Contacts of the helix formed by residues 239 - 269 (chain A) in PDB entry 3VOC
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 SER 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TRP 6.1 1.3 - - - -
235A GLY 3.1 16.2 + - - -
236A GLY* 2.6 22.1 + - - -
238A ASN* 1.3 82.6 - - - +
240A ALA* 1.3 64.8 + - - +
241A TYR* 3.5 12.2 + - - +
242A GLY 2.8 17.0 + - - -
243A LYS* 3.0 24.5 + - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TYR* 6.0 0.4 - - - +
211A ALA* 3.3 26.7 - - + +
212A TRP* 3.9 11.9 + - + +
238A ASN 3.9 0.6 + - - -
239A SER* 1.3 72.4 - - - +
241A TYR* 1.3 65.0 + - - +
243A LYS* 3.4 8.4 + - - +
244A ASP* 2.9 27.6 + - - +
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Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 4.0 16.4 - + - -
212A TRP* 3.6 56.3 + + + +
214A THR* 5.4 3.4 - - + -
223A ASN 2.7 28.8 + - - -
224A PRO* 3.1 21.1 + - - +
225A PRO* 3.1 7.8 - - + +
231A PHE* 4.2 20.6 - + - -
236A GLY* 5.4 2.2 - - - -
239A SER* 3.1 11.7 + - - +
240A ALA* 1.3 78.9 - - - +
242A GLY* 1.3 61.1 + - - +
244A ASP* 3.2 2.6 + - - +
245A PHE* 2.8 32.0 + - + +
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Residues in contact with GLY 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.4 17.7 - - - -
236A GLY 3.1 21.1 - - - -
237A TYR 4.3 3.6 - - - -
239A SER* 2.8 14.1 + - - -
241A TYR* 1.3 77.5 - - - +
243A LYS* 1.3 56.3 - - - +
245A PHE* 3.4 2.2 + - - +
246A LEU* 2.9 35.5 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 3.6 27.6 + - + +
238A ASN* 3.7 26.4 + - - +
239A SER 3.0 19.4 + - - +
240A ALA* 3.8 6.7 - - - +
242A GLY* 1.3 73.1 - - - +
244A ASP* 1.3 59.0 + - - +
246A LEU* 4.1 0.6 - - - +
247A SER* 2.9 32.4 + - - -
303A TYR* 3.9 30.8 - - + +
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 3.9 2.9 - - - -
198A MET* 3.8 20.5 - - - +
201A LYS* 2.8 30.5 + - - +
202A TYR* 2.6 23.7 + - - -
212A TRP* 2.7 28.9 + - + +
240A ALA* 2.9 15.7 + - - +
241A TYR 3.5 4.0 - - - +
243A LYS* 1.3 77.0 - - - +
245A PHE* 1.3 61.6 + - - +
247A SER* 4.0 4.5 - - - -
248A TRP* 3.0 25.5 + - - +
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.7 31.9 - + + -
185A ALA* 4.2 5.2 - - + -
194A PHE* 3.6 21.9 - + + -
224A PRO* 3.6 26.5 - - + -
225A PRO* 3.5 33.2 - - + -
231A PHE* 4.5 3.8 - + - -
241A TYR* 2.8 28.1 + - + +
242A GLY* 3.8 4.0 - - - +
243A LYS 3.3 0.2 - - - -
244A ASP* 1.3 74.1 - - - +
246A LEU* 1.3 69.8 + - + +
248A TRP* 3.3 30.7 + + - +
249A TYR* 2.8 49.3 + + - +
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.7 34.3 - - + -
231A PHE* 3.9 12.8 - - + -
237A TYR* 3.4 39.3 - - + -
242A GLY 2.9 19.1 + - - +
243A LYS 4.1 0.2 - - - +
245A PHE* 1.3 82.1 - - + +
247A SER* 1.3 56.8 + - - +
