Contacts of the helix formed by residues 158 - 189 (chain A) in PDB entry 5I75
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 PHE 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TRP* 3.6 16.9 - - + -
155A CYS* 2.8 27.2 + - + +
157A ILE* 1.3 86.8 - - + +
159A LYS* 1.3 57.9 + - - +
160A GLY 3.1 2.7 - - - -
161A ILE* 2.9 39.7 + - + +
507A ILE* 4.7 9.6 - - + -
510A VAL* 6.1 1.3 - - + -
511A ALA* 3.4 31.4 - - + -
515A PHE* 4.0 38.4 - + - -
589A ILE* 4.5 12.6 - - + -
593A ILE* 3.7 24.5 - - + -
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Residues in contact with LYS 159 (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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148A ILE* 3.5 27.5 - - + +
151A TRP* 3.5 13.4 - - + -
152A ARG* 3.0 36.2 - - + +
155A CYS 3.6 2.0 + - - -
156A PRO* 2.9 18.5 + - + +
157A ILE 3.2 0.2 - - - -
158A PHE* 1.3 78.1 - - - +
160A GLY* 1.3 63.0 + - - +
162A GLY* 2.9 17.8 + - - -
163A TYR* 3.5 12.2 + - + +
453A GLU* 2.7 43.6 + - - -
592A TYR* 3.4 29.4 + - + +
596A ARG* 5.0 3.8 - - - +
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Residues in contact with GLY 160 (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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157A ILE 4.1 0.8 + - - -
158A PHE 3.1 1.8 - - - -
159A LYS* 1.3 79.1 - - - +
161A ILE* 1.3 49.5 + - - +
163A TYR* 2.9 15.3 + - - +
164A ALA* 2.6 36.7 + - - +
588A CYS* 3.4 10.0 - - - -
589A ILE* 4.0 24.9 - - - -
592A TYR* 3.9 12.9 - - - -
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Residues in contact with ILE 161 (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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151A TRP* 3.5 37.7 - - + +
158A PHE* 2.9 23.8 + - + +
160A GLY* 1.3 75.0 - - - +
162A GLY* 1.3 64.1 + - - +
164A ALA* 2.9 8.4 + - - +
165A ILE* 2.9 30.3 + - + +
504A VAL* 3.5 15.7 - - + -
507A ILE* 3.4 26.5 - - + -
508A GLU* 3.3 32.5 - - + +
589A ILE* 3.7 21.0 - - + +
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Residues in contact with GLY 162 (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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147A CYS* 3.2 33.1 + - - +
148A ILE* 3.4 18.0 - - - +
151A TRP* 4.0 1.2 - - - -
159A LYS 2.9 10.4 + - - -
161A ILE* 1.3 79.8 - - - +
163A TYR* 1.3 57.0 + - - +
165A ILE* 4.2 4.0 + - - +
166A CYS* 3.2 25.8 + - - -
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Residues in contact with TYR 163 (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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148A ILE* 3.6 37.0 - - + +
159A LYS* 3.5 8.0 + - + +
160A GLY* 2.9 19.7 + - - +
162A GLY* 1.3 77.6 - - - +
164A ALA* 1.3 66.0 + - - +
165A ILE 3.3 0.2 - - - -
166A CYS* 2.9 24.6 + - + +
167A ILE* 3.0 12.5 + - + +
453A GLU* 4.0 9.4 + - + +
454A PHE* 3.6 27.3 - + - -
588A CYS* 4.0 17.3 - - + -
592A TYR* 5.1 19.5 - + + -
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Residues in contact with ALA 164 (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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160A GLY 2.6 19.8 + - - +
