Contacts of the helix formed by residues 291 - 324 (chain A) in PDB entry 1TQN
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 291 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ALA 3.3 4.0 + - - -
290A LEU* 1.3 69.4 - - - +
292A ASP* 1.3 58.7 + - - +
293A LEU* 2.8 17.6 + - - +
294A GLU* 2.5 55.4 + - - -
295A LEU 2.8 12.0 + - - -
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Residues in contact with ASP 292 (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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254A LYS* 4.8 18.5 - - + -
257A LYS* 3.5 20.6 + - + +
258A GLU* 5.4 1.4 - - - +
279A GLN* 2.8 21.6 - - - +
290A LEU 3.9 0.9 - - - +
291A SER* 1.3 73.4 + - - +
293A LEU* 1.3 57.7 + - - +
295A LEU* 3.9 3.9 - - - +
296A VAL* 2.9 30.5 + - - +
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Residues in contact with LEU 293 (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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113A PHE* 3.8 30.3 - - + -
116A SER* 4.9 2.0 - - - +
250A ARG* 2.9 49.8 - - + +
291A SER* 2.7 11.6 + - - +
292A ASP* 1.3 77.4 - - - +
294A GLU* 1.3 69.2 + - + +
296A VAL* 3.1 5.6 + - + +
297A ALA* 2.9 17.7 + - - +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 4.0 22.9 + - - -
125A GLU* 3.8 12.8 - - - +
128A ARG* 2.8 39.9 + - - -
129A LEU* 4.1 5.1 - - - +
290A LEU* 3.2 19.7 - - + +
291A SER* 2.5 45.7 + - - +
293A LEU* 1.3 71.2 - - + +
295A LEU* 1.3 54.8 + - - +
297A ALA* 2.4 29.7 + - - +
298A GLN* 2.8 19.1 + - - +
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Residues in contact with LEU 295 (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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253A VAL* 3.8 24.2 - - + -
257A LYS* 3.2 35.0 - - + +
272A LEU* 4.0 6.7 - - + -
275A MET* 3.9 33.0 - - + +
276A ILE* 4.4 3.1 - - + +
279A GLN* 3.4 13.9 - - - +
290A LEU* 4.4 9.5 - - + +
291A SER 2.8 16.7 + - - +
292A ASP* 3.9 4.3 - - - +
294A GLU* 1.3 72.6 - - - +
296A VAL* 1.3 65.1 + - + +
298A GLN* 3.1 12.1 + - - +
299A SER* 3.0 39.7 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.4 0.9 - - + -
249A LEU 4.6 2.9 - - - +
250A ARG* 3.6 52.3 - - + +
253A VAL* 4.2 26.7 - - + -
254A LYS* 5.6 1.3 - - + +
292A ASP* 2.9 21.7 + - + +
293A LEU* 3.1 10.5 + - + +
294A GLU 3.1 1.0 - - - -
295A LEU* 1.3 79.5 - - + +
297A ALA* 1.3 62.4 + - - +
299A SER* 3.5 4.8 + - - -
300A ILE* 3.2 36.5 + - + +
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Residues in contact with ALA 297 (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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113A PHE* 3.9 8.0 - - + +
114A MET* 3.6 27.3 - - - +
116A SER* 3.4 24.9 - - - +
117A ALA* 4.0 11.0 - - - +
293A LEU 2.9 8.6 + - - +
294A GLU 2.4 22.1 + - - +
296A VAL* 1.3 72.5 - - - +
298A GLN* 1.3 62.8 + - - +
300A ILE* 3.4 0.9 + - - +
301A ILE* 3.0 24.5 + - - +
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Residues in contact with GLN 298 (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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116A SER 3.0 26.1 + - - -