249A TYR* 3.4 7.1 + - + +
250A GLN* 3.0 28.8 + - - +
298A GLN* 4.0 23.8 - - + +
301A GLY 5.3 0.6 - - - +
303A TYR* 3.5 29.9 - - + +
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LYS* 6.3 1.1 - - - -
243A LYS 2.9 19.7 + - - -
244A ASP* 4.0 6.1 - - - -
246A LEU* 1.3 77.8 - - - +
248A TRP* 1.3 57.0 + - - +
251A SER* 2.8 26.6 + - - -
303A TYR* 3.8 18.3 - - - -
307A ARG* 2.8 35.7 + - - +
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Residues in contact with TRP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 5.0 2.9 - - + -
166A TYR* 5.2 1.1 - - - -
185A ALA* 3.9 19.5 - - + -
190A ALA* 3.5 23.8 - - + -
193A ALA* 3.8 20.1 + - + +
194A PHE* 3.6 44.9 - + + -
197A ALA* 3.5 22.8 - - + +
198A MET* 4.4 7.4 - - + -
224A PRO* 5.5 0.2 - - + -
244A ASP 3.0 18.6 + - - +
245A PHE* 3.7 26.0 - + - +
247A SER* 1.3 73.5 - - - +
249A TYR* 1.3 89.1 + + - +
251A SER* 2.7 30.8 + - - -
252A VAL* 3.1 31.0 + - + +
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Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 2.6 72.0 + + - +
183A PHE* 3.5 16.7 - + - -
184A GLN 2.9 30.5 + - - -
185A ALA* 4.0 16.8 - - + -
245A PHE* 2.8 37.6 + + + +
246A LEU* 3.5 11.7 - - + +
248A TRP* 1.3 84.0 - + + +
250A GLN* 1.3 62.6 + - - +
252A VAL* 3.6 3.6 + - - +
253A LEU 3.9 0.3 + - - -
298A GLN 3.2 18.8 - - - -
299A ALA 2.6 29.5 + - - -
301A GLY* 3.6 13.5 - - - -
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU 3.0 17.1 + - - +
249A TYR* 1.3 74.6 - - - +
251A SER* 1.3 63.1 + - - +
253A LEU* 3.0 10.3 + - + +
254A GLU* 2.8 48.3 + - + +
301A GLY 3.3 20.9 + - - +
302A TYR* 3.6 2.2 - - - -
303A TYR* 2.6 35.6 + - + -
304A ASP* 2.8 30.8 + - - +
307A ARG* 3.8 16.3 - - - +
308A LEU* 3.5 19.6 - - + +
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 2.8 19.0 + - - -
248A TRP* 2.7 32.3 + - - -
250A GLN* 1.3 72.5 - - - +
252A VAL* 1.3 53.1 + - - +
254A GLU* 3.2 18.1 - - - +
255A LYS* 2.8 35.6 + - - +
307A ARG* 3.6 3.1 - - - +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 3.9 24.0 - - + +
125A LEU* 3.8 31.4 - - + -
166A TYR* 3.2 26.9 - - + +
248A TRP* 3.1 46.6 + - + +
250A GLN 3.2 0.4 + - - -
251A SER* 1.3 77.0 + - - +
253A LEU* 1.3 60.7 + - - +
255A LYS* 4.0 4.8 - - - +
256A HIS* 3.1 22.5 + - - +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE* 6.0 0.9 - - + -
124A PRO* 4.9 12.6 - - + -
158A GLY 5.1 2.2 - - - +
164A LEU* 3.5 31.3 - - + +
165A ARG* 3.8 35.4 - - - +
166A TYR* 3.7 29.2 - - + +
250A GLN* 3.0 9.8 + - + +
252A VAL* 1.3 74.4 - - - +
254A GLU* 1.3 59.8 + - - +
256A HIS* 3.2 6.7 + - - +
257A LEU* 2.9 25.3 + - - +
300A GLY 3.7 22.2 - - - +
301A GLY* 3.8 17.5 - - - +
302A TYR* 4.4 5.6 - - + -
308A LEU* 5.2 3.8 - - + -