161A ILE* 3.4 10.5 - - - +
163A TYR* 1.3 71.4 - - - +
165A ILE* 1.3 52.7 + - - +
167A ILE* 2.9 6.3 + - - +
168A ILE* 2.7 40.2 + - + +
504A VAL* 4.6 11.2 - - + -
585A SER 3.8 11.6 - - - +
586A PHE* 4.2 15.3 - - + -
588A CYS* 3.4 17.4 - - - -
589A ILE* 5.0 2.5 - - + -
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Residues in contact with ILE 165 (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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147A CYS* 4.8 16.8 - - + +
151A TRP* 6.0 0.2 - - - +
161A ILE* 2.9 22.4 + - + +
162A GLY* 4.3 4.3 - - - +
164A ALA* 1.3 73.5 - - - +
166A CYS* 1.3 53.1 + - - +
168A ILE* 2.9 11.9 + - - +
169A ALA* 2.6 34.5 + - - +
340A GLY 3.8 3.4 - - - +
341A PHE* 3.1 59.5 - - + +
342A GLY* 4.4 0.7 - - - +
446A VAL* 4.9 7.0 - - + -
504A VAL* 4.2 18.6 - - + +
508A GLU* 3.3 25.6 - - - +
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Residues in contact with CYS 166 (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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147A CYS* 6.2 0.2 - - - -
148A ILE* 4.1 9.6 - - - -
162A GLY 3.2 20.4 - - - -
163A TYR* 2.9 19.4 + - + +
165A ILE* 1.3 77.3 - - - +
167A ILE* 1.3 62.6 + - + +
169A ALA* 2.9 15.7 + - - +
170A PHE* 3.1 11.7 + - - +
446A VAL* 3.6 35.3 - - + +
449A ALA* 5.5 1.3 - - - -
450A VAL* 4.0 17.7 - - - -
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Residues in contact with ILE 167 (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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163A TYR* 3.0 12.7 + - + +
164A ALA 2.9 6.8 + - - +
166A CYS* 1.3 74.2 - - + +
168A ILE* 1.3 65.9 + - - +
170A PHE* 2.9 20.9 + - + +
171A TYR* 3.2 31.7 + - + +
584A SER 4.3 7.2 - - - +
585A SER* 3.4 36.6 - - - +
587A ILE* 5.4 4.0 - - + -
588A CYS* 4.4 15.0 - - + -
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Residues in contact with ILE 168 (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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164A ALA* 2.7 25.5 + - + +
165A ILE* 3.1 13.7 - - - +
167A ILE* 1.3 72.0 - - - +
169A ALA* 1.3 62.4 + - - +
171A TYR* 2.9 13.6 + - + +
172A ILE* 2.9 26.5 + - + +
341A PHE* 3.4 25.6 - - + -
496A ALA 5.9 0.2 - - - -
497A THR* 4.6 9.2 - - - +
500A ALA* 3.4 36.6 - - + +
501A VAL* 3.6 17.9 - - + -
504A VAL* 5.3 5.6 - - + -
582A GLY* 6.1 0.2 - - - -
585A SER* 3.5 19.3 - - - +
586A PHE* 6.5 0.2 - - + -
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Residues in contact with ALA 169 (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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165A ILE 2.6 15.5 + - - +
166A CYS 3.2 9.4 - - - +
168A ILE* 1.3 72.5 - - - +
170A PHE* 1.3 58.2 + - - +
172A ILE* 3.0 2.1 + - - +
173A ALA* 2.8 34.3 + - - +
341A PHE* 4.1 14.6 - - + -
443A LEU* 5.9 2.9 - - + -
446A VAL* 3.6 28.0 - - + -
473A CYS* 6.0 0.4 - - - -
701A 68P 4.1 15.3 - - + -
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Residues in contact with PHE 170 (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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166A CYS 3.1 8.8 + - - +
