Contacts of the helix formed by residues 198 - 220 (chain K) in PDB entry 1XFB
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 198 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K ASP 3.8 1.2 + - - -
197K HIS* 1.3 79.1 - - - +
199K LEU* 1.3 65.3 + - - +
200K LYS* 3.1 37.0 + - - +
201K ARG* 3.2 27.2 + - - +
202K CYS* 3.3 7.8 + - - +
236K PRO* 4.1 2.2 - - - -
240K CYS* 4.0 15.7 - - - -
242K ILE* 4.3 9.1 - - + +
244K TYR* 3.4 14.6 + - - +
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Residues in contact with LEU 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198K ASP* 1.3 74.3 - - - +
200K LYS* 1.3 65.2 + - - +
202K CYS* 3.1 4.2 + - - +
203K GLN* 3.0 21.0 + - - +
234K VAL* 3.3 20.0 - - + +
235K THR* 3.2 33.9 - - - -
236K PRO* 3.8 13.5 - - + +
244K TYR* 3.3 41.8 + - + -
248K GLU* 3.7 28.7 - - + +
249K ILE* 4.4 5.2 - - + -
252K ALA* 3.9 14.1 - - + -
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Residues in contact with LYS 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J SER* 6.3 0.2 - - - -
6J PRO* 4.1 23.6 - - - +
198K ASP* 3.1 21.1 + - - +
199K LEU* 1.3 78.4 - - - +
201K ARG* 1.3 63.6 + - - +
203K GLN* 3.1 10.8 + - - +
204K TYR* 3.0 21.2 + - - +
244K TYR* 4.8 0.2 + - - -
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Residues in contact with ARG 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I ARG* 3.0 25.2 - - - +
3J HIS* 2.7 47.3 + - - +
4J SER* 3.5 20.3 + - - +
154K ILE* 3.4 20.2 - - + +
155K SER 3.3 18.8 + - - -
158K THR 5.5 0.2 - - - +
159K PRO* 4.8 1.8 - - - +
197K HIS* 3.7 22.0 - - + +
198K ASP* 3.2 19.8 + - - +
200K LYS* 1.3 78.5 - - - +
202K CYS* 1.3 65.0 + - - +
204K TYR* 3.1 7.7 + - - +
205K VAL* 2.9 35.4 + - + +
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Residues in contact with CYS 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K ILE* 4.1 18.4 - - - -
191K ILE* 5.2 4.0 - - - -
192K LEU 6.1 0.2 - - - -
197K HIS* 4.0 11.4 - - + +
198K ASP 3.3 2.9 + - - +
199K LEU 3.1 8.3 + - - +
201K ARG* 1.3 78.8 - - - +
203K GLN* 1.3 58.2 + - - +
205K VAL* 4.0 0.7 - - - +
206K THR* 2.8 41.6 + - - -
232K ASN* 4.2 7.0 - - - -
233K MET 4.4 0.9 - - - -
234K VAL* 3.5 11.0 - - - -
235K THR 3.2 44.2 - - - +
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Residues in contact with GLN 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199K LEU 3.0 11.2 + - - +
200K LYS* 3.1 13.2 + - - +
202K CYS* 1.3 78.2 - - - +
204K TYR* 1.3 57.1 + - - +
206K THR* 3.2 3.0 + - - -
207K GLU* 2.6 59.0 + - - +
234K VAL* 3.8 15.2 - - + +
252K ALA* 3.4 37.2 + - + +
255K THR* 3.7 15.2 - - - +
256K ALA* 3.9 6.5 - - + +
259K ARG* 3.2 16.6 - - - +
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Residues in contact with TYR 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I GLY 4.6 1.8 + - - -
3J HIS* 2.9 48.7 + + + +
4J SER* 3.3 33.7 - - - -
5J TYR 5.0 0.7 - - - -
221J HIS* 3.0 31.6 - - + -
200K LYS 3.0 11.7 + - - +
201K ARG* 3.3 10.1 - - - +
203K GLN* 1.3 75.3 - - - +
205K VAL* 1.3 67.0 + - + +
207K GLU* 3.1 13.5 + - - +
208K LYS* 3.0 54.0 + - + +
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Residues in contact with VAL 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J HIS* 3.8 26.0 - - + +
154K ILE* 3.9 25.8 - - + -
159K PRO* 3.6 31.2 - - + -
164K ILE* 6.0 0.2 - - + -
191K ILE* 3.7 16.4 - - + -
201K ARG* 2.9 30.9 + - + +
