Contacts of the helix formed by residues 250 - 283 (chain A) in PDB entry 4DUB
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 ASP 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASN* 5.0 7.5 + - - -
98A LYS* 4.8 4.5 - - - +
248A PRO 3.7 2.4 + - - -
249A LEU* 1.3 74.3 - - - +
251A ASP* 1.3 65.8 + - - +
252A GLU* 3.5 10.5 + - - +
253A ASN* 2.9 38.0 + - - +
254A ILE* 2.9 15.3 + - - +
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Residues in contact with ASP 251 (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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217A ASP* 5.0 1.1 - - - +
220A ILE* 3.7 21.5 - - + +
224A LYS* 2.7 46.1 + - - +
238A LEU* 4.3 1.7 - - - +
249A LEU 5.0 0.7 - - - +
250A ASP* 1.3 75.9 - - - +
252A GLU* 1.3 62.7 + - - +
254A ILE* 3.4 14.9 + - - +
255A ARG* 3.0 22.9 + - - +
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Residues in contact with GLU 252 (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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84A ASP* 5.0 4.2 - - - +
217A ASP* 5.6 0.9 - - - -
250A ASP* 3.1 12.1 + - - +
251A ASP* 1.3 80.5 - - - +
253A ASN* 1.3 62.6 + - - +
255A ARG* 3.2 29.3 + - - +
256A TYR* 3.1 47.3 + - + -
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Residues in contact with ASN 253 (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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84A ASP* 2.9 47.6 + - - +
85A GLY 4.3 0.4 - - - +
95A ASN* 3.8 22.7 - - - +
99A ALA* 4.1 0.7 - - - +
249A LEU* 3.4 21.1 - - + +
250A ASP* 2.9 26.9 + - - +
252A GLU* 1.3 78.2 - - - +
254A ILE* 1.3 58.0 + - - +
256A TYR* 3.0 7.8 + - - +
257A GLN* 2.8 49.2 + - - +
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Residues in contact with ILE 254 (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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220A ILE* 3.9 9.0 - - + -
234A LEU* 3.7 26.7 - - + -
237A MET* 3.9 36.3 - - + +
238A LEU* 3.9 26.7 - - + -
249A LEU* 3.6 31.0 - - + +
250A ASP 2.9 14.4 + - - +
251A ASP* 3.7 14.8 - - - +
253A ASN* 1.3 74.1 - - - +
255A ARG* 1.3 64.6 + - - +
257A GLN* 3.1 12.2 + - - +
258A ILE* 3.0 22.6 + - + +
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Residues in contact with ARG 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ASN* 3.5 37.9 + - - +
216A VAL* 3.5 29.6 - - + -
217A ASP* 2.7 44.6 + - - +
220A ILE* 3.6 4.4 - - + +
251A ASP 3.0 13.6 + - - +
252A GLU* 3.2 27.2 + - - +
254A ILE* 1.3 77.1 - - - +
256A TYR* 1.3 99.0 + - - +
258A ILE* 3.3 2.3 + - - +
259A ILE* 3.1 31.5 + - + +
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Residues in contact with TYR 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP 5.5 3.0 + - - -
81A PHE* 3.5 22.7 - - - -
82A ALA* 3.3 24.6 - - - +
83A GLY* 3.6 17.4 - - - -
84A ASP* 3.6 18.8 - - - -
85A GLY* 4.0 11.0 - - - +
213A ASN* 4.6 5.1 + - - -
252A GLU* 3.1 41.9 + - + -
253A ASN* 3.0 8.7 + - - +
255A ARG* 1.3 106.2 + - - +
257A GLN* 1.3 57.8 + - - +
259A ILE* 3.9 3.5 - - + +
