Contacts of the helix formed by residues 329 - 360 (chain C) in PDB entry 5NC5
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PHE 4.5 9.9 - - - +
137C LEU* 3.3 34.1 + - - +
299C ALA* 5.8 0.3 - - - +
327C TYR* 5.0 5.4 - - + -
328C ASP* 1.3 73.9 + - - +
330C THR* 1.4 64.4 + - - +
331C PRO* 3.4 0.7 - - - -
332C PHE* 3.2 18.8 + - - +
333C VAL* 3.3 16.6 + - - +
569C GLN* 4.4 13.7 - - - +
571C VAL* 4.8 7.4 - - + -
668C LEU* 4.3 23.8 - - + -
672C VAL* 6.0 3.8 - - + -
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Residues in contact with THR 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 4.2 20.0 - - + -
138C MET* 4.4 1.3 - - + -
299C ALA* 4.5 7.6 - - + +
300C LEU* 4.4 12.1 - - - -
303C ALA* 3.4 32.6 - - + +
328C ASP* 2.9 25.1 + - - +
329C THR* 1.4 74.8 - - - +
331C PRO* 1.3 77.6 - - - +
333C VAL* 3.0 19.9 + - - +
334C LYS* 3.0 27.8 + - - +
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Residues in contact with PRO 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ASP* 3.2 29.2 - - + +
330C THR* 1.3 98.3 - - - +
332C PHE* 1.3 61.2 + - - +
334C LYS* 3.5 12.1 + - + +
335C ILE* 3.1 24.4 + - - +
634C TRP* 4.2 14.7 - - + -
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Residues in contact with PHE 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLN* 3.3 38.8 - - - -
328C ASP 4.9 0.2 + - - -
329C THR* 3.2 11.0 + - - +
330C THR 3.1 1.2 - - - -
331C PRO* 1.3 79.4 - - - +
333C VAL* 1.3 67.2 + - + +
335C ILE* 3.2 2.9 + - - +
336C SER* 2.8 33.9 + - - -
567C GLU* 3.9 23.8 - - + -
568C ASP 3.6 23.8 - - - -
569C GLN* 3.4 49.5 + - + +
634C TRP* 3.8 13.9 - + + -
995C ALA* 4.3 5.6 - - + -
996C GLY* 4.0 20.9 - - - -
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Residues in contact with VAL 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA* 4.8 0.2 - - - -
34C GLN* 3.5 48.2 - - + +
299C ALA* 5.7 8.1 - - + -
300C LEU* 3.6 31.0 - - + -
329C THR* 3.3 14.7 + - - +
330C THR* 3.0 11.6 + - - +
332C PHE* 1.3 79.2 - - + +
334C LYS* 1.3 64.5 + - - +
336C SER* 3.4 6.6 + - - -
337C ILE* 3.2 26.7 + - + +
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Residues in contact with LYS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 3.9 27.1 - - + -
303C ALA* 6.4 1.1 - - - -
330C THR* 3.0 26.2 + - - +
331C PRO* 3.8 11.4 - - + +
333C VAL* 1.3 77.9 - - - +
335C ILE* 1.3 57.9 + - - +
337C ILE* 3.3 4.7 + - - +
338C HIS* 3.0 26.0 + - - +
1102C D10 4.4 33.1 - - + +
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Residues in contact with ILE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C PRO 3.1 13.8 + - - +
332C PHE* 3.4 10.8 - - - +
334C LYS* 1.3 76.0 - - - +
336C SER* 1.3 71.3 + - - +
338C HIS* 3.2 23.9 + - + +
339C GLU* 2.8 37.7 + - + +
634C TRP* 4.0 20.6 - - + -
995C ALA* 3.5 26.9 - - + -
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Residues in contact with SER 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLN* 4.0 11.1 - - - +
332C PHE* 2.8 40.7 + - - -
333C VAL* 3.5 7.3 + - - -
335C ILE* 1.3 74.7 - - - +
337C ILE* 1.3 62.2 + - - +
339C GLU* 3.4 2.3 + - - +
340C VAL* 2.9 32.4 + - - +
392C THR* 3.5 21.0 - - - +
995C ALA 4.1 14.6 - - - -
996C GLY* 4.8 4.5 - - - -
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Residues in contact with ILE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 3.3 26.0 - - + -
