Contacts of the helix formed by residues 307 - 337 (chain C) in PDB entry 2VIG
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 LEU 307 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLN* 3.8 15.3 - - - +
299C ALA* 5.2 9.6 - - + +
300C PHE* 5.6 6.1 - - + -
303C PRO 4.8 2.7 - - - +
304C LEU* 2.9 31.7 + - + +
306C LYS* 1.3 80.5 - - + +
308C GLN* 1.3 65.4 + - - +
309C VAL* 4.4 0.7 - - + -
310C ILE* 3.1 25.1 + - + +
311C GLN* 3.1 14.1 + - - +
501D FAD 3.4 55.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU* 4.2 17.7 - - + +
501A FAD 2.9 34.1 + - - -
307B LEU* 3.8 14.1 - - - +
308B GLN* 3.3 24.0 + - + +
309B VAL* 3.2 38.3 + - + +
306C LYS 3.5 4.5 + - - +
307C LEU* 1.3 70.9 - - - +
309C VAL* 1.3 63.0 + - - +
311C GLN* 3.1 12.9 + - - +
312C PHE* 3.0 30.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLN* 3.4 28.2 + - + +
309B VAL* 4.8 3.8 - - + +
312B PHE* 3.3 45.3 - - + -
307C LEU* 4.4 0.4 - - + -
308C GLN* 1.3 75.4 - - - +
310C ILE* 1.3 68.4 + - + +
312C PHE* 3.4 9.1 + - - +
313C LYS* 3.0 34.8 + - - +
396D GLU* 4.7 5.2 - - + -
501D FAD 3.3 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ALA* 4.3 11.9 - - + -
304C LEU* 3.4 38.6 - - + +
305C THR* 4.3 4.3 - - - -
307C LEU* 3.1 19.4 + - + +
309C VAL* 1.3 79.4 - - + +
311C GLN* 1.3 59.2 + - - +
313C LYS* 3.3 15.9 + - + +
314C LEU* 3.0 45.9 + - + +
366C ILE* 4.0 25.6 - - + -
501D FAD 4.0 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU* 3.3 26.3 - - + +
403A ALA* 3.3 31.3 - - + +
404A GLY 6.2 0.2 - - - -
407A LEU* 4.8 9.4 - - + +
305C THR* 2.8 30.6 + - - +
306C LYS* 3.6 19.4 + - - +
307C LEU 3.1 7.4 + - - +
308C GLN* 3.1 12.5 + - - +
310C ILE* 1.3 76.3 - - - +
312C PHE* 1.3 55.9 + - + +
314C LEU* 3.4 7.7 + - + +
315C ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 3.7 34.1 - - + -
399A ARG* 3.8 30.1 - - + -
400A LEU* 3.8 28.0 - - + -
501A FAD 4.9 1.1 - + - -
309B VAL* 3.4 44.2 - - + -
313B LYS* 5.7 1.8 - - - -
308C GLN 3.0 16.7 + - - +
309C VAL* 3.5 11.2 - - - +
311C GLN* 1.3 76.2 - - - +
313C LYS* 1.3 65.3 + - + +
315C ALA* 3.3 5.5 + - - +
316C ASP* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 5.8 2.0 - - - -
309C VAL* 3.0 20.7 + - - +
310C ILE* 3.5 20.0 - - + +
312C PHE* 1.3 75.7 - - + +
314C LEU* 1.3 58.1 + - - +
316C ASP* 3.3 6.2 + - - +
317C MET* 2.9 37.0 + - - +
362C GLN* 2.9 34.5 + - + +
365C GLN* 4.3 5.9 - - - +
366C ILE* 3.8 31.0 - - + -
396D GLU* 3.0 43.6 + - - +
501D FAD 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ALA* 5.3 1.8 - - + -
406A LEU* 3.6 14.0 - - + +
407A LEU* 4.1 28.0 - - + -
