Contacts of the helix formed by residues 305 - 329 (chain 5) in PDB entry 3J7Y
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 GLN 305 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125 ARG* 3.8 11.7 - - - +
3005 ARG* 4.6 16.3 + - - +
3035 ARG* 3.5 12.9 + - - +
3045 LEU* 1.3 88.4 + - - +
3065 PRO* 1.3 76.8 - - + +
3075 ASP* 3.4 1.8 - - + +
3085 GLN* 3.2 19.0 + - - +
3095 LEU* 3.0 16.7 + - - +
2389A C 3.1 50.8 + - + +
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Residues in contact with PRO 306 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3055 GLN* 1.3 90.7 - - + +
3075 ASP* 1.3 60.5 + - + +
3095 LEU* 3.2 9.7 + - + +
3105 ARG* 2.9 48.2 + - - +
3515 VAL* 5.8 0.7 - - + -
3535 HIS* 3.5 27.2 + - + +
3795 ASP* 5.0 6.3 - - + -
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Residues in contact with ASP 307 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165 GLY* 3.2 21.9 - - - -
1175 VAL* 3.2 31.0 + - - +
1185 LYS* 5.4 3.5 + - - -
3055 GLN* 6.0 0.2 - - + -
3065 PRO* 1.3 81.4 - - + +
3085 GLN* 1.3 65.5 + - - +
3105 ARG* 3.2 32.3 + - - +
3115 ALA* 2.9 29.4 + - - +
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Residues in contact with GLN 308 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125 ARG* 3.0 30.2 - - + +
1135 LEU* 3.1 33.5 + - - +
1145 LEU 4.0 12.4 + - - +
1165 GLY* 4.8 4.2 - - - +
3045 LEU* 3.0 25.2 - - + +
3055 GLN* 3.2 14.3 + - - +
3075 ASP* 1.3 85.0 - - - +
3095 LEU* 1.3 56.3 + - - +
3115 ALA* 3.2 9.5 + - - +
3125 LYS* 2.9 29.0 + - - +
2388A A 4.8 1.6 - - - +
2389A C 2.7 33.6 + - - +
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Residues in contact with LEU 309 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2955 ASP* 3.7 18.4 - - + +
3045 LEU* 3.7 20.3 - - + +
3055 GLN 3.0 12.2 + - - +
3065 PRO* 3.2 12.8 - - + +
3085 GLN* 1.3 77.4 - - - +
3105 ARG* 1.3 56.4 + - - +
3125 LYS* 3.2 18.7 + - - +
3135 MET* 2.9 47.6 + - + +
3475 THR* 2.9 49.6 - - + +
3485 ASP* 5.6 1.6 - - + -
3535 HIS* 4.3 17.3 - - + +
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Residues in contact with ARG 310 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175 VAL* 5.1 14.2 - - + +
3065 PRO* 2.9 29.9 + - - +
3075 ASP* 3.3 46.1 + - - +
3095 LEU* 1.3 75.5 - - - +
3115 ALA* 1.3 58.8 + - - +
3135 MET* 3.2 16.5 + - + +
3145 ILE* 2.9 36.2 + - + +
3535 HIS* 4.0 23.7 - - + -
3765 VAL* 5.2 17.6 - - + +
3785 SER* 2.8 40.0 + - - +
3795 ASP* 4.6 4.0 + - - -
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Residues in contact with ALA 311 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135 LEU* 3.4 19.3 - - + -
1165 GLY 3.2 27.1 - - - +
1175 VAL* 4.8 1.3 - - - +
1205 ALA* 3.4 15.1 - - + +
3075 ASP 2.9 11.0 + - - +
3085 GLN 3.3 9.4 - - - +
3105 ARG* 1.3 77.6 - - - +
3125 LYS* 1.3 56.1 + - - +
3145 ILE* 3.2 8.8 + - - +