117A ALA* 3.9 1.0 - - - +
118A ILE* 3.1 34.9 + - - +
129A LEU* 3.9 15.4 - - - +
133A LEU* 3.7 12.0 - - + +
275A MET* 3.3 34.8 - - + -
290A LEU* 4.7 4.9 - - + -
294A GLU* 2.8 26.2 + - - +
295A LEU* 3.1 4.9 + - - +
297A ALA* 1.3 73.6 - - - +
299A SER* 1.3 67.2 + - - +
301A ILE* 3.1 7.1 + - - +
302A PHE* 2.8 34.7 + - + -
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Residues in contact with SER 299 (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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188A SER* 4.6 14.9 + - - -
253A VAL* 4.7 13.5 - - - +
271A PHE* 6.4 0.2 - - - -
272A LEU* 4.9 5.4 - - - +
275A MET* 4.1 7.9 - - - -
295A LEU* 3.0 28.5 + - - +
296A VAL* 3.8 6.5 - - - -
298A GLN* 1.3 76.6 - - - +
300A ILE* 1.3 63.5 + - - +
302A PHE* 3.4 11.8 + - - +
303A ILE* 3.2 30.6 + - - +
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Residues in contact with ILE 300 (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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113A PHE* 4.0 25.1 - - + -
114A MET* 3.9 18.8 - - + -
210A LEU* 4.1 22.7 - - + +
241A PHE* 4.7 7.6 - - + -
246A THR* 4.2 26.9 - - + +
249A LEU* 3.7 25.8 - - + -
253A VAL* 6.5 0.2 - - + -
296A VAL* 3.2 27.0 + - + +
297A ALA 3.7 3.4 - - - +
298A GLN 3.2 0.4 - - - -
299A SER* 1.3 75.2 - - - +
301A ILE* 1.3 60.5 + - - +
303A ILE* 3.1 11.7 + - - +
304A PHE* 2.9 25.1 + - - +
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Residues in contact with ILE 301 (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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114A MET* 3.6 18.2 - - + -
117A ALA* 3.7 12.8 - - + -
118A ILE* 4.2 7.9 - - + -
119A SER* 3.3 28.5 - - - +
120A ILE* 4.4 2.9 - - + -
241A PHE* 4.1 10.1 - - + -
297A ALA 3.0 14.8 + - - +
298A GLN* 3.1 25.8 - - - +
300A ILE* 1.3 74.4 - - - +
302A PHE* 1.3 74.0 + - + +
304A PHE* 3.1 28.3 + - + +
305A ALA* 2.6 39.7 + - + +
508A HEM 4.8 4.0 - - + -
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Residues in contact with PHE 302 (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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118A ILE* 4.3 7.2 - - + -
133A LEU* 3.4 35.7 - - + -
136A THR* 5.3 0.9 - - + -
137A PHE* 3.5 37.0 - + - -
184A ILE* 5.4 2.1 - - - +
271A PHE* 4.5 25.1 - + + -
275A MET* 4.0 21.5 - - + -
298A GLN* 2.8 25.5 + - + +
299A SER* 3.6 9.6 - - - +
300A ILE 3.2 0.2 - - - -
301A ILE* 1.3 87.9 - - + +
303A ILE* 1.3 58.6 + - + +
305A ALA* 4.4 0.7 - - - -
306A GLY* 3.1 23.9 + - - -
443A ILE* 4.9 0.7 - - + -
508A HEM 3.9 32.9 - - + +
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Residues in contact with ILE 303 (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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181A MET* 5.1 1.1 - - + -
184A ILE* 3.5 37.9 - - + -
185A THR* 6.4 0.4 - - + -
188A SER* 6.4 3.6 - - - -
203A PHE* 6.2 1.3 - - + -
207A THR* 4.2 23.1 - - + +
210A LEU* 3.3 34.8 - - + -
249A LEU* 4.4 14.8 - - + -
299A SER* 3.2 18.6 - - - +
300A ILE 3.3 6.1 - - - +
302A PHE* 1.3 76.8 - - + +
304A PHE* 1.3 60.3 + - - +
307A TYR* 2.8 39.6 + - + +