287C LEU* 3.9 22.6 - - + +
290C ALA* 4.1 8.7 - - + -
291C VAL* 3.9 17.0 - - + +
294C ALA* 5.0 1.8 - - + -
305C THR* 4.3 9.2 - - + -
310C ILE* 3.0 33.4 + - + +
311C GLN* 3.6 7.6 - - - +
313C LYS* 1.3 78.6 - - - +
315C ALA* 1.3 56.8 + - - +
317C MET* 3.4 7.5 + - - +
318C ALA* 2.9 29.3 + - - +
366C ILE* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 3.4 39.5 - - + +
402A ILE* 3.6 26.0 - - + +
403A ALA* 4.0 4.5 - - - +
406A LEU* 4.7 0.4 - - - +
311C GLN 2.8 18.7 + - - +
312C PHE 3.9 4.3 - - - +
313C LYS 3.3 0.2 - - - -
314C LEU* 1.3 72.1 - - - +
316C ASP* 1.3 59.9 + - - +
318C ALA* 3.3 3.4 + - - +
319C LEU* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 4.8 3.1 - - - +
399A ARG* 2.8 41.5 + - - +
312C PHE* 3.0 22.0 + - - +
313C LYS* 3.7 5.8 - - - +
315C ALA* 1.3 73.3 - - - +
317C MET* 1.3 58.6 + - + +
319C LEU* 3.4 8.1 + - - +
320C ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 3.8 25.8 - - + -
290C ALA* 4.0 19.7 - - + -
313C LYS 2.9 28.0 + - - +
314C LEU* 3.5 17.0 - - - +
316C ASP* 1.3 77.4 - - + +
318C ALA* 1.3 62.0 + - - +
320C ALA* 3.4 0.4 + - - -
321C LEU* 3.1 19.4 + - - +
359C ILE* 3.3 63.6 - - + +
362C GLN* 3.9 23.3 - - + -
363C ALA* 4.0 5.2 - - + +
366C ILE* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 3.7 16.4 - - + -
402A ILE* 4.6 1.6 - - + -
406A LEU* 3.8 29.8 - - + -
287C LEU* 4.0 11.4 - - + +
314C LEU 2.9 17.1 + - - +
315C ALA* 3.7 5.4 - - - +
317C MET* 1.3 73.3 - - - +
319C LEU* 1.3 65.4 + - - +
321C LEU* 3.3 1.7 + - - +
322C GLU* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.5 29.6 - - + -
347A MET* 3.6 35.1 - - + +
350A LEU* 3.8 35.0 - - + -
351A ALA* 4.3 14.1 - - + +
354A GLU* 5.9 0.9 - - - +
399A ARG* 5.7 2.0 - - - +
402A ILE* 5.6 1.3 - - + -
315C ALA 2.9 17.6 + - - +
316C ASP* 3.7 8.7 - - - +
318C ALA* 1.3 75.5 - - - +
320C ALA* 1.3 63.5 + - - +
322C GLU* 4.1 0.2 - - - -
323C SER* 3.1 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ASP 2.9 18.6 + - - +
317C MET 3.9 3.4 - - - +
319C LEU* 1.3 76.7 - - - +
321C LEU* 1.3 57.4 - - - +
323C SER* 3.8 4.9 - - - -
324C ALA* 3.2 27.9 + - - +
351C ALA 5.1 0.2 - - - +
355C ALA* 3.8 22.0 - - + +
358C ALA* 6.0 3.1 - - + -
359C ILE* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 3.8 32.5 - - + +
283C ALA* 3.9 16.4 - - + +
284C GLN* 3.6 42.2 - - - +
287C LEU* 4.0 18.8 - - + -
317C MET 3.1 16.5 + - - +
318C ALA* 3.8 3.8 - - - +
320C ALA* 1.3 76.0 - - - +
322C GLU* 1.3 64.6 + - + +
324C ALA* 3.3 3.8 + - - +
325C ARG* 2.9 43.0 + - - +
355C ALA* 4.7 1.6 - - + -