33C ALA 3.2 32.8 - - - +
34C GLN 4.0 1.3 - - - +
300C LEU* 4.7 0.7 - - + -
333C VAL* 3.2 22.4 + - + +
334C LYS* 3.8 4.7 - - - +
336C SER* 1.3 79.2 + - - +
338C HIS* 1.3 66.0 + - - +
340C VAL* 3.3 7.0 + - - +
341C VAL* 3.0 28.4 + - + +
390C ILE* 4.5 8.5 - - + +
391C ASN* 5.0 1.1 - - - -
392C THR* 4.4 10.8 - - + +
395C MET* 5.4 5.8 - - + -
1102C D10 4.2 30.3 - - + -
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Residues in contact with HIS 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C LYS 3.0 14.4 + - - +
335C ILE* 3.5 26.9 - - + +
337C ILE* 1.3 77.0 - - - +
339C GLU* 1.3 65.2 + - - +
341C VAL* 3.1 10.1 + - + +
342C LYS* 2.9 35.8 + - + +
1102C D10 6.3 1.3 - - - +
3F GLU* 6.1 0.4 - - - -
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Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ILE* 2.8 33.5 + - + +
336C SER 3.6 5.2 - - - +
337C ILE 3.3 0.2 - - - -
338C HIS* 1.3 80.2 - - - +
340C VAL* 1.3 57.9 + - - +
342C LYS* 3.1 30.1 - - - +
343C THR* 3.0 30.0 + - - -
992C SER* 4.6 5.2 + - - -
994C GLY* 3.8 21.9 + - - -
995C ALA 3.8 24.7 - - - +
1000C GLN* 3.7 10.9 + - - +
3F GLU* 4.2 7.2 - - - +
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Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C SER* 2.9 21.6 + - - +
337C ILE* 3.3 6.0 + - - +
339C GLU* 1.3 73.1 - - - +
341C VAL* 1.3 64.4 + - - +
343C THR* 3.4 4.1 + - + -
344C LEU* 3.1 23.2 + - - +
392C THR* 4.6 12.8 - - + -
395C MET* 3.4 36.6 - - + +
396C PHE* 3.7 30.1 - - + -
399C VAL* 4.8 5.2 - - + -
1000C GLN* 3.6 18.6 - - + +
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Residues in contact with VAL 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ILE* 3.0 24.3 + - + +
338C HIS* 3.7 9.4 - - + +
340C VAL* 1.3 77.7 - - - +
342C LYS* 1.3 64.1 + - - +
344C LEU* 3.3 10.0 + - + +
345C VAL* 3.2 30.9 + - + +
395C MET* 4.5 11.9 - - + -
1102C D10 4.0 42.2 - - + -
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Residues in contact with LYS 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C HIS* 2.9 20.2 + - + +
339C GLU* 3.1 36.6 - - - +
341C VAL* 1.3 78.2 - - - +
343C THR* 1.3 62.9 + - - +
345C VAL* 3.3 7.1 + - - +
346C GLU* 3.1 44.8 + - - +
3F GLU* 3.3 29.6 - - - +
4F LEU* 3.6 33.2 - - + +
7F SER* 3.9 14.8 + - - -
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Residues in contact with THR 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C GLU 3.0 11.0 + - - -
340C VAL* 3.5 10.1 - - - -
342C LYS* 1.3 80.1 - - - +
344C LEU* 1.3 57.7 + - - +
346C GLU* 3.4 5.2 + - - +
347C ALA* 2.9 27.9 + - - +
399C VAL* 3.8 13.7 - - + -
988C PRO* 4.0 23.5 + - + +
989C LEU* 3.4 33.2 - - + -
992C SER* 5.2 1.4 - - - -
1000C GLN* 3.2 19.4 + - - -
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C VAL 3.1 17.2 + - - +
341C VAL* 3.3 13.9 + - + +
343C THR* 1.3 75.2 - - - +
345C VAL* 1.3 66.4 + - + +
347C ALA* 3.4 4.0 + - - +
348C ILE* 3.1 30.5 + - + +
376C LEU* 5.7 4.0 - - + -
380C PHE* 5.9 0.9 - - + -
395C MET* 3.5 34.8 - - + +
398C MET* 3.6 21.1 - - + +
399C VAL* 3.2 45.1 - - + +
402C ILE* 4.9 6.8 - - + +
1102C D10 5.5 5.8 - - + -
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Residues in contact with VAL 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C VAL* 3.2 21.5 + - + +
342C LYS* 3.7 8.1 - - - +