260A THR* 2.6 39.0 + - - -
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Residues in contact with GLN 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP 3.9 2.2 + - - -
85A GLY* 3.7 9.1 - - - -
86A LEU* 3.0 34.8 + - - +
95A ASN 4.6 0.4 + - - -
99A ALA* 3.2 24.0 - - - +
103A LEU* 4.3 6.4 - - + +
237A MET* 3.8 25.1 - - - -
249A LEU* 4.3 2.0 - - + -
253A ASN* 2.8 47.1 + - - +
254A ILE* 3.1 6.3 + - - +
256A TYR* 1.3 78.5 - - - +
258A ILE* 1.3 57.4 + - - +
260A THR* 3.2 3.3 + - - -
261A PHE* 2.8 46.1 + - + -
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Residues in contact with ILE 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY* 4.7 6.1 - - - +
158A PHE* 3.9 47.6 - - + -
216A VAL* 3.9 30.3 - - + -
220A ILE* 4.2 4.5 - - + -
234A LEU* 4.1 14.8 - - + -
237A MET* 3.9 14.6 - - + -
254A ILE* 3.0 33.6 + - + +
255A ARG 3.8 6.1 - - - +
256A TYR 3.3 0.2 - - - -
257A GLN* 1.3 72.4 - - - +
259A ILE* 1.3 66.9 + - - +
261A PHE* 3.2 12.7 + - + +
262A LEU* 3.2 26.3 + - + +
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Residues in contact with ILE 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.6 42.2 - - + +
82A ALA* 4.3 5.6 - - + -
173A PHE* 4.5 9.2 - - + -
177A MET* 4.6 1.0 - - - +
212A MET* 4.2 24.5 - - + -
213A ASN* 3.6 23.8 - - - +
216A VAL* 4.2 15.5 - - + -
255A ARG* 3.1 31.6 + - + +
256A TYR* 3.9 5.6 - - + +
258A ILE* 1.3 75.2 - - - +
260A THR* 1.4 59.3 + - - +
262A LEU* 3.3 8.2 + - - +
263A ALA* 2.8 29.2 + - + +
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Residues in contact with THR 260 (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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82A ALA* 3.7 27.0 + - + +
85A GLY* 3.8 7.1 - - - -
86A LEU 4.4 2.2 - - - +
87A PHE* 3.6 38.4 - - + +
256A TYR 2.6 26.0 + - - -
257A GLN* 3.5 8.3 - - - +
258A ILE 3.1 0.2 - - - -
259A ILE* 1.4 73.2 - - - +
261A PHE* 1.3 64.3 + - + +
263A ALA* 4.5 1.3 - - - +
264A ALA* 2.8 40.1 + - + +
500A HEM 4.1 15.3 - - + -
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Residues in contact with PHE 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 4.9 1.1 - - + -
103A LEU* 4.0 23.1 - - + -
107A PHE* 3.7 30.7 - + - -
153A ILE* 3.7 22.8 - - + +
157A GLY* 5.1 6.3 - - - -
233A LEU* 3.9 27.1 - - + -
237A MET* 4.1 20.6 - - + -
257A GLN* 2.8 33.9 + - + -
258A ILE* 3.2 12.5 + - + +
260A THR* 1.3 78.6 - - - +
262A LEU* 1.3 57.0 + - - +
265A GLY* 2.9 27.9 + - - -
500A HEM 3.9 40.2 - - + +
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Residues in contact with LEU 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.9 15.5 - - + +
153A ILE* 3.6 29.6 - - + +
154A GLY 3.9 3.6 - - - +
158A PHE* 4.2 13.5 - - + -
162A PHE* 3.8 22.7 - - + -
173A PHE* 3.7 28.7 - - + -
177A MET* 3.7 14.4 - - + -
258A ILE* 3.2 27.9 + - + +
259A ILE 3.6 5.6 - - - +
261A PHE* 1.3 76.9 - - - +
263A ALA* 1.3 59.3 + - - +
266A HIS* 2.8 37.1 + - - +
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Residues in contact with ALA 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 5.6 3.6 - - + -