202K CYS 4.0 0.2 - - - +
204K TYR* 1.3 75.4 - - + +
206K THR* 1.3 64.0 + - - +
208K LYS* 3.2 6.5 + - + +
209K VAL* 2.9 25.6 + - + +
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Residues in contact with THR 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K ILE* 3.4 16.4 - - + +
202K CYS* 2.8 27.7 + - - -
203K GLN* 3.5 6.5 - - - -
205K VAL* 1.3 77.2 - - - +
207K GLU* 1.3 64.8 + - - +
209K VAL* 3.8 0.3 - - - +
210K LEU* 2.9 46.4 + - + +
231K PRO* 5.8 1.8 - - + -
232K ASN* 3.3 28.5 + - - +
234K VAL* 4.4 8.8 - - + +
256K ALA* 4.1 15.5 - - + -
257K LEU* 5.9 0.9 - - + -
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Residues in contact with GLU 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218J SER* 5.5 0.2 - - - -
203K GLN* 2.6 51.5 + - - +
204K TYR* 3.1 12.6 + - - +
206K THR* 1.3 77.8 - - - +
208K LYS* 1.3 62.1 + - + +
210K LEU* 4.8 0.4 - - - -
211K ALA* 2.9 30.6 + - - +
256K ALA* 3.7 23.3 - - - +
259K ARG* 3.0 31.6 + - - +
260K THR* 3.4 16.4 - - + +
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Residues in contact with LYS 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J HIS* 6.5 0.2 - - + -
218J SER* 2.6 41.1 + - - +
219J ASP* 4.8 2.0 + - - +
221J HIS* 2.9 23.6 + - + +
164K ILE* 4.7 13.4 - - + +
204K TYR* 3.0 61.7 + - + +
205K VAL* 3.7 7.4 - - + +
207K GLU* 1.3 75.9 - - - +
209K VAL* 1.3 67.4 + - - +
211K ALA* 3.4 5.9 + - - +
212K ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K LEU* 3.3 36.8 - - + -
159K PRO* 4.8 0.7 - - + -
164K ILE* 4.4 21.2 - - + +
189K PRO* 4.2 14.4 - - + -
191K ILE* 3.6 19.5 - - + -
205K VAL* 2.9 28.0 + - + +
206K THR 3.8 2.7 - - - +
208K LYS* 1.3 77.0 - - + +
210K LEU* 1.3 66.6 + - + +
212K ALA* 3.0 5.7 + - - +
213K VAL* 2.9 37.0 + - + +
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Residues in contact with LEU 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K PRO* 4.0 18.4 - - + -
191K ILE* 6.5 0.2 - - + -
206K THR* 2.9 39.1 + - + +
209K VAL* 1.3 76.8 - - + +
211K ALA* 1.3 65.8 + - - +
213K VAL* 2.9 16.3 + - + +
214K TYR* 2.9 22.8 + - + -
229K LEU* 3.9 33.0 - - + -
231K PRO* 4.7 6.7 - - + -
256K ALA 5.0 1.1 - - - +
257K LEU* 3.8 26.2 - - + -
260K THR* 3.5 29.2 - - - +
261K VAL* 4.5 0.4 - - + -
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Residues in contact with ALA 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J LYS* 3.9 11.4 - - + +
218J SER* 3.4 33.0 - - - +
207K GLU 2.9 18.8 + - - +
208K LYS 3.6 5.2 - - - +
209K VAL 3.3 0.2 - - - -
210K LEU* 1.3 77.8 - - - +
212K ALA* 1.3 62.1 + - - +
214K TYR* 3.8 4.2 + - - +
215K LYS* 3.3 21.0 + - - +
260K THR* 4.1 14.9 - - + +
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Residues in contact with ALA 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J LYS* 4.0 20.2 - - - +
164K ILE* 3.5 29.8 - - + +
165K LEU* 6.1 0.4 - - - -
168K ALA* 4.1 9.4 - - + +
208K LYS 3.1 8.2 + - - +
209K VAL 3.0 8.2 + - - +
211K ALA* 1.3 74.5 - - - +
213K VAL* 1.3 66.7 + - - +
215K LYS* 3.2 3.5 + - - +
216K ALA* 3.0 23.7 + - - +
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Residues in contact with VAL 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K ILE* 6.4 0.2 - - + -
168K ALA* 4.0 16.6 - - + +
171K LEU* 4.2 12.3 - - + -
187K VAL* 3.9 27.6 - - + -
189K PRO* 4.1 18.2 - - + -
209K VAL* 2.9 34.9 + - + +
210K LEU* 2.9 11.4 + - + +
212K ALA* 1.3 77.5 - - - +