359C ILE* 3.7 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.6 1.8 - - + -
330A ARG* 2.9 44.6 + - - +
343A LYS* 3.1 30.5 + - - +
347A MET* 3.4 22.2 - - - +
406A LEU* 4.7 5.4 - - - +
318C ALA* 3.0 23.1 + - - +
319C LEU 4.2 0.2 - - - +
321C LEU* 1.3 76.6 - - + +
323C SER* 1.3 64.6 + - - +
325C ARG* 3.3 22.6 + - - +
326C LEU* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SER* 2.1 35.8 + - - +
327A LEU* 4.1 27.4 - - - +
351A ALA* 5.8 0.2 - - - +
319C LEU* 3.1 20.9 + - - -
320C ALA* 3.8 6.1 - - - -
322C GLU* 1.3 77.5 - - - +
324C ALA* 1.3 60.5 + - - -
326C LEU* 3.4 5.7 + - - +
327C LEU* 3.2 25.7 + - - +
351C ALA* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU* 3.6 16.6 - - + -
320C ALA 3.2 16.3 + - - +
321C LEU* 3.3 6.9 + - - +
323C SER* 1.3 75.5 - - - +
325C ARG* 1.3 65.1 + - - +
327C LEU* 3.4 4.8 + - - +
328C THR* 3.0 24.8 + - - -
348C ALA* 4.9 1.6 - - - +
351C ALA* 4.0 17.5 - - + +
352C ALA* 3.7 26.7 - - - +
355C ALA* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLU* 2.8 36.6 + - - -
280C LEU* 3.6 15.8 - - + +
284C GLN* 3.0 24.6 + - - +
321C LEU* 2.9 38.0 + - - +
322C GLU* 3.5 32.9 - - - +
323C SER 3.2 0.2 - - - -
324C ALA* 1.3 78.4 - - - +
326C LEU* 1.3 59.8 + - + +
328C THR* 3.0 4.2 + - - -
329C TRP* 2.9 67.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.7 43.2 - - + +
327A LEU* 3.8 30.3 - - + +
330A ARG* 4.1 31.2 - - + +
322C GLU 3.1 16.7 + - - +
323C SER* 3.9 4.5 - - - +
324C ALA 3.4 0.2 - - - -
325C ARG* 1.3 78.2 - - + +
327C LEU* 1.3 57.9 + - - +
329C TRP* 3.4 18.4 + - + +
330C ARG* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.5 22.9 - - + -
322A GLU 4.6 0.2 - - - -
323A SER* 4.2 26.5 - - - +
326A LEU* 3.6 22.6 - - + +
323C SER 3.2 13.1 + - - +
324C ALA* 3.5 7.0 - - - +
326C LEU* 1.3 76.8 - - - +
328C THR* 1.3 61.4 + - - +
330C ARG* 3.6 28.1 + - - +
331C ALA* 3.2 18.0 + - - +
344C GLU 4.1 2.6 - - - +
347C MET* 3.9 6.5 - - + +
348C ALA* 3.5 19.0 - - - +
351C ALA* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA* 4.3 12.1 - - + -
273C ILE* 4.2 13.5 - - + +
276C ALA* 3.5 20.6 - - + +
277C SER* 3.6 24.5 - - - +
280C LEU* 3.7 19.5 - - + +
324C ALA 3.0 13.5 + - - -
325C ARG 3.0 9.5 + - - -
327C LEU* 1.3 74.6 - - - +
329C TRP* 1.3 62.6 + - + +
331C ALA* 3.2 4.5 + - - +
332C ALA* 2.9 25.6 + - - +
348C ALA* 3.5 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.7 33.7 - - + -
42C LEU* 5.7 3.1 - - + -
96C LEU* 3.8 16.8 - - + -
99C ALA* 4.5 9.3 - - + +
100C ILE* 4.2 28.3 - - + +
103C GLU* 4.8 7.2 + - - -
280C LEU* 5.3 1.6 - - - +
325C ARG* 2.9 50.8 + - + +
326C LEU* 3.9 18.4 - - + +