3155 LEU* 2.9 34.6 + - - +
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Residues in contact with LYS 312 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075 PHE* 3.8 29.8 - - + -
1085 HIS 4.1 5.4 - - - +
1095 HIS* 3.8 25.4 - - - +
1115 CYS 4.7 5.4 - - - +
1135 LEU* 6.2 0.2 - - + -
2935 LEU* 3.3 35.7 - - + +
2945 LEU 5.5 3.3 + - - -
2955 ASP* 5.9 0.4 - - - +
3045 LEU* 3.8 28.2 - - + +
3085 GLN 2.9 12.7 + - - +
3095 LEU* 3.3 19.3 - - - +
3115 ALA* 1.3 76.1 - - - +
3135 MET* 1.3 56.1 + - - +
3155 LEU* 3.2 2.4 + - - +
3165 PHE* 2.9 52.7 + - + -
3475 THR* 5.0 1.4 - - - +
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Residues in contact with MET 313 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2935 LEU* 3.9 24.5 - - + -
3095 LEU* 2.9 33.7 + - + +
3105 ARG* 3.3 15.3 - - + +
3125 LYS* 1.3 76.6 - - - +
3145 ILE* 1.3 57.4 + - - +
3165 PHE* 3.2 9.1 + - - +
3175 ALA* 2.9 28.8 + - - +
3445 SER* 3.6 18.0 + - - +
3455 VAL 4.1 2.7 - - - +
3465 GLY* 3.6 20.4 - - - -
3535 HIS* 3.1 36.6 - - + +
3545 PHE 4.2 1.1 - - - +
3555 LEU* 3.5 26.0 - - + -
3765 VAL* 5.6 1.1 - - + -
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Residues in contact with ILE 314 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175 VAL* 3.8 28.9 - - + -
1205 ALA* 4.5 10.8 - - + +
1215 LEU* 4.3 7.6 - - + -
1245 THR* 3.9 27.4 - - + +
1265 THR* 4.9 4.5 - - + -
1285 LEU* 4.2 15.9 - - + -
3105 ARG* 2.9 20.0 + - + +
3115 ALA* 3.4 10.1 - - - +
3135 MET* 1.3 75.2 - - - +
3155 LEU* 1.3 58.8 + - - +
3175 ALA* 3.2 9.0 + - - +
3185 PHE* 2.9 27.0 + - - +
3555 LEU* 3.6 25.4 - - + -
3575 PHE* 4.5 8.8 - - + -
3745 ALA* 5.0 1.1 - - + -
3765 VAL* 4.8 3.4 - - + -
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Residues in contact with LEU 315 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075 PHE* 3.3 49.8 - - + -
1135 LEU* 4.1 3.8 - - + -
1205 ALA* 3.9 16.4 - - + -
1235 LEU* 3.8 27.8 - - + -
1245 THR* 4.0 16.6 - - - +
2135 TRP* 4.7 8.7 - - + -
2205 LEU* 5.7 1.6 - - + -
2225 VAL* 3.9 27.0 - - + +
2655 LEU* 5.4 1.1 - - + -
3115 ALA 2.9 17.0 + - - +
3125 LYS 3.2 7.8 + - - +
3145 ILE* 1.3 77.3 - - - +
3165 PHE* 1.3 57.2 - - - +
3185 PHE* 3.2 4.8 + - - +
3195 GLY* 2.9 27.0 + - - -
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Residues in contact with PHE 316 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075 PHE* 4.0 16.8 - + - -
1085 HIS 4.1 7.0 - - - -
1095 HIS* 4.1 13.5 - - + -
2095 PHE* 3.7 14.0 - + + -
2225 VAL* 6.2 2.2 - - + -
2235 ARG 4.2 8.3 - - - -
2245 GLY 3.6 19.5 - - - -
2255 SER* 3.3 36.6 - - - -
2265 GLY 5.0 0.4 - - - -
2915 LEU* 4.5 17.3 - - + -
2935 LEU* 4.5 22.4 - - + -
3125 LYS* 2.9 47.0 + - + +
3135 MET* 3.2 10.7 + - - +
3155 LEU* 1.3 76.8 - - - +
3175 ALA* 1.3 58.1 + - - +
3195 GLY* 3.2 1.1 + - - -
3205 SER* 2.9 33.7 + - - -