167A ILE* 2.9 15.2 + - + +
169A ALA* 1.3 76.5 - - - +
171A TYR* 1.3 86.3 + + - +
173A ALA* 4.3 4.5 - - - +
174A SER* 2.9 26.6 + - - -
472A THR* 3.9 40.6 - - + -
473A CYS* 5.0 11.0 - - - -
476A GLY* 4.1 19.7 - - - -
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Residues in contact with TYR 171 (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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167A ILE* 3.2 31.2 + - + +
168A ILE* 2.9 12.6 + - + +
170A PHE* 1.3 103.4 - + - +
172A ILE* 1.3 67.6 + - - +
174A SER* 2.9 22.9 + - - -
175A TYR* 3.6 8.5 - - - -
492A LEU* 4.4 11.4 - - + +
496A ALA* 5.7 0.9 - - + -
497A THR* 3.9 19.5 - - + -
581A ILE* 3.5 41.8 - - + +
582A GLY* 6.0 0.4 - - - -
584A SER* 3.3 17.5 + - - -
585A SER* 4.0 11.7 - - - -
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Residues in contact with ILE 172 (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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168A ILE* 2.9 34.3 + - + +
169A ALA 3.6 5.2 - - - +
171A TYR* 1.3 75.8 - - - +
173A ALA* 1.3 59.1 + - - +
174A SER 3.0 6.1 + - - -
175A TYR* 3.1 14.4 + - - +
176A TYR* 3.1 25.9 + - + +
341A PHE* 3.7 11.0 - - + -
497A THR* 4.0 14.4 - - + -
701A 68P 3.4 88.2 - - + -
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Residues in contact with ALA 173 (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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169A ALA 2.8 15.7 + - - +
170A PHE 4.3 2.0 - - - +
172A ILE* 1.3 72.7 - - - +
174A SER* 1.3 60.7 + - - +
175A TYR 3.3 0.8 + - - -
176A TYR* 4.7 0.9 - - - +
177A ASN* 3.1 31.8 + - - +
263A PHE* 4.4 2.0 - - + -
443A LEU* 4.9 1.8 - - + -
473A CYS* 3.5 33.2 - - + +
477A SER* 3.2 11.0 + - - -
701A 68P 3.5 21.9 - - - -
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Residues in contact with SER 174 (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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170A PHE* 2.9 24.4 + - - -
171A TYR* 2.9 18.1 + - - -
173A ALA* 1.3 79.1 - - - +
175A TYR* 1.3 53.9 + - - +
178A THR* 3.6 2.0 - - - +
473A CYS* 4.9 1.2 + - - -
476A GLY* 2.9 27.2 + - - -
477A SER* 3.2 19.9 + - - -
480A THR* 2.8 29.8 + - - -
492A LEU* 4.6 11.9 - - - -
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Residues in contact with TYR 175 (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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171A TYR 3.6 9.0 - - - -
172A ILE* 3.5 24.2 - - + -
174A SER* 1.3 79.5 - - - +
176A TYR* 1.3 89.3 + + + +
177A ASN 3.1 2.7 - - - -
178A THR* 2.5 27.2 + - - -
179A ILE* 3.4 12.4 + - + +
480A THR* 4.1 4.3 - - + +
488A VAL 5.7 0.2 - - - -
489A VAL* 3.8 39.9 - - + -
492A LEU* 4.1 22.9 - - + -
493A GLU* 3.4 36.2 - - + +
497A THR* 3.3 29.1 + - + -
701A 68P 3.9 17.9 - + - -
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Residues in contact with TYR 176 (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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98A ASP* 3.2 29.0 + - + +
99A LEU* 4.8 10.8 + - + +