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLN* 2.8 37.9 + - + +
251A SER* 3.2 14.9 + - - +
253A LEU* 1.3 76.8 - - - +
255A LYS* 1.3 61.1 + - - +
257A LEU* 3.2 5.2 + - - +
258A GLY 3.0 9.9 + - - -
307A ARG* 2.9 53.3 + - - +
308A LEU* 4.0 20.6 - - + -
311A LYS* 3.0 43.5 - - + -
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A SER 2.8 20.7 + - - +
252A VAL* 4.0 5.4 - - - +
254A GLU* 1.3 71.6 - - - +
256A HIS* 1.3 58.3 + - - +
258A GLY* 3.2 2.6 + - - +
259A VAL* 2.9 42.4 + - + +
311A LYS* 4.6 5.8 - - - +
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU 5.1 3.1 + - - -
124A PRO* 3.6 36.4 - - + +
129A THR* 3.8 26.6 - - + +
130A GLY* 6.3 0.2 - - - -
133A TYR* 4.0 13.1 + + - -
158A GLY 3.4 30.7 + - - -
159A GLY* 5.5 0.2 - - - -
164A LEU* 4.1 8.7 - - + -
252A VAL 3.1 15.7 + - - +
253A LEU* 3.2 9.6 + - + +
255A LYS* 1.3 77.4 - - - +
257A LEU* 1.3 61.3 + - - +
259A VAL* 3.1 9.4 + - + +
260A ILE* 2.9 54.1 + - + +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLY* 5.9 0.2 - - - -
164A LEU* 4.0 25.3 - - + +
253A LEU 2.9 13.1 + - - +
254A GLU* 3.2 8.7 + - - +
256A HIS* 1.3 75.4 - - - +
258A GLY* 1.3 57.5 + - - +
260A ILE* 3.6 11.9 - - + +
261A GLY* 2.8 29.6 + - - -
278A ALA* 4.0 20.4 - - + -
308A LEU* 4.8 1.1 - - + +
311A LYS* 3.9 23.8 - - + +
312A PHE* 3.5 42.2 - - + +
315A ALA* 4.5 2.0 - - + +
317A LEU* 3.6 24.8 - - + +
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Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLU 3.0 12.6 + - - -
255A LYS* 3.2 4.2 + - - -
257A LEU* 1.3 77.2 - - - +
259A VAL* 1.3 56.8 + - - +
261A GLY 3.9 0.2 - - - -
262A ALA* 3.0 31.2 + - - +
311A LYS* 4.0 17.2 - - - +
315A ALA* 4.7 10.3 - - - +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY* 3.8 30.1 - - - +
255A LYS* 2.9 35.6 + - + +
256A HIS* 3.1 12.5 + - + +
258A GLY* 1.3 78.3 - - - +
260A ILE* 1.3 61.3 + - + +
262A ALA* 3.8 3.5 - - - +
263A ALA* 3.1 27.8 + - + +
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 5.6 0.9 - - + -
130A GLY* 5.7 0.7 - - - -
133A TYR* 3.4 27.6 - - + -
137A TYR* 3.5 15.8 - - - +
156A LEU* 3.9 18.4 - - + -
157A SER 3.9 9.9 - - - +
158A GLY* 3.9 28.9 - - - -
256A HIS* 2.9 41.4 + - + +
257A LEU* 3.6 18.4 - - + +
259A VAL* 1.3 79.1 - - + +
261A GLY* 1.3 62.6 + - - +
263A ALA* 3.4 5.1 + - - -
264A ALA* 2.9 30.5 + - - +
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.1 6.3 - - - -
257A LEU 2.8 18.0 + - - -
258A GLY 4.0 0.7 - - - -
260A ILE* 1.3 78.5 - - - +
262A ALA* 1.3 57.0 + - - +
264A ALA* 3.3 1.4 + - - +
265A HIS* 2.9 38.7 + - - -
315A ALA* 5.0 5.2 - - - -
317A LEU* 4.0 23.6 - - - -
505A EDO 5.1 0.2 - - - -
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY 3.0 20.3 + - - +