81A PHE* 3.9 27.1 - - + -
82A ALA* 5.7 1.1 - - + -
177A MET* 3.6 21.3 - - + -
181A LEU* 3.9 23.6 - - + +
259A ILE* 2.8 23.9 + - + +
260A THR* 4.5 2.5 - - - +
262A LEU* 1.3 74.7 - - - +
264A ALA* 1.3 57.4 + - + +
266A HIS* 3.7 12.2 + - - -
267A GLU* 4.9 3.8 + - - +
437A LEU* 4.7 4.3 - - - +
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Residues in contact with ALA 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PHE* 3.9 31.9 - - + -
260A THR* 2.8 26.3 + - + +
263A ALA* 1.3 74.5 - - + +
265A GLY* 1.3 62.2 + - - +
266A HIS 3.6 0.4 - - - -
267A GLU* 5.1 0.4 - - - -
268A ALA* 4.4 6.8 + - - +
437A LEU* 5.0 8.1 - - - -
438A VAL* 5.4 1.2 - - - +
500A HEM 4.9 4.0 - - + -
501A LDP 3.2 36.5 + - - +
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Residues in contact with GLY 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 3.7 5.4 - - - -
260A THR 3.8 0.2 + - - -
261A PHE 2.9 17.1 + - - -
264A ALA* 1.3 81.9 - - - +
266A HIS* 1.3 62.8 + - - +
267A GLU 3.4 0.7 - - - -
268A ALA 3.8 0.6 + - - -
269A THR* 2.7 31.5 + - - -
500A HEM 3.5 29.1 - - - +
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Residues in contact with HIS 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR* 3.8 20.8 - - + +
149A THR* 2.8 27.0 + - - +
150A LEU* 3.4 32.7 - - + +
153A ILE* 3.5 16.4 - - + +
177A MET* 3.7 19.9 - - + +
178A VAL* 4.8 9.4 - - + +
181A LEU* 3.9 20.0 - - + -
262A LEU 2.8 27.7 + - - +
263A ALA 3.7 4.1 + - - -
265A GLY* 1.3 78.3 - - - +
267A GLU* 1.3 86.9 + - + +
269A THR 3.4 0.5 + - - -
270A SER* 2.9 18.0 + - - -
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Residues in contact with GLU 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR* 4.9 7.2 - - + +
181A LEU* 4.1 14.0 - - - +
263A ALA 4.9 4.1 + - - +
264A ALA 4.9 1.2 + - - +
266A HIS* 1.3 105.8 + - + +
268A ALA* 1.4 62.2 + - - +
269A THR 3.1 1.3 - - - -
270A SER* 3.6 4.8 - - - -
271A GLY* 2.9 26.9 + - - -
436A THR* 3.3 13.8 + - - +
437A LEU* 4.8 7.6 - - - +
438A VAL* 3.5 30.3 - - + +
440A LYS* 3.2 28.9 + - + +
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Residues in contact with ALA 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA 4.4 5.2 + - - +
265A GLY 3.8 1.6 + - - +
266A HIS 3.5 0.2 - - - -
267A GLU* 1.4 77.7 - - - +
269A THR* 1.3 58.7 + - - +
271A GLY 3.4 0.2 + - - -
272A LEU* 3.1 19.6 + - - +
327A THR* 2.9 30.4 + - - +
438A VAL* 3.8 21.7 - - + +
500A HEM 3.5 34.6 - - + +
501A LDP 4.1 11.9 - - + -
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Residues in contact with THR 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR* 3.8 18.8 - - + -
153A ILE* 5.6 0.9 - - - -
265A GLY 2.7 22.7 + - - -
266A HIS 3.9 2.9 - - - -
267A GLU 3.1 0.6 - - - -
268A ALA* 1.3 77.9 - - - +
270A SER* 1.3 67.3 + - - +
272A LEU* 3.2 4.3 + - + +
273A LEU* 3.2 25.2 + - + +
405A PHE* 6.2 0.9 - - + -
406A ALA* 4.1 18.8 - - + +
409A GLU* 3.9 21.3 - - + -
410A ALA* 5.1 2.9 - - + -
500A HEM 3.4 33.6 - - + +