172A ILE* 3.1 25.2 + - + +
175A TYR* 1.3 91.2 - + + +
177A ASN* 1.3 62.1 + - - +
179A ILE* 3.9 22.6 - - + +
180A MET* 4.1 8.9 + - + +
435A GLY* 3.6 31.3 - - - -
438A SER* 3.1 28.8 - - - -
439A SER* 4.3 13.0 - - - -
701A 68P 4.2 39.7 - + + -
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Residues in contact with ASN 177 (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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173A ALA* 3.1 36.5 + - - +
175A TYR 3.1 0.8 - - - -
176A TYR* 1.3 78.6 - - - +
178A THR* 1.3 64.5 + - - +
179A ILE 3.1 2.5 - - - -
180A MET* 2.9 40.4 + - + +
181A ALA* 2.9 10.6 + - - +
259A ILE* 4.2 9.6 - - + +
262A ILE* 4.3 6.8 - - + +
263A PHE* 3.4 37.9 - - + -
266A ILE* 4.5 2.3 - - - +
439A SER* 3.3 20.7 + - - -
701A 68P 5.4 0.8 - - - -
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Residues in contact with THR 178 (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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174A SER 3.6 10.8 - - - +
175A TYR* 2.5 18.7 + - - +
177A ASN* 1.3 77.6 - - - +
179A ILE* 1.3 63.5 + - - +
181A ALA* 2.9 13.0 + - - +
182A TRP* 2.9 34.7 + - - -
259A ILE* 3.6 20.0 - - + -
477A SER* 4.1 2.2 - - - +
480A THR* 3.3 41.6 - - + +
481A LEU* 4.0 15.3 - - + -
489A VAL* 4.3 4.7 - - - +
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Residues in contact with ILE 179 (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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99A LEU* 3.5 32.5 - - + -
175A TYR* 3.8 16.4 - - + +
176A TYR* 3.9 19.7 - - + +
177A ASN 3.1 0.8 - - - -
178A THR* 1.3 77.9 + - - +
180A MET* 1.3 62.5 + - - +
182A TRP* 2.9 45.5 + - + +
183A ALA* 3.0 11.7 + - + +
403A PRO* 5.5 9.4 - - + -
407A PHE* 4.2 13.9 - - + -
431A LEU* 6.2 0.2 - - + -
489A VAL* 4.7 16.4 - - + -
493A GLU* 5.3 5.6 - - - +
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Residues in contact with MET 180 (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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99A LEU* 5.5 4.5 - - + -
176A TYR* 4.2 9.0 - - + +
177A ASN* 2.9 40.8 + - - +
179A ILE* 1.3 81.3 - - + +
181A ALA* 1.3 62.8 + - - +
183A ALA* 3.1 10.1 + - - +
184A LEU* 2.8 20.6 + - - +
262A ILE* 3.4 29.7 - - + +
266A ILE* 5.5 0.2 - - + -
431A LEU 4.7 2.7 - - - +
432A ILE* 3.9 19.1 - - - +
435A GLY* 3.4 37.9 - - - +
436A LEU* 3.5 13.9 - - + -
439A SER* 4.4 13.2 - - - -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASN 2.9 7.2 + - - +
178A THR* 2.9 22.6 + - - +
180A MET* 1.3 74.6 - - - +
182A TRP* 1.3 60.4 + - + +
184A LEU* 3.1 4.0 + - - +
185A TYR 2.9 19.8 + - - -
255A LEU* 3.6 23.1 - - + +
258A CYS* 3.6 5.2 - - + +
259A ILE* 3.9 30.7 - - + +
262A ILE* 3.3 11.8 - - - +
481A LEU* 5.0 0.7 - - + -
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Residues in contact with TRP 182 (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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178A THR* 2.9 30.6 + - - -
179A ILE* 2.9 31.6 + - + +
181A ALA* 1.3 75.7 - - + +
183A ALA* 1.3 62.9 + - - +
185A TYR* 3.1 4.3 + - - +