214K TYR* 1.3 66.0 + - + +
216K ALA* 3.3 3.6 + - - +
217K LEU* 3.0 35.3 + - + +
229K LEU* 5.3 0.7 - - + -
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Residues in contact with TYR 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K VAL* 5.7 1.8 - - + +
210K LEU* 2.9 25.1 + - + +
211K ALA* 4.5 2.9 - - - +
213K VAL* 1.3 78.7 - - + +
215K LYS* 1.3 66.3 + - - +
217K LEU* 3.2 16.8 + - + +
218K SER* 2.9 22.9 + - - -
224K LEU* 3.6 35.1 - - + +
227K THR* 5.1 2.3 + - - -
228K LEU 5.2 0.5 - - - -
229K LEU* 3.4 40.5 + - + +
260K THR 3.9 17.0 - - - +
261K VAL* 3.7 21.6 - - + +
262K PRO* 3.7 20.2 - - + -
265K VAL* 3.5 26.2 - - + +
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Residues in contact with LYS 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211J ALA* 3.8 23.6 - - + +
212J ALA* 4.0 26.5 - - - +
215J LYS* 3.8 32.3 - - + -
211K ALA 3.3 16.6 + - - +
212K ALA 3.2 5.7 + - - +
214K TYR* 1.3 78.3 - - - +
216K ALA* 1.3 58.2 + - - +
218K SER* 3.2 5.6 + - - -
219K ASP* 2.9 68.2 + - - +
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Residues in contact with ALA 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K ALA* 3.4 35.2 - - + +
169K ASN* 4.3 4.7 - - - +
172K ALA* 3.8 6.1 - - + -
212K ALA 3.0 12.6 + - - +
213K VAL 3.4 7.6 - - - +
215K LYS* 1.3 75.3 - - - +
217K LEU* 1.3 67.1 + - - +
219K ASP* 2.9 10.5 + - - +
220K HIS* 2.9 28.9 + - + -
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Residues in contact with LEU 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K LEU 4.7 0.2 - - - -
172K ALA* 3.7 22.4 - - + +
175K ALA* 3.9 9.0 - - + -
187K VAL* 4.4 18.2 - - + -
213K VAL* 3.0 27.5 + - + +
214K TYR* 3.2 39.7 + - + +
216K ALA* 1.3 76.4 - - - +
218K SER* 1.3 62.4 + - - +
220K HIS 3.2 1.6 + - - -
221K HIS 3.1 4.0 + - - -
222K VAL* 3.0 59.8 + - + +
224K LEU* 4.0 15.3 - - + -
227K THR* 5.5 2.0 - - - +
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Residues in contact with SER 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J GLU 5.1 0.3 + - - -
208J LYS* 2.9 38.0 + - - +
211J ALA* 3.5 30.3 - - - +
214K TYR 2.9 12.9 + - - -
215K LYS* 3.3 11.2 - - - -
216K ALA 3.1 0.2 - - - -
217K LEU* 1.3 77.1 - - - +
219K ASP* 1.3 63.0 + - - +
221K HIS* 2.9 13.9 + - - +
222K VAL 5.0 3.1 - - - +
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Residues in contact with ASP 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208J LYS* 4.9 2.9 - - - +
215K LYS* 2.9 50.8 + - - +
216K ALA* 2.9 10.8 + - - +
218K SER* 1.3 78.4 + - - +
220K HIS* 1.3 67.0 + - + +
221K HIS* 3.4 12.2 + - - -
162L LEU* 3.3 24.1 - - + +
165L LEU* 3.8 26.0 - - + +
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Residues in contact with HIS 220 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ASN* 2.8 29.4 + - - -
172K ALA* 3.4 29.3 - - + +
173K ARG* 3.8 35.2 + - + +
176K SER* 3.7 18.6 + - - -
216K ALA* 2.9 22.2 + - - +
217K LEU 3.9 2.2 - - - +
218K SER 3.1 0.4 - - - -
219K ASP* 1.3 79.1 - - + +
221K HIS* 1.3 75.3 + - - +
222K VAL* 3.3 3.9 + - + -
116L LEU* 5.4 3.7 - - + +
117L ALA* 3.9 4.2 - - - +
162L LEU* 3.6 29.5 - - + +
165L LEU* 4.2 2.8 - - + +
166L GLU* 4.0 11.9 - - + -
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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
------------------------------------------------------------
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