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Residues in contact with ALA 317 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2915 LEU* 5.6 0.9 - - - -
3135 MET 2.9 13.4 + - - +
3145 ILE 3.4 8.5 - - - +
3165 PHE* 1.3 76.2 - - - +
3185 PHE* 1.3 56.9 + - - +
3205 SER* 2.9 19.4 + - - -
3215 ALA* 2.9 19.9 + - - +
3425 VAL* 4.1 14.2 - - + +
3445 SER* 4.6 5.1 + - - +
3555 LEU* 3.6 14.1 - - + -
3575 PHE* 3.4 29.2 - - + -
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Residues in contact with PHE 318 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245 THR* 3.2 55.6 - - + +
2135 TRP* 3.3 50.9 - + + -
3145 ILE 2.9 12.4 + - - +
3155 LEU* 3.4 9.0 - - + +
3175 ALA* 1.3 76.6 - - - +
3195 GLY* 1.3 57.4 + - - +
3215 ALA* 3.2 1.7 + - - +
3225 LEU* 2.6 69.0 + - + +
3575 PHE* 3.5 21.2 - + + -
3595 LEU* 4.3 5.2 - - + +
3645 LEU* 4.1 10.1 - - + -
3725 ASN* 4.0 8.5 - - - -
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Residues in contact with GLY 319 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2095 PHE* 3.6 8.3 - - - -
2115 ALA* 3.5 10.3 - - - +
2225 VAL* 3.8 24.7 - - - -
3155 LEU 2.9 13.4 + - - -
3165 PHE 3.6 2.7 - - - -
3185 PHE* 1.3 82.6 - - - +
3205 SER* 1.3 56.4 + - - +
3225 LEU 3.2 1.2 + - - -
3235 ALA* 2.9 26.9 + - - +
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Residues in contact with SER 320 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2095 PHE* 3.4 23.4 - - - -
2295 ARG* 5.4 4.3 - - - -
2885 PRO* 4.7 8.7 - - - +
2915 LEU* 4.0 14.7 - - - +
3165 PHE 2.9 12.8 + - - -
3175 ALA* 2.9 11.4 + - - -
3195 GLY* 1.3 73.7 - - - +
3215 ALA* 1.3 63.3 + - - +
3235 ALA* 3.2 7.1 + - - +
3245 GLN* 2.9 33.7 + - - +
3425 VAL* 3.4 21.0 - - - +
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Residues in contact with ALA 321 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3175 ALA 2.9 16.5 + - - +
3185 PHE 3.5 4.5 - - - +
3205 SER* 1.3 81.7 + - - +
3225 LEU* 1.3 58.5 + - - +
3245 GLN* 3.2 5.9 + - - +
3255 ALA* 2.9 25.8 + - - +
3405 VAL* 3.4 20.8 - - + +
3425 VAL* 3.9 14.4 - - + -
3575 PHE* 4.3 3.6 - - + -
3595 LEU* 3.6 28.7 - - + -
----------------------------------------------------------
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Residues in contact with LEU 322 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2115 ALA* 3.5 24.2 - - + -
2125 THR 4.1 13.5 - - - +
2135 TRP* 4.4 4.7 - - + -
3185 PHE* 2.6 54.0 + - + +
3195 GLY 3.5 4.0 - - - +
3215 ALA* 1.3 73.5 - - - +
3235 ALA* 1.3 55.6 + - - +
3255 ALA* 3.2 8.3 + - - +
3265 ARG* 2.9 68.7 + - - +
3595 LEU* 4.2 8.5 - - + +
3625 THR* 4.8 10.5 - - + +
3645 LEU* 4.6 11.4 - - + -
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Residues in contact with ALA 323 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2095 PHE* 5.1 2.5 - - + -
2105 SER 3.9 18.8 - - - +
2115 ALA* 5.0 0.2 - - - -
2755 ASN* 5.5 2.9 - - - +