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Residues in contact with PHE 304 (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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108A PHE* 6.4 0.4 - + - -
119A SER* 5.9 0.2 - - - -
210A LEU* 3.9 27.3 - - + +
211A LEU 3.1 29.2 - - - -
212A ARG* 3.2 67.4 + - - -
213A PHE* 3.4 40.6 - + - -
241A PHE* 3.9 19.7 - + + -
300A ILE 2.9 15.8 + - - +
301A ILE* 3.5 27.1 - - + +
303A ILE* 1.3 81.7 - - - +
305A ALA* 1.3 60.5 + - + +
306A GLY 3.5 0.2 + - - -
307A TYR 4.1 2.9 + - - -
308A GLU 4.8 1.9 + - - -
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Residues in contact with ALA 305 (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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212A ARG* 3.4 13.2 + - - +
301A ILE* 2.6 22.8 + - + +
302A PHE* 3.9 1.6 - - - +
304A PHE* 1.3 77.2 - - + +
306A GLY* 1.3 51.1 + - - +
309A THR* 2.6 32.9 + - - +
508A HEM 3.4 52.4 + - + +
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Residues in contact with GLY 306 (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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180A SER* 3.5 1.9 + - - -
184A ILE* 4.1 8.3 - - - -
302A PHE 3.1 13.7 + - - -
305A ALA* 1.3 77.9 - - - +
307A TYR* 1.3 64.5 + - - +
309A THR* 3.1 10.2 + - - -
310A THR* 2.7 24.8 + - - -
508A HEM 3.4 22.0 - - - -
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Residues in contact with TYR 307 (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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177A GLY* 3.4 34.0 + - - -
180A SER* 2.7 27.5 + - - -
181A MET* 4.1 13.0 - - + -
184A ILE* 3.4 20.1 - - + +
207A THR 4.3 7.2 - - - -
208A LYS* 2.9 54.6 - - + +
210A LEU 3.8 19.7 - - - +
211A LEU* 3.5 14.7 - - + +
303A ILE* 2.8 26.4 + - + +
304A PHE 4.1 1.0 + - - +
305A ALA 3.7 0.6 - - - -
306A GLY* 1.3 73.0 - - - +
308A GLU* 1.3 68.0 + - + +
311A SER* 3.5 10.0 + - - -
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Residues in contact with GLU 308 (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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210A LEU 5.3 0.6 + - - +
211A LEU* 3.6 27.3 - - + +
212A ARG* 3.1 45.7 + - + +
304A PHE 4.8 2.8 + - - -
307A TYR* 1.3 86.6 - - + +
309A THR* 1.3 60.5 + - - +
311A SER* 3.9 6.9 - - - -
312A SER* 2.9 43.8 + - - +
482A LEU* 4.5 9.5 - - + +
484A GLN* 5.4 7.8 + - - +
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Residues in contact with THR 309 (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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212A ARG* 4.3 25.1 - - + +
305A ALA 2.6 30.0 + - - +
306A GLY* 3.1 9.9 + - - -
308A GLU* 1.3 74.6 - - - +
310A THR* 1.3 72.2 + - - +
312A SER* 3.1 3.5 + - - -
313A VAL* 2.9 30.2 + - - +
369A ILE* 3.5 28.9 - - + -
508A HEM 3.7 22.0 - - + +
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Residues in contact with THR 310 (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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179A TYR* 5.0 1.3 - - + -
180A SER* 3.7 12.3 - - - +