186A TYR* 2.9 29.5 + - + -
232A TYR* 3.3 31.4 - + + -
236A VAL* 4.5 12.8 - - + -
237A LEU* 3.7 27.3 - - + +
255A LEU* 3.3 30.1 - - + +
403A PRO* 4.6 12.8 - - + -
407A PHE* 4.0 22.0 - + + -
480A THR 5.3 6.4 + - - -
481A LEU* 5.9 1.2 - - - +
485A GLY 5.2 0.7 - - - -
486A ALA* 4.2 25.1 - - + -
489A VAL* 4.4 14.6 - - + -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ILE* 3.0 12.3 + - + +
180A MET* 3.1 11.4 + - - +
182A TRP* 1.3 75.6 - - - +
184A LEU* 1.3 57.5 + - - +
186A TYR* 3.1 8.2 + - - +
187A LEU* 2.8 27.4 + - - +
407A PHE* 3.9 11.7 - - + -
428A PHE* 3.7 8.1 - - + +
431A LEU* 4.0 29.8 - - + -
432A ILE* 3.7 18.4 - - + +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A MET 2.8 16.3 + - - +
181A ALA 3.1 9.2 + - - +
183A ALA* 1.3 72.0 - - - +
185A TYR* 1.3 58.3 + - - +
187A LEU* 2.9 12.6 + - + +
188A ILE* 2.9 49.7 + - + +
258A CYS* 3.4 37.9 - - + +
261A LEU* 3.7 29.2 - - + -
262A ILE* 3.8 13.9 - - + -
432A ILE* 3.6 21.7 - - + +
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA 2.9 9.5 + - - +
182A TRP 3.1 7.2 + - - +
184A LEU* 1.3 76.7 - - - +
186A TYR* 1.3 59.9 + + - +
188A ILE* 3.4 21.0 - - + +
189A SER* 2.8 37.9 + - - -
231A PHE* 5.1 3.1 - + - -
235A HIS* 3.0 44.9 + + - -
236A VAL* 3.5 32.5 - - + -
254A GLN* 3.4 39.6 + - + +
255A LEU* 4.1 3.8 - - + -
258A CYS* 3.6 25.1 - - - -
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Residues in contact with TYR 186 (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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182A TRP* 2.9 21.8 + - + +
183A ALA* 3.3 10.3 - - - +
185A TYR* 1.3 77.0 - - - +
187A LEU* 1.3 62.6 + - - +
189A SER* 3.6 5.6 + - - -
190A SER* 3.3 16.8 + - - -
197A TRP* 3.8 17.6 - + - -
228A ALA 4.6 0.7 + - - -
231A PHE* 3.4 28.4 - + - -
232A TYR* 3.2 35.3 + + - +
236A VAL* 3.5 26.2 - - + -
407A PHE* 3.5 41.1 + + - -
411A ALA* 5.1 0.2 - - + -
428A PHE* 3.3 48.9 - + + -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA 2.8 12.1 + - - +
184A LEU* 2.9 17.4 + - + +
186A TYR* 1.3 73.8 - - - +
188A ILE* 1.3 59.8 + - + +
189A SER 3.1 4.5 - - - -
190A SER* 3.1 20.1 + - - -
191A PHE* 3.8 20.8 - - + -
425A ILE* 3.5 49.4 - - + +
428A PHE* 4.0 9.2 - - + -
429A LEU* 3.7 30.5 - - + +
432A ILE* 3.8 16.6 - - + -
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 2.9 32.0 + - + +
185A TYR* 3.4 41.5 - - + +
187A LEU* 1.3 77.9 - - + +
189A SER* 1.3 63.4 + - - +
190A SER 3.3 0.4 - - - -
191A PHE* 4.1 28.5 + - + +
258A CYS* 4.4 8.5 - - - -
261A LEU* 6.1 2.2 - - + -
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Residues in contact with SER 189 (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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185A TYR* 2.8 37.2 + - - -
186A TYR* 3.8 5.6 - - - -
187A LEU 3.1 0.8 - - - -
188A ILE* 1.3 80.1 - - - +
190A SER* 1.3 57.3 + - - +
191A PHE 3.4 4.6 + - - -
192A THR* 3.9 11.1 + - - -
196A PRO* 3.3 36.6 - - - +
197A TRP* 5.2 1.8 - - - -
231A PHE* 4.5 12.0 - - - -
235A HIS* 5.4 1.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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