3.0 31.3 + - - -
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Residues in contact with ILE 218 (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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38A THR 4.6 9.0 - - - +
39A THR* 4.5 10.3 - - + -
40A LEU* 4.5 23.6 - - + +
43A LEU* 4.2 6.1 - - + -
214B ARG* 3.3 47.5 + - + +
215B ARG* 3.2 10.4 + - + +
217B HIS* 1.3 74.2 - - + +
219B LYS* 1.3 67.8 + - - +
221B SER* 3.1 9.5 + - - -
222B PHE* 3.0 45.7 + - + -
239B ARG* 4.0 12.1 - - - +
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Residues in contact with LYS 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 2.9 17.2 + - - +
216B ASP* 3.5 15.0 - - - +
218B ILE* 1.3 77.6 - - - +
220B ASP* 1.3 65.0 + - - +
222B PHE* 3.1 6.4 + - + +
223B HIS* 3.0 57.9 + - + +
239B ARG* 3.9 19.1 - - - +
309G A 2.9 33.8 + - - +
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Residues in contact with ASP 220 (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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216B ASP* 2.9 20.7 + - - +
217B HIS* 3.6 15.9 - - - +
219B LYS* 1.3 79.3 - - - +
221B SER* 1.3 58.2 + - - +
223B HIS* 3.2 18.8 + - - +
224B SER* 2.9 33.7 + - - +
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Residues in contact with SER 221 (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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40A LEU* 3.4 19.0 - - - +
43A LEU* 4.0 30.5 - - - +
44A THR* 4.6 5.2 + - - -
47A LYS* 5.9 0.2 - - - +
217B HIS 3.0 15.1 + - - -
218B ILE* 3.1 10.7 + - - -
220B ASP* 1.3 74.7 - - - +
222B PHE* 1.3 62.8 + - - +
224B SER* 3.8 7.3 - - - -
225B LEU* 3.2 22.2 + - - +
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Residues in contact with PHE 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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17A LEU* 5.3 4.3 - - + -
21A LEU* 5.3 2.2 - - + -
39A THR* 4.8 7.4 - - + -
43A LEU* 3.7 20.9 - - + -
218B ILE* 3.0 36.6 + - + -
219B LYS* 3.1 8.5 + - - +
221B SER* 1.3 74.5 - - - +
223B HIS* 1.3 71.3 + - + +
225B LEU* 3.2 4.7 + - - +
226B ARG* 2.9 24.9 + - - +
239B ARG* 3.5 67.3 - - + +
242B ILE* 3.8 27.8 - - + +
243B LEU* 3.9 29.2 - - + -
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Residues in contact with HIS 223 (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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219B LYS* 3.0 60.2 + - + +
220B ASP* 3.4 19.7 - - - +
222B PHE* 1.3 81.4 - - + +
224B SER* 1.3 61.5 + - - +
226B ARG* 3.4 38.8 + - - +
227B ASP* 3.2 29.1 + - - +
242B ILE* 5.7 2.2 - - - +
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Residues in contact with SER 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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47A LYS* 3.7 30.1 + - - +
220B ASP* 2.9 18.5 + - - +
221B SER* 4.0 7.7 - - - -
223B HIS* 1.3 74.1 - - - +
225B LEU* 1.3 61.3 + - - +
227B ASP* 3.5 6.3 + - - +
228B SER* 3.0 26.5 + - - -
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Residues in contact with LEU 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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24A LEU* 4.3 14.1 - - + -
43A LEU* 4.0 28.9 - - + +
46A ALA* 4.2 6.5 - - + -
47A LYS* 3.9 25.7 - - - +
50A ILE* 3.8 25.8 - - + -
221B SER 3.2 18.7 + - - +
222B PHE 3.8 3.8 - - - +
224B SER* 1.3 73.9 - - - +
226B ARG* 1.3 66.6 + - - +
228B SER* 3.1 12.6 + - - -
229B VAL* 3.4 14.9 - - - +
242B ILE* 3.8 20.2 - - + -
243B LEU* 4.4 2.9 - - + -
246B ALA* 4.1 17.7 - - + -
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Residues in contact with ARG 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 PHE 2.9 16.2 + - - +
223B HIS* 3.4 43.4 + - - +
225B LEU* 1.3 78.6 - - - +
227B ASP* 1.3 94.4 + - - +
229B VAL* 2.7 34.7 + - - +
232B LEU* 3.7 27.1 - - + +
233B GLN 3.6 3.3 + - - -
234B GLY* 4.5 3.3 - - - +
235B GLU 3.4 18.9 + - - +
236B LYS* 5.6 1.8 - - - +
237B ALA* 4.7 8.4 + - + +
242B ILE* 3.6 29.9 - - + +
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Residues in contact with ASP 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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51A LYS* 4.7 2.7 + - - -
223B HIS* 3.2 15.8 + - - +
224B SER* 3.9 6.2 - - - +
225B LEU 3.2 0.6 - - - -
226B ARG* 1.3 107.3 + - - +
228B SER* 1.3 59.6 + - - +
229B VAL 3.2 5.3 + - - -
233B GLN* 3.3 36.1 + - + +
234B GLY* 3.4 18.9 + - - -
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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