Contacts of the helix formed by residues 329 - 360 (chain A) in PDB entry 4C48
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 THR 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.2 39.3 - - - +
136A PHE 4.1 4.5 + - - -
137A LEU* 2.6 39.0 + - - -
327A TYR* 4.9 5.0 + - - -
328A ASP* 1.3 73.0 + - - +
330A THR* 1.3 66.4 + - - +
332A PHE* 3.2 23.5 - - - +
333A VAL* 3.7 3.0 + - + +
569A GLN* 4.1 16.4 - - - +
571A VAL* 5.9 3.8 - - - -
672A VAL* 5.5 6.3 - - + +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.8 6.7 - - + -
300A LEU* 4.3 26.2 - - + -
303A ALA* 3.8 29.4 - - + -
328A ASP* 3.1 16.4 + - - +
329A THR* 1.3 76.9 - - - +
331A PRO* 1.4 69.5 - - - +
333A VAL* 2.5 35.1 + - + +
334A LYS* 3.0 18.8 + - - +
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Residues in contact with PRO 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASP* 3.4 29.2 - - + +
330A THR* 1.4 98.1 - - - +
332A PHE* 1.3 60.0 + - - +
334A LYS* 3.9 13.0 - - + +
335A ILE* 3.0 38.7 + - + +
634A TRP* 5.0 3.6 - - + -
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Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.8 16.8 - - + -
35A TYR* 5.5 6.7 - + - -
328A ASP 5.0 1.5 + - - +
329A THR* 3.2 13.6 + - - +
330A THR 3.0 0.4 - - - -
331A PRO* 1.3 80.8 - - - +
333A VAL* 1.3 62.2 + - + +
335A ILE* 3.7 2.8 - - + +
336A SER* 2.8 39.0 + - - -
392A THR* 5.7 5.6 - - - -
567A GLU* 3.9 26.0 - - + -
568A ASP 4.3 6.7 - - - -
569A GLN* 3.6 46.7 - - + +
634A TRP* 4.3 26.3 - + + -
995A ALA 4.7 4.5 - - - -
996A GLY* 4.1 15.9 - - - -
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 5.4 3.6 - - + -
33A ALA 5.4 0.7 - - - -
34A GLN* 3.3 52.7 - - + +
300A LEU* 3.4 34.1 - - + -
329A THR* 3.8 8.7 - - + +
330A THR* 2.5 26.7 + - + +
332A PHE* 1.3 73.3 - - + +
334A LYS* 1.3 68.3 + - - +
335A ILE 3.1 1.3 - - - -
336A SER* 3.1 12.5 + - - +
337A ILE* 3.1 28.8 + - + +
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Residues in contact with LYS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 5.4 3.2 - - + +
300A LEU* 3.4 45.0 - - + +
330A THR* 3.0 21.0 + - - +
331A PRO* 4.0 14.1 - - + +
333A VAL* 1.3 76.5 - - + +
335A ILE* 1.3 61.1 + - + +
337A ILE* 3.3 14.4 - - + +
338A HIS* 3.1 26.5 + - - +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PRO* 3.0 26.6 + - + +
332A PHE* 3.7 4.0 - - + +
334A LYS* 1.3 78.6 - - + +
336A SER* 1.3 65.8 + - - +
337A ILE 3.1 2.0 - - - -
338A HIS* 3.4 9.4 - - + +
339A GLU* 2.9 27.2 + - + +
633A ASP* 5.1 5.4 - - - +
634A TRP* 3.7 27.6 - - + -
995A ALA* 3.6 37.2 - - + +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A PHE* 2.8 36.3 + - - -
333A VAL* 3.1 14.1 + - - +
335A ILE* 1.3 79.3 - - - +
337A ILE* 1.3 67.2 + - - +
339A GLU* 4.0 5.7 - - - +
340A VAL* 3.5 23.4 + - - +
392A THR* 4.7 16.1 - - - -
995A ALA 4.9 5.8 - - - -
996A GLY 6.2 0.2 - - - -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 5.5 16.2 - - + -