343C THR 3.2 0.2 - - - -
344C LEU* 1.3 79.2 - - + +
346C GLU* 1.3 63.6 + - - +
348C ILE* 3.1 22.3 + - + +
349C ILE* 3.1 30.3 + - + +
4F LEU* 4.4 15.7 - - + -
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Residues in contact with GLU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LYS* 3.1 41.2 + - - +
343C THR* 4.0 7.9 + - - +
345C VAL* 1.3 76.0 - - - +
347C ALA* 1.3 63.5 + - - +
349C ILE* 3.2 9.6 + - + +
350C LEU* 2.9 32.9 + - + +
988C PRO* 3.7 27.4 - - + +
991C ILE* 5.4 8.2 - - - +
4F LEU* 4.7 10.7 - - + +
7F SER* 3.9 19.7 + - - +
8F LEU* 5.5 0.4 - - - -
11F ALA* 3.7 24.2 - - + +
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Residues in contact with ALA 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C THR 2.9 18.0 + - - +
344C LEU* 3.7 6.5 - - - +
345C VAL 3.2 0.4 - - - -
346C GLU* 1.3 76.8 - - - +
348C ILE* 1.3 57.8 + - - +
350C LEU* 3.5 2.0 + - - +
351C VAL* 2.9 35.3 + - - +
399C VAL* 4.4 9.4 - - + -
402C ILE* 4.2 14.1 - - + -
985C GLY* 3.1 33.4 - - - +
988C PRO* 4.1 6.7 - - + +
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Residues in contact with ILE 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 3.1 21.2 + - + +
345C VAL* 3.1 17.7 + - + +
347C ALA* 1.3 77.9 - - - +
349C ILE* 1.3 63.9 + - + +
351C VAL* 4.0 2.3 - - - +
352C PHE* 3.0 28.8 + - + +
369C THR* 6.0 6.3 - - + -
372C VAL* 4.0 23.6 - - + -
376C LEU* 4.7 6.1 - - + -
402C ILE* 3.4 31.0 - - + -
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Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C VAL* 3.1 32.0 + - + +
346C GLU* 3.9 9.6 - - + +
348C ILE* 1.3 79.0 - - + +
350C LEU* 1.3 63.2 + - + +
352C PHE* 3.2 9.0 + - + +
353C LEU* 2.9 46.9 + - + +
4F LEU* 4.9 11.0 - - + -
8F LEU* 6.5 0.7 - - + -
12F VAL* 5.7 3.8 - - + -
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLU* 2.9 24.0 + - + +
347C ALA 3.8 3.4 - - - +
349C ILE* 1.3 79.3 - - + +
351C VAL* 1.3 57.6 + - - +
353C LEU* 3.4 8.6 + - + +
354C VAL* 3.0 32.6 + - - +
984C LEU* 3.4 40.2 - - + +
987C MET* 4.5 8.3 - - + -
988C PRO* 4.1 17.3 - - + -
11F ALA* 3.7 34.1 - - + +
12F VAL* 4.6 2.2 - - + +
15F VAL* 3.6 25.1 - - + +
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Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ALA 2.9 20.3 + - - +
348C ILE* 4.0 2.9 - - - +
350C LEU* 1.3 72.7 - - - +
352C PHE* 1.3 67.1 + - - +
354C VAL* 3.2 6.5 + - - +
355C MET* 2.9 36.5 + - + +
372C VAL* 5.9 1.1 - - + -
402C ILE* 3.6 21.1 - - + -
403C GLY* 4.7 2.0 - - - -
406C VAL* 4.1 29.8 - - + -
981C ALA* 3.2 36.1 - - + +
985C GLY* 4.0 7.2 - - - +
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Residues in contact with PHE 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ILE* 3.0 18.0 + - + +
349C ILE* 3.2 13.2 + - + +
351C VAL* 1.3 78.8 - - - +
353C LEU* 1.3 69.2 + - + +
355C MET* 3.5 8.9 + - - -
356C TYR* 2.9 45.4 + + + +
362C PHE* 4.8 13.5 - + - -
365C THR* 3.5 23.8 - - + +
366C LEU* 4.7 14.8 - - + -
369C THR* 3.5 27.1 - - + +
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Residues in contact with LEU 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ILE* 2.9 44.7 + - + +
350C LEU* 3.7 8.5 - - + +
351C VAL 3.3 0.2 - - - -
352C PHE* 1.3 86.0 - - + +
354C VAL* 1.3 67.4 + - - +
356C TYR* 3.1 5.4 + - + +
357C LEU* 2.8 29.7 + - + +
12F VAL* 3.7 39.3 - - + +
15F VAL* 4.0 22.9 - - + -