328C THR* 1.3 86.7 - - + +
330C ARG* 1.3 58.9 + - - +
332C ALA* 3.4 5.1 + - - +
333C MET* 2.9 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 2.7 32.1 + - - +
326A LEU* 4.1 19.0 - - + +
502A EDO 3.4 37.4 + - - -
326C LEU 3.0 17.2 + - - +
327C LEU* 3.6 22.7 + - - +
328C THR 3.3 0.2 - - - -
329C TRP* 1.3 75.2 - - - +
331C ALA* 1.3 56.6 + - - +
333C MET* 3.2 8.8 + - - +
334C LEU* 3.0 42.6 + - + +
343C LYS* 4.7 0.6 - - - +
344C GLU* 3.6 30.8 + - - +
347C MET* 3.4 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ILE* 3.7 16.7 - - + +
327C LEU 3.2 6.0 + - - +
328C THR 3.2 9.0 + - - +
330C ARG* 1.3 77.8 - - - +
332C ALA* 1.3 63.4 + - - +
334C LEU* 3.5 3.9 + - - +
335C LYS* 3.1 23.7 + - - +
341C PHE* 4.0 4.7 - - - +
344C GLU* 3.7 40.2 - - + +
345C ALA* 3.9 10.8 - - + +
348C ALA* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.7 26.8 - - - +
96C LEU* 3.8 12.8 - - + -
99C ALA* 4.3 8.1 - - + -
273C ILE* 4.0 15.3 - - + +
328C THR 2.9 13.9 + - - +
329C TRP* 3.6 11.7 - - - +
331C ALA* 1.3 76.2 - - - +
333C MET* 1.3 56.2 + - - +
335C LYS* 3.4 3.6 + - - +
336C ASP* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 5.5 1.3 - - + -
96C LEU* 3.6 45.1 - - + -
329C TRP* 2.9 41.7 + - + +
330C ARG* 3.2 6.9 + - - +
332C ALA* 1.3 71.2 - - - +
334C LEU* 1.3 60.2 + - - +
336C ASP* 3.4 7.5 + - - +
337C ASN* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ARG* 3.0 29.6 + - + +
331C ALA 3.7 4.3 - - - +
333C MET* 1.3 73.6 - - + +
335C LYS* 1.3 65.2 + - - +
337C ASN* 3.1 8.4 + - - -
339C LYS* 2.9 49.5 + - + +
340C PRO 3.7 10.3 - - - +
341C PHE* 3.9 8.7 - - + -
344C GLU* 3.3 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 3.6 19.6 + - - -
95C TYR* 3.6 44.8 - - + +
270C MET* 3.7 24.8 - - + -
273C ILE* 4.4 3.6 - - + -
331C ALA 3.1 12.4 + - - +
332C ALA 3.4 4.0 + - - +
334C LEU* 1.3 77.9 - - - +
336C ASP* 1.3 61.6 + - - +
338C LYS* 3.1 24.1 + - - +
339C LYS 4.2 0.7 - - - -
341C PHE* 3.5 48.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 4.7 2.8 - - - +
94C ASP* 3.4 20.7 - - + +
95C TYR* 2.7 28.9 + - - +
96C LEU* 3.0 29.6 + - - +
332C ALA 2.9 18.5 + - - +
333C MET* 3.7 8.8 - - - +
334C LEU 3.2 0.2 - - - -
335C LYS* 1.3 79.1 + - - +
337C ASN* 1.3 64.1 + - - +
338C LYS* 3.3 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C MET* 2.9 32.4 + - - +
334C LEU* 3.1 3.7 + - - +
336C ASP* 1.3 83.2 - - - +
338C LYS* 1.3 70.2 - - - +
339C LYS* 3.1 33.9 + - + +
----------------------------------------------------------
Back to top of page
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