306A GLY* 2.7 24.9 + - - -
309A THR* 1.3 82.3 + - - +
311A SER* 1.3 65.9 + - - +
313A VAL* 3.4 1.4 + - - +
314A LEU* 3.0 36.2 + - + +
448A ALA* 5.1 3.0 - - - +
451A ASN* 3.6 26.2 + - + +
452A MET* 3.7 21.4 - - + +
508A HEM 4.2 21.8 - - - +
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS* 3.6 14.6 + - - +
176A PHE* 3.7 26.8 - - - +
177A GLY* 3.4 20.5 + - - -
180A SER* 4.1 0.8 + - - -
307A TYR* 3.5 17.8 + - - -
308A GLU* 4.0 7.0 - - - -
309A THR 3.3 0.6 - - - -
310A THR* 1.3 82.1 - - - +
312A SER* 1.3 57.0 + - - +
314A LEU* 3.5 3.0 + - - +
315A SER* 3.0 32.3 + - - -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 2.9 33.8 + - - +
309A THR* 3.6 4.5 - - - -
311A SER* 1.3 73.3 + - - +
313A VAL* 1.3 65.6 + - - +
315A SER* 3.3 7.4 + - - -
316A PHE* 3.0 42.6 + - - -
369A ILE* 4.5 11.4 - - - -
483A LEU 4.9 5.2 + - - -
484A GLN* 5.3 8.2 + - - +
485A PRO* 6.4 0.4 - - - -
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Residues in contact with VAL 313 (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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309A THR 2.9 19.7 + - - +
312A SER* 1.3 73.4 - - - +
314A LEU* 1.3 66.3 + - - +
316A PHE* 2.9 9.5 + - + +
317A ILE* 2.9 41.1 + - + +
363A THR* 5.1 3.1 - - + -
364A LEU* 3.9 28.0 - - + -
367A PHE 5.1 0.7 - - - +
369A ILE* 4.0 20.9 - - + -
452A MET* 3.3 33.0 - - + -
508A HEM 3.5 17.7 - - + -
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Residues in contact with LEU 314 (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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176A PHE* 3.8 34.8 - - + +
179A TYR* 4.1 20.4 - - + -
310A THR* 3.0 38.0 + - + +
311A SER* 3.7 4.7 - - - +
313A VAL* 1.3 77.5 - - - +
315A SER* 1.3 56.5 + - - +
317A ILE* 3.4 5.2 + - + +
318A MET* 3.0 33.8 + - - +
452A MET* 3.6 25.8 - - + +
455A ALA* 4.4 4.9 - - + -
456A LEU* 3.6 36.3 - - + -
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Residues in contact with SER 315 (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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172A LEU* 3.5 33.0 - - - +
173A LYS* 3.6 12.9 + - - -
176A PHE* 3.5 11.3 - - - -
311A SER 3.0 18.2 + - - -
312A SER* 3.6 8.0 - - - -
313A VAL 3.1 0.2 - - - -
314A LEU* 1.3 74.5 - - - +
316A PHE* 1.3 67.0 + - - +
318A MET 3.4 0.3 + - - -
319A TYR* 3.0 22.7 + - - +
485A PRO* 6.1 4.5 - - - -
489A VAL* 4.8 8.3 - - - +
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Residues in contact with PHE 316 (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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312A SER* 3.0 31.3 + - - -
313A VAL* 2.9 10.3 + - - +
315A SER* 1.3 75.6 - - - +
317A ILE* 1.3 64.8 + - - +
319A TYR* 3.0 8.9 + - - +
320A GLU* 2.9 24.1 + - - +
363A THR* 3.5 18.6 - - + -
367A PHE* 3.5 55.9 - + + -
369A ILE* 4.1 11.7 - - + -
475A LEU* 3.9 13.7 - - + -
477A LEU* 4.2 4.5 - - + -
483A LEU* 3.7 23.3 - - + -
484A GLN* 3.8 3.6 - - - -
485A PRO* 3.7 37.5 - - + -
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 2.9 30.9 + - + +
314A LEU* 3.6 11.0 - - + +
316A PHE* 1.3 75.0 - - - +