16F PRO* 6.0 0.7 - - + -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LEU 3.0 15.3 + - - +
351C VAL* 3.2 6.5 + - - +
353C LEU* 1.3 76.2 - - - +
355C MET* 1.3 66.4 + - + +
357C LEU* 3.2 12.2 + - + +
358C PHE* 3.3 26.9 + - + -
977C MET* 4.1 8.5 - - + +
980C LEU* 3.7 27.6 - - + +
981C ALA* 4.0 12.1 - - + +
984C LEU* 3.4 39.9 - - + -
15F VAL* 3.8 15.5 - - + +
19F MET* 5.7 1.8 - - + -
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Residues in contact with MET 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C VAL* 2.9 34.8 + - + +
352C PHE* 4.5 3.8 - - - -
354C VAL* 1.3 80.2 - - + +
356C TYR* 1.3 56.4 + - - +
358C PHE* 3.3 2.1 + - - -
359C LEU* 2.8 37.1 + - + +
365C THR* 3.6 11.9 - - + +
368C PRO* 3.3 32.3 - - + +
369C THR* 3.3 41.1 - - - +
406C VAL* 4.6 5.2 - - + -
410C ILE* 3.8 28.7 - - + -
977C MET* 4.7 10.3 - - + -
981C ALA* 5.4 0.7 - - + -
----------------------------------------------------------
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Residues in contact with TYR 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C PHE* 2.9 34.8 + + + +
353C LEU* 3.1 6.9 + - + +
355C MET* 1.3 72.6 - - - +
357C LEU* 1.3 71.7 + - + +
360C GLN* 2.8 25.0 + - - +
361C ASN* 4.0 11.1 - - - -
362C PHE* 3.3 59.4 - + - -
365C THR* 3.4 22.8 - - + +
513C PHE* 3.6 31.5 - + - -
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 2.8 12.6 + - + +
354C VAL* 3.4 11.0 - - - +
356C TYR* 1.3 82.9 - - + +
358C PHE* 1.3 57.4 + - - +
360C GLN* 3.4 15.2 - - - +
512C PHE* 4.0 29.6 - - + -
513C PHE* 4.4 7.3 - - + -
516C PHE* 3.6 21.3 - - + -
15F VAL* 4.2 31.2 - - + +
16F PRO* 5.0 10.5 - - + -
19F MET* 3.1 34.3 - - + -
----------------------------------------------------------
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Residues in contact with PHE 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C VAL* 3.3 25.9 + - + +
355C MET 3.3 6.2 + - - +
356C TYR 3.1 0.2 - - - -
357C LEU* 1.3 79.7 - - - +
359C LEU* 1.3 63.7 + - - +
360C GLN* 3.4 7.5 - - - +
516C PHE* 4.3 13.2 - + - -
520C PHE* 4.0 29.4 - + - -
973C ARG* 3.1 41.8 + - + -
976C LEU* 4.6 7.2 - - + -
977C MET* 3.5 53.8 - - + -
980C LEU* 4.8 3.8 - - + -
19F MET* 3.3 40.2 - - + -
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Residues in contact with LEU 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C MET* 2.8 21.4 + - + +
358C PHE* 1.3 74.1 - - - +
360C GLN* 1.3 73.2 + - - +
361C ASN* 3.1 14.3 + - - -
364C ALA* 3.1 44.2 - - + +
365C THR* 3.8 12.6 - - + +
368C PRO* 4.3 11.9 - - + -
410C ILE* 6.5 0.2 - - - -
413C VAL* 4.0 18.8 - - + -
414C GLU* 5.0 8.5 - - + +
417C GLU* 3.9 22.6 - - - +
509C LYS* 5.4 0.9 + - - -
973C ARG* 5.6 3.6 - - - +
977C MET* 4.1 26.2 - - + -
----------------------------------------------------------
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Residues in contact with GLN 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C TYR* 2.8 25.4 + - - -
357C LEU 3.4 21.7 - - - +
358C PHE 3.4 14.2 - - - +
359C LEU* 1.3 78.2 + - - +
361C ASN* 1.3 61.5 + - - +
506C GLY* 5.0 3.4 - - - -
509C LYS* 3.6 31.2 + - - +
513C PHE* 3.9 38.2 - - + +
516C PHE* 4.3 1.8 - - - -
517C ASN* 2.4 46.4 + - - -
973C ARG* 3.9 4.8 + - - -
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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