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Residues in contact with SER 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 3.4 9.9 + - - +
145A MET* 3.4 11.9 - - - +
146A THR* 2.8 43.4 + - - -
149A THR* 3.7 10.0 - - - +
266A HIS 2.9 17.5 + - - -
267A GLU* 3.6 6.3 - - - -
269A THR* 1.3 77.8 - - - +
271A GLY* 1.3 61.8 + - - +
273A LEU* 3.3 2.0 + - - +
274A SER* 3.0 27.9 + - - -
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Residues in contact with GLY 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 6.4 0.2 - - - -
267A GLU 2.9 17.0 + - - -
270A SER* 1.3 76.1 - - - +
272A LEU* 1.3 53.6 + - - +
274A SER* 3.2 6.3 + - - -
275A PHE* 2.8 40.4 + - - -
327A THR* 3.5 16.8 - - - -
439A LEU 4.0 10.8 - - - -
440A LYS* 4.6 8.7 - - - -
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Residues in contact with LEU 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA 3.1 14.4 + - - +
269A THR* 3.5 9.4 - - + +
271A GLY* 1.3 76.4 - - - +
273A LEU* 1.3 65.5 + - - +
275A PHE* 3.4 2.3 + - + +
276A ALA* 2.9 26.2 + - - +
318A LEU* 3.6 29.6 - - + +
321A ALA* 4.1 10.8 - - + -
322A LEU* 3.5 30.1 - - + -
327A THR* 3.6 6.8 - - - +
406A ALA 5.0 2.0 - - - +
407A LEU* 4.2 19.1 - - + -
410A ALA* 4.0 20.4 - - + -
500A HEM 3.9 22.4 - - + -
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Residues in contact with LEU 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A MET* 3.7 25.0 - - + +
148A LEU* 3.8 29.2 - - + -
149A THR* 4.6 7.2 - - + -
269A THR* 3.2 14.0 + - + +
270A SER 3.9 4.0 - - - +
272A LEU* 1.3 81.2 - - - +
274A SER* 1.4 62.6 + - - +
276A ALA* 3.8 4.4 - - - +
277A LEU* 3.1 25.3 + - - +
318A LEU* 4.9 2.2 - - + -
409A GLU* 4.8 3.4 - - + +
410A ALA* 3.4 45.5 - - + +
413A VAL* 4.1 10.3 - - + -
414A LEU* 4.0 24.2 - - + +
417A MET* 4.8 4.9 - - - +
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Residues in contact with SER 274 (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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141A VAL* 3.9 13.7 - - - -
142A PRO* 3.2 31.7 - - - +
145A MET* 3.6 6.4 - - - +
270A SER 3.0 17.9 + - - -
271A GLY* 3.6 6.1 - - - -
273A LEU* 1.4 76.3 - - - +
275A PHE* 1.3 57.8 + - - +
277A LEU 3.4 0.2 + - - -
278A TYR* 2.9 28.1 + - - +
441A PRO* 3.6 25.1 - - - -
444A PHE* 3.6 6.8 - - - -
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Residues in contact with PHE 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLY 2.8 29.8 + - - +
272A LEU* 4.1 3.4 - - + +
274A SER* 1.3 69.1 - - - +
276A ALA* 1.3 61.1 + - - +
278A TYR* 3.3 6.1 + + - +
279A PHE* 2.9 43.5 + + + -
321A ALA* 4.4 12.6 - - + +
325A TRP* 3.8 34.8 - + + +
327A THR* 3.7 22.4 - - + -
431A LEU* 4.1 8.1 - - + -
433A ILE* 3.8 31.0 - - + -
439A LEU* 3.8 9.9 - - + -
440A LYS* 3.7 35.7 - - - -
441A PRO* 4.0 16.2 - - + -
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Residues in contact with ALA 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU 2.9 18.7 + - - +
273A LEU* 3.8 4.3 - - - +
274A SER 3.3 0.2 - - - -
275A PHE* 1.3 79.1 - - - +
277A LEU* 1.3 60.0 - - - +