2765 ASP 4.1 12.1 - - - +
2775 THR* 4.3 18.6 + - - +
3195 GLY 2.9 12.9 + - - +
3205 SER* 3.2 12.8 + - - +
3225 LEU* 1.3 77.5 - - - +
3245 GLN* 1.3 58.5 + - + +
3265 ARG* 3.2 8.4 + - - +
3275 LEU* 2.9 29.6 + - - +
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Residues in contact with GLN 324 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2295 ARG* 4.7 1.4 - - - +
2775 THR* 4.0 19.8 + - - -
2865 PRO* 3.4 21.4 + - - +
2875 TYR* 3.5 33.9 - - + -
2885 PRO* 3.4 34.4 - - + +
3205 SER 2.9 12.2 + - - +
3215 ALA* 3.4 12.3 - - - +
3235 ALA* 1.3 77.5 - - - +
3255 ALA* 1.3 56.9 + - - +
3275 LEU* 3.2 16.6 + - - +
3285 LEU* 2.9 29.9 + - - +
3405 VAL* 4.5 14.4 - - + -
3425 VAL* 5.5 0.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 325 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3215 ALA 2.9 13.2 + - - +
3225 LEU 3.4 8.5 - - - +
3245 GLN* 1.3 75.5 - - - +
3265 ARG* 1.3 59.0 + - - +
3285 LEU* 3.2 3.7 + - - +
3295 TYR* 2.9 44.6 + - + +
3365 LEU* 4.4 7.0 - - + -
3405 VAL* 4.8 6.7 - - + +
3595 LEU* 4.1 11.2 - - + -
3625 THR* 3.6 29.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 326 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2125 THR 4.5 10.2 + - - -
2135 TRP* 5.3 4.9 - - - +
2755 ASN* 3.5 42.6 - - - +
3225 LEU* 2.9 57.4 + - - +
3235 ALA* 3.2 5.8 + - - +
3255 ALA* 1.3 76.4 - - + +
3275 LEU* 1.3 57.2 + - - +
3295 TYR 2.8 26.0 - - - +
3305 GLY 4.5 11.7 - - - +
3315 ASN* 3.4 31.3 + - - +
3335 ALA* 4.6 10.3 - - - +
3625 THR* 4.1 25.9 + - + -
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Residues in contact with LEU 327 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2775 THR* 3.4 34.3 - - + +
2795 PHE 5.5 0.4 - - - +
2815 GLU* 6.4 2.0 - - - -
2875 TYR* 5.2 11.9 - - + +
3235 ALA 2.9 12.7 + - - +
3245 GLN* 3.2 21.7 + - - +
3265 ARG* 1.3 76.8 - - - +
3285 LEU* 1.3 66.4 - - - +
3295 TYR 4.0 1.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 328 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875 TYR* 4.6 20.4 - - + +
3245 GLN 2.9 12.9 + - - +
3255 ALA 3.2 7.8 + - - +
3275 LEU* 1.3 84.3 - - - +
3295 TYR* 1.3 100.7 + - + +
3385 GLN* 4.9 11.4 - - + +
3405 VAL* 4.8 13.5 - - + -
----------------------------------------------------------
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Residues in contact with TYR 329 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3255 ALA* 2.9 30.8 + - + +
3265 ARG 2.8 18.7 - - - +
3275 LEU 4.0 1.7 - - - +
3285 LEU* 1.3 107.5 - - + +
3305 GLY* 1.3 67.2 + - - +
3325 ASP 5.7 0.2 - - - +
3345 LYS* 4.0 26.7 - - - +
3365 LEU* 3.4 39.5 - - + -
3375 GLU* 4.4 13.4 + - + -
3385 GLN* 2.8 39.7 + - + +
3405 VAL* 5.5 0.7 - - + -
3625 THR* 5.2 1.1 - - + -
----------------------------------------------------------
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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