318A MET* 1.3 58.3 + - - +
320A GLU* 3.1 4.7 + - - +
321A LEU* 2.9 34.2 + - + +
359A VAL* 4.0 22.7 - - + -
360A VAL* 4.2 22.0 - - + -
363A THR* 3.4 26.5 - - + +
452A MET* 4.9 2.0 - - - -
456A LEU* 3.9 39.9 - - + -
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Residues in contact with MET 318 (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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172A LEU* 3.7 22.2 - - + -
176A PHE* 3.4 24.2 - - + -
314A LEU 3.0 21.1 + - - +
316A PHE 3.3 0.2 - - - -
317A ILE* 1.3 75.3 - - - +
319A TYR* 1.3 62.6 + - - +
321A LEU* 3.9 16.1 - - + +
322A ALA* 3.0 25.3 + - - +
328A GLN* 5.2 0.2 - - - +
456A LEU* 3.5 27.1 - - + -
459A VAL* 5.1 2.0 - - + -
460A LEU* 4.3 14.4 - - + -
465A PHE* 3.2 48.5 - - + -
491A LEU* 3.7 6.3 - - + +
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Residues in contact with TYR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.4 0.6 - - - +
315A SER 3.0 13.8 + - - +
316A PHE* 3.0 11.9 + - - +
318A MET* 1.3 78.7 - - - +
320A GLU* 1.3 83.9 + - - +
322A ALA* 3.3 2.6 + - - +
323A THR* 3.0 49.8 + - + +
324A HIS* 6.0 0.2 - + - -
367A PHE* 5.8 0.7 - + - -
471A THR* 4.1 13.0 - - + -
472A GLN 3.1 20.9 + - - -
473A ILE* 3.7 12.5 - - - +
474A PRO* 3.6 4.5 - - - +
475A LEU* 2.9 50.3 + - + -
489A VAL* 4.2 28.9 - - + -
491A LEU* 4.4 8.7 - - + -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE 2.9 17.4 + - - +
317A ILE* 3.5 7.0 - - - +
319A TYR* 1.3 91.2 - - - +
321A LEU* 1.3 63.1 + - - +
323A THR* 3.1 3.7 + - - -
324A HIS* 2.9 41.6 + - - +
363A THR* 4.3 10.8 - - + +
366A LEU* 4.1 4.1 - - - +
367A PHE* 3.2 28.6 - - + -
414A PHE* 3.5 56.8 - - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 2.9 29.5 + - + +
318A MET* 3.9 27.8 - - + +
320A GLU* 1.3 76.0 - - - +
322A ALA* 1.3 60.5 + - - +
324A HIS 3.1 21.8 - - - +
325A PRO 3.7 0.3 - - - -
327A VAL* 3.6 31.4 - - + -
328A GLN* 3.0 34.9 + - + +
331A LEU* 4.1 8.3 - - + -
359A VAL* 3.9 13.5 - - + -
414A PHE* 4.8 2.2 - - + -
456A LEU* 5.0 0.9 - - + -
460A LEU* 3.9 29.4 - - + -
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A MET 3.0 18.9 + - - +
319A TYR 3.7 3.8 - - - +
321A LEU* 1.3 77.4 - - - +
323A THR* 1.3 63.0 + - + +
324A HIS 3.2 0.7 + - - -
325A PRO* 3.9 10.4 - - - +
328A GLN* 3.8 0.6 + - - +
465A PHE* 3.5 26.2 - - + +
466A LYS* 5.2 0.3 + - - -
467A PRO* 3.3 27.1 - - + +
491A LEU* 3.7 28.7 - - + -
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Residues in contact with THR 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR* 3.0 47.2 + - + +
320A GLU* 3.1 9.0 + - - -
322A ALA* 1.3 79.5 - - + +
324A HIS* 1.3 90.4 + - - +
325A PRO* 3.5 6.9 - - - +
467A PRO* 4.5 6.1 - - + -
471A THR* 5.1 1.8 - - + -
473A ILE* 4.0 24.5 - - + -
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Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU* 2.9 30.3 + - - +
321A LEU 3.1 6.7 - - - +
323A THR* 1.3 115.9 + - - +
325A PRO* 1.3 68.7 - - - +
326A ASP* 3.2 14.4 - - - +
327A VAL* 3.0 26.9 + - + +
328A GLN 3.1 8.8 + - - -
414A PHE* 3.7 36.4 + + + +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il