333A VAL* 3.3 15.9 - - + +
334A LYS* 3.3 21.1 - - + +
336A SER* 1.3 86.0 + - - +
338A HIS* 1.3 68.1 + - - +
339A GLU 3.2 1.6 - - - -
340A VAL* 3.9 5.0 - - - +
341A VAL* 2.9 31.5 + - + +
390A ILE* 5.5 7.9 - - + +
391A ASN 4.6 17.5 - - - +
392A THR* 5.6 0.4 - - - -
395A MET* 4.7 13.6 - - + +
2044A LMT 4.4 23.8 - - + -
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Residues in contact with HIS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS 3.1 20.2 + - - +
335A ILE* 3.4 14.4 - - + +
337A ILE* 1.3 79.8 - - - +
339A GLU* 1.3 70.9 + - - +
341A VAL* 3.5 6.2 + - - +
342A LYS* 3.0 32.5 + - + +
3C GLU* 4.9 14.4 - - - -
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ILE* 2.9 21.6 + - + +
336A SER* 4.0 6.1 - - - +
338A HIS* 1.3 85.3 + - - +
340A VAL* 1.3 61.4 + - + +
342A LYS* 3.4 17.6 + - - +
343A THR* 3.0 37.0 + - + +
992A SER* 4.1 16.6 + - - +
993A THR 5.9 1.6 - - - -
994A GLY 5.5 0.2 - - - +
995A ALA* 3.8 32.1 - - + +
1000A GLN* 5.8 6.7 - - - +
3C GLU* 5.3 3.6 - - - +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER 3.5 14.0 + - - +
337A ILE* 3.4 4.3 + - - +
339A GLU* 1.3 79.1 - - + +
341A VAL* 1.3 65.9 + - - +
343A THR* 2.5 28.6 + - + +
344A LEU* 2.9 11.4 + - + +
395A MET* 3.6 42.4 - - + +
396A PHE* 4.0 34.3 - - + +
398A MET* 5.7 0.7 - - + -
399A VAL* 4.9 13.0 - - + +
989A LEU* 6.1 1.1 - - + -
1000A GLN* 5.8 2.7 - - + -
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 2.9 23.7 + - + +
338A HIS* 3.8 7.0 - - - +
340A VAL* 1.3 77.0 - - - +
342A LYS* 1.3 61.0 + - + +
344A LEU* 3.1 10.9 + - + +
345A VAL* 3.0 37.2 + - + +
395A MET* 3.7 20.6 - - + -
2044A LMT 4.0 41.5 - - + -
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A HIS* 3.0 31.0 + - + +
339A GLU* 3.8 18.5 + - - +
341A VAL* 1.3 78.3 - - + +
343A THR* 1.3 63.0 + - + +
345A VAL* 4.0 6.3 - - + +
346A GLU* 3.0 55.6 + - + +
3C GLU* 3.7 47.7 + - + +
4C LEU* 5.3 11.8 - - + +
6C LYS* 3.9 16.3 - - - +
7C SER* 5.7 0.9 - - - -
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Residues in contact with THR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 3.0 23.8 + - + +
340A VAL* 2.5 29.6 + - + +
342A LYS* 1.3 76.3 - - + +
344A LEU* 1.3 57.6 + - - +
346A GLU* 3.4 13.4 - - - +
347A ALA* 2.9 30.5 + - - +
399A VAL* 4.5 6.5 - - - +
985A GLY 4.5 0.5 - - - +
988A PRO* 3.6 23.6 - - + +
989A LEU* 3.7 29.9 - - + +
992A SER* 5.6 4.0 - - - +
1000A GLN* 5.8 2.7 - - + -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A VAL* 2.9 14.5 + - + +
341A VAL* 3.1 14.3 + - + +
343A THR* 1.3 76.3 + - - +
345A VAL* 1.3 75.5 + - + +
347A ALA* 3.1 8.1 + - - +
348A ILE* 2.9 34.5 + - + +
376A LEU* 3.9 35.0 - - + -
395A MET* 5.1 10.8 - - + -
398A MET* 5.0 12.3 - - + -
399A VAL* 5.4 6.7 - - + -
402A ILE* 3.7 32.0 - - + +
2044A LMT 5.0 12.8 - - + -
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 3.0 23.1 + - + +
342A LYS* 4.0 6.7 - - + +
344A LEU* 1.3 86.0 - - + +