279A PHE* 3.4 4.0 + - - +
280A LEU* 3.0 29.9 + - - +
317A VAL* 4.3 8.6 - - + +
318A LEU* 3.8 24.0 - - + -
321A ALA* 4.0 14.9 - - + +
414A LEU* 3.8 15.3 - - + -
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Residues in contact with LEU 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TRP* 4.9 2.7 - - + -
141A VAL* 4.0 33.0 - - + -
273A LEU 3.1 17.4 + - - +
274A SER 3.9 3.4 - - - +
276A ALA* 1.3 71.9 - - - +
278A TYR* 1.4 61.9 + - - +
280A LEU* 4.4 15.0 - - + -
281A VAL* 2.9 43.3 + - + +
287A LEU* 5.2 1.3 - - + -
414A LEU* 4.9 4.2 - - + +
417A MET* 3.7 33.7 - - + -
418A LEU* 5.6 0.9 - - + -
423A PHE* 4.2 29.6 - - + -
444A PHE* 3.9 7.2 - - + -
446A VAL* 4.4 6.3 - - + -
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Residues in contact with TYR 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A SER 2.9 15.6 + - - +
275A PHE* 3.5 11.7 - + - +
276A ALA 3.2 0.2 - - - -
277A LEU* 1.4 77.9 - - - +
279A PHE* 1.4 98.7 + + - +
281A VAL* 3.3 1.7 + - - +
282A LYS* 3.0 66.8 + - + +
429A TYR* 3.6 32.5 - + - -
431A LEU* 3.4 45.5 + - + +
441A PRO* 4.9 3.6 - - + -
444A PHE* 3.4 22.1 - + + -
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Residues in contact with PHE 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A PHE* 2.9 37.3 + + + +
276A ALA 3.8 1.8 - - - +
278A TYR* 1.4 98.7 - + - +
280A LEU* 1.3 57.6 + - - +
282A LYS* 3.5 2.0 + - + -
283A ASN* 2.8 40.2 + - - +
321A ALA* 4.3 11.0 - - + -
324A LEU* 3.7 29.2 - - + -
325A TRP* 3.6 34.8 - + - -
372A GLU 5.6 2.5 - - - -
374A PHE* 3.3 50.3 - + + -
431A LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ALA 3.0 22.5 + - - +
277A LEU* 3.8 8.1 - - + +
278A TYR 3.2 0.2 - - - -
279A PHE* 1.3 76.6 - - - +
281A VAL* 1.3 63.8 + - - +
283A ASN 3.0 22.9 + - - +
284A PRO 3.8 0.5 - - - -
286A VAL* 3.6 30.3 - - + +
287A LEU* 3.6 31.6 - - + +
290A ALA* 4.6 2.9 - - + -
317A VAL* 3.8 26.5 - - + -
374A PHE* 4.6 1.6 - - + -
414A LEU* 4.0 28.0 - - + -
418A LEU* 4.2 23.1 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 2.9 27.7 + - + +
278A TYR 3.5 9.6 - - - +
280A LEU* 1.3 78.5 - - - +
282A LYS* 1.3 65.5 + - + +
283A ASN 3.5 0.5 + - - -
284A PRO* 3.8 14.8 - - - +
287A LEU* 4.1 10.1 - - + -
423A PHE* 3.8 32.3 - - + +
425A ASP* 3.8 33.7 - - + +
444A PHE* 4.0 18.8 - - + -
446A VAL* 4.4 9.9 - - + -
----------------------------------------------------------
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.0 57.3 + - + +
279A PHE* 4.4 2.0 - - + -
280A LEU 3.2 0.2 - - - -
281A VAL* 1.3 77.6 - - + +
283A ASN* 1.3 74.3 + - - +
284A PRO* 3.5 7.3 - - - +
425A ASP* 2.8 32.3 + - - +
428A ASN* 3.4 18.2 + - - -
429A TYR* 2.6 32.0 + - - +
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 2.8 29.8 + - - +
280A LEU 3.0 8.5 + - - +
282A LYS* 1.3 90.6 + - - +
284A PRO* 1.4 56.2 - - - +
285A HIS* 3.2 2.9 - - - -
286A VAL* 2.8 42.2 + - + +
287A LEU 3.0 9.2 + - - -
374A PHE* 4.0 30.3 + - + +
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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