259A VAL* 3.8 4.7 - - - +
261A GLY* 1.3 72.1 - - - +
263A ALA* 1.3 60.3 + - - +
265A HIS* 3.4 1.9 + - - +
266A LYS* 2.9 31.1 + - - +
315A ALA* 5.8 0.4 - - - +
505A EDO 4.3 17.5 - - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 4.9 3.4 - - - +
133A TYR* 5.0 0.9 - - + -
134A ASP* 4.1 27.8 - - + +
137A TYR* 3.8 16.6 - - + -
259A VAL* 3.1 18.3 + - + +
260A ILE* 3.8 5.6 - - - +
262A ALA* 1.3 77.5 - - - +
264A ALA* 1.3 60.6 + - - +
266A LYS* 3.4 7.0 + - - +
267A ASN* 2.9 31.7 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 3.6 10.7 - - + -
156A LEU* 3.7 32.1 - - + -
260A ILE 2.9 19.1 + - - +
261A GLY 3.7 3.6 - - - +
262A ALA 3.3 0.2 - - - -
263A ALA* 1.3 72.3 - - - +
265A HIS* 1.3 62.4 + - - +
267A ASN 3.3 0.7 + - - -
268A PHE* 2.8 46.6 + - + +
276A ILE* 3.8 11.2 - - + -
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Residues in contact with HIS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLY 2.9 26.1 + - - +
262A ALA 3.8 3.6 - - - +
264A ALA* 1.3 76.4 - - - +
266A LYS* 1.3 63.5 + - - +
269A ASP* 2.6 64.4 + - - +
274A VAL 5.6 1.8 - - - -
275A ARG* 5.5 1.6 - - - -
276A ILE* 3.8 15.2 - - + +
315A ALA 3.2 16.8 + - - -
316A ASP* 2.8 46.9 + - + +
317A LEU* 4.2 6.2 - - + +
505A EDO 3.8 22.6 - - - +
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 2.8 42.3 + - - -
262A ALA 2.9 18.8 + - - +
263A ALA* 3.7 5.2 - - - +
264A ALA 3.2 0.2 - - - -
265A HIS* 1.3 79.7 - - - +
267A ASN* 1.3 67.1 + - - +
269A ASP 4.7 0.9 + - - -
270A SER* 4.7 9.0 + - - -
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 2.8 37.1 + - - +
137A TYR* 3.8 24.5 - - + +
138A ALA* 3.3 29.3 - - - +
141A ALA* 3.4 17.8 - - + +
263A ALA 2.9 22.2 + - - +
266A LYS* 1.3 86.5 - - - +
268A PHE* 1.3 60.9 + - + +
270A SER* 5.1 1.5 + - - -
271A VAL* 3.7 13.4 - - - +
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Residues in contact with PHE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 4.5 3.6 - - + -
137A TYR* 3.3 47.8 - + + -
140A PHE* 4.0 23.8 - + - -
141A ALA* 4.0 1.8 - - + -
154A ILE* 3.8 35.0 - - + -
156A LEU* 4.3 7.4 - - + -
264A ALA* 2.8 42.2 + - + +
267A ASN* 1.3 80.5 - - - +
269A ASP* 1.3 60.6 + - - +
270A SER 3.3 2.5 - - - -
271A VAL 3.8 0.7 - - - -
272A PHE* 2.7 51.8 + + + +
273A GLY 3.0 5.4 + - - +
274A VAL* 5.8 1.8 - - + +
276A ILE* 4.1 14.4 - - + -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A HIS* 2.6 60.1 + - - +
268A PHE* 1.3 76.7 - - - +
270A SER* 1.3 59.0 + - - +
273A GLY* 3.2 25.4 + - - +
274A VAL 4.5 7.6 - - - +
276A ILE* 3.8 9.4 - - - +
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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).
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