346A GLU* 1.3 59.3 + - - +
348A ILE* 2.9 23.1 + - + +
349A ILE* 3.0 31.5 + - + +
2044A LMT 6.3 2.7 - - + -
4C LEU* 4.8 23.1 - - + -
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LYS* 3.0 49.4 + - + +
343A THR* 3.4 19.4 + - - +
345A VAL* 1.3 80.4 - - + +
347A ALA* 1.3 55.7 + - - +
349A ILE* 3.3 12.0 - - + +
350A LEU* 2.9 35.4 + - + +
988A PRO* 3.1 34.7 - - + +
991A ILE* 5.9 1.1 - - - +
4C LEU* 6.0 2.7 - - + -
6C LYS* 5.5 0.7 + - - -
7C SER* 3.9 28.7 - - - -
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A THR 2.9 20.4 + - - +
344A LEU* 3.2 7.0 - - - +
346A GLU* 1.3 74.5 - - - +
348A ILE* 1.3 58.6 + - - +
350A LEU* 3.1 6.4 + - - +
351A VAL* 2.8 35.0 + - - +
399A VAL* 5.9 1.1 - - + -
402A ILE* 3.8 23.3 - - + -
985A GLY* 3.3 30.3 - - - +
988A PRO* 5.4 0.2 - - - -
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Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 2.9 33.1 + - + +
345A VAL* 2.9 12.1 + - + +
347A ALA* 1.3 72.5 - - + +
349A ILE* 1.3 74.5 + - + +
351A VAL* 3.6 8.9 + - + +
352A PHE* 3.0 23.0 + - + +
369A THR* 4.6 14.6 - - + +
372A VAL* 3.8 32.5 - - + -
373A PRO* 4.5 13.5 - - + -
376A LEU* 4.4 4.0 - - + -
402A ILE* 5.8 3.6 - - + -
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL* 3.0 32.5 + - + +
346A GLU* 3.3 16.2 - - + +
348A ILE* 1.3 84.8 - - + +
350A LEU* 1.3 60.2 + - - +
352A PHE* 2.8 23.8 + - - +
353A LEU* 3.0 34.7 + - + +
7C SER* 5.2 10.8 - - - +
8C LEU* 5.4 8.3 - - + -
11C ALA* 4.2 15.7 - - + -
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 2.9 28.4 + - + +
347A ALA* 3.1 5.8 + - - +
349A ILE* 1.3 75.0 - - + +
351A VAL* 1.3 63.8 + - - +
353A LEU* 3.2 5.8 + - - +
354A VAL* 3.0 26.4 + - - +
981A ALA 5.4 0.2 - - - -
984A LEU* 2.9 47.8 - - + +
987A MET* 4.1 14.6 - - + -
988A PRO* 4.5 6.7 - - + -
11C ALA* 3.3 41.7 - - + +
14C MET* 5.9 0.9 - - + -
15C VAL* 4.5 9.8 - - + +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA 2.8 18.8 + - - +
348A ILE* 3.7 9.2 - - + +
350A LEU* 1.3 76.2 - - - +
352A PHE* 1.3 60.2 + - - +
353A LEU 3.0 0.3 + - - -
354A VAL* 3.0 3.5 + - - +
355A MET* 2.9 42.4 + - + +
368A PRO* 5.5 6.1 - - + +
369A THR* 4.8 11.9 - - + -
372A VAL* 5.6 4.3 - - + -
402A ILE* 5.5 1.8 - - + -
406A VAL* 4.0 29.2 - - + -
410A ILE* 5.7 2.5 - - + -
981A ALA* 4.0 37.5 - - + +
985A GLY* 5.2 3.4 - - - -
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 3.0 14.4 + - + +
349A ILE* 2.8 17.1 + - + +
351A VAL* 1.3 75.5 - - - +
353A LEU* 1.3 66.7 + - + +
355A MET* 3.7 6.9 - - - +
356A TYR* 3.0 36.1 + + + +
362A PHE* 5.0 3.4 - - + -
365A THR* 3.2 37.0 - - + -
366A LEU* 4.5 8.1 - - + -
369A THR* 3.3 26.7 - - + -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 3.0 47.4 + - + +
350A LEU* 3.5 8.1 - - - +
351A VAL 3.1 0.2 - - - -
352A PHE* 1.3 86.4 - - + +
354A VAL* 1.3 60.2 + - - +
356A TYR* 3.3 4.1 + - - +
357A LEU* 2.8 32.7 + - - +
8C LEU* 5.3 5.8 - - + -
11C ALA* 4.0 4.0 - - + -
12C VAL* 3.9 36.8 - - + +
15C VAL* 3.8 28.7 - - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU 3.0 12.6 + - - +
351A VAL 3.8 5.2 - - - +
353A LEU* 1.3 75.0 - - - +
355A MET* 1.3 66.6 + - + +
357A LEU* 3.7 5.5 + - - -
358A PHE* 3.1 43.0 + - + +
977A MET* 3.6 25.4 - - - +
980A LEU* 3.8 17.5 - - + -
981A ALA* 3.9 14.6 - - + +
984A LEU* 3.4 32.8 - - + -
15C VAL* 4.4 7.2 - - + -
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 2.9 32.1 + - + +
352A PHE* 3.7 8.3 - - - +
354A VAL* 1.3 86.6 - - + +
356A TYR* 1.3 61.1 + - - +
358A PHE* 3.2 1.1 + - - -
359A LEU* 2.8 43.2 + - + +
365A THR* 3.5 18.2 - - + +
368A PRO* 3.6 31.4 - - + -
369A THR* 5.5 0.7 - - + -
410A ILE* 3.7 35.0 - - + -
413A VAL* 5.2 0.4 - - - -
977A MET* 3.7 26.5 - - + +
981A ALA* 5.0 3.6 - - + -
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Residues in contact with TYR 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 3.0 29.4 + + + +
353A LEU* 3.8 4.7 - - - +
355A MET* 1.3 74.6 - - - +
357A LEU* 1.3 62.1 + - - +
358A PHE 2.8 1.6 + - - -
360A GLN* 2.6 47.2 + - - +
361A ASN* 4.2 1.5 - - - -
362A PHE* 3.5 40.6 + - + -
365A THR* 3.3 19.7 - - + +
513A PHE* 3.6 35.4 - + - -
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU 2.8 18.7 + - - +
354A VAL* 4.0 4.5 - - - +
356A TYR* 1.3 80.8 - - - +
358A PHE* 1.3 59.3 + - + +
360A GLN* 4.1 8.5 + - - +
512A PHE* 4.4 26.9 - - + -
513A PHE* 5.6 3.4 - - - -
516A PHE* 3.2 34.6 - - + -
980A LEU* 5.3 0.7 - - + -
15C VAL* 3.8 25.6 - - + -
16C PRO* 5.2 11.0 - - + -
19C MET* 3.6 33.4 - - + -
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Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 3.1 35.4 + - + +
355A MET 3.9 0.4 - - - +
356A TYR 2.8 1.8 + - - -
357A LEU* 1.3 81.2 - - + +
359A LEU* 1.3 64.6 + - - +
360A GLN* 3.4 8.5 - - - +
516A PHE* 4.0 16.2 - + - -
517A ASN* 5.3 2.9 - - - +
520A PHE* 3.7 33.2 - + - -
973A ARG* 4.2 15.6 + - + -
976A LEU* 4.4 5.8 - - + -
977A MET* 3.3 60.1 - - + -
980A LEU* 4.1 4.7 - - + -
19C MET* 3.2 33.4 - - + -
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 2.8 29.2 + - - +
358A PHE* 1.3 72.8 - - - +
360A GLN* 1.3 70.0 + - - +
361A ASN* 2.9 15.0 + - - +
364A ALA* 3.9 33.3 - - + +
365A THR* 5.2 1.1 - - + +
368A PRO* 5.3 0.2 - - + -
413A VAL* 4.3 23.3 - - + -
414A GLU* 5.0 3.6 - - - -
417A GLU* 3.8 37.4 - - + +
497A LEU* 6.0 2.7 - - + -
509A LYS* 5.4 1.2 + - - -
973A ARG* 4.0 20.2 - - - +
977A MET* 4.1 14.4 - - + -
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 2.6 41.8 + - - +
357A LEU 4.1 9.2 + - - +
358A PHE 4.4 5.1 - - - +
359A LEU* 1.3 72.4 - - - +
361A ASN* 1.3 73.4 + - - +
506A GLY* 5.7 0.2 - - - -
509A LYS* 4.1 22.7 + - + +
512A PHE* 5.3 0.6 - - - -
513A PHE* 3.1 50.1 + - + +
516A PHE* 3.9 15.7 - - - +
517A ASN* 2.7 38.3 + - - +
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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