Contacts of the helix formed by residues 3139 - 3165 (chain B) in PDB entry 5NUG
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 HIS3139 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3115B LEU* 3.4 33.4 - - + +
3117B LYS* 3.2 42.6 + - + +
3120B TYR* 3.2 42.6 - + + +
3138B SER* 1.3 78.6 + - - +
3140B ARG* 1.3 60.8 + - - +
3141B GLU 3.2 0.7 - - - -
3142B ALA* 3.2 1.7 + - - +
3143B ILE* 3.1 50.8 + - + +
3504B ALA* 4.4 14.9 - - + +
3541B ILE* 4.2 18.4 - - + +
3542B GLN* 5.9 0.4 - - + -
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Residues in contact with ARG3140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3107B LYS* 5.2 9.0 - - + +
3110B THR* 3.5 42.0 - - - +
3111B SER* 3.9 21.6 + - - +
3113B MET 4.7 2.2 - - - -
3115B LEU* 4.2 19.9 + - + +
3116B GLU* 3.4 40.1 + - - +
3138B SER* 3.5 10.3 + - - +
3139B HIS* 1.3 79.3 - - - +
3141B GLU* 1.3 66.7 + - - +
3143B ILE* 3.4 13.2 - - - +
3144B VAL* 3.3 21.5 - - - +
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Residues in contact with GLU3141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3103B TYR* 2.9 29.6 + - + +
3107B LYS* 3.3 32.4 + - - +
3133B LEU* 4.6 10.4 - - + +
3134B PRO* 4.4 14.6 - - + +
3137B PRO* 4.0 17.3 - - + -
3138B SER* 3.7 25.1 - - - +
3139B HIS 3.2 0.2 - - - -
3140B ARG* 1.3 86.6 + - - +
3142B ALA* 1.3 61.2 + - - +
3143B ILE 3.3 0.4 - - - -
3144B VAL* 3.2 5.8 + - - +
3145B ASN* 2.9 28.6 + - - +
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Residues in contact with ALA3142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3120B TYR* 3.0 34.5 - - + +
3126B MET* 5.9 4.7 - - + -
3133B LEU* 6.1 0.7 - - - -
3137B PRO* 4.8 7.4 - - + +
3138B SER 3.8 5.9 + - - +
3139B HIS 3.2 10.8 + - - +
3141B GLU* 1.3 80.3 - - - +
3143B ILE* 1.3 56.9 + - - +
3145B ASN* 3.2 9.3 + - - +
3146B SER* 2.9 30.8 + - - -
3539B ALA* 5.3 4.0 - - + +
3541B ILE* 3.8 10.1 - - + -
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Residues in contact with ILE3143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3110B THR* 4.0 12.8 - - + -
3115B LEU* 2.5 47.1 - - + -
3139B HIS* 3.1 27.4 + - + +
3140B ARG* 3.4 14.6 - - - +
3142B ALA* 1.3 80.6 - - - +
3144B VAL* 1.3 59.2 + - - +
3146B SER* 3.2 4.1 + - - -
3147B CYS* 2.9 32.3 + - - -
3183B TYR* 3.5 27.1 - - + +
3504B ALA* 5.0 4.3 - - + -
3505B GLY* 6.2 0.4 - - - -
3508B LEU* 4.7 5.5 - - + +
3541B ILE* 3.8 23.6 - - + -
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Residues in contact with VAL3144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3103B TYR* 3.4 50.9 - - + +
3106B GLY* 3.7 15.9 - - - -
3107B LYS* 3.9 6.3 - - + +
3110B THR* 3.5 30.7 - - + +
3140B ARG 3.3 16.4 - - - +
3141B GLU* 3.2 8.6 + - - +
3143B ILE* 1.3 76.3 - - - +
3145B ASN* 1.3 56.8 + - - +
3147B CYS* 3.2 11.4 - - - +
3148B VAL* 2.9 28.8 + - + +
3176B TYR* 5.0 0.7 - - - +
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Residues in contact with ASN3145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3103B TYR* 4.7 2.9 - - + -
3126B MET* 5.5 2.4 - - + +
3127B PRO 3.3 22.1 - - - +
3128B VAL* 3.7 5.7 - - - +
3129B VAL* 3.6 9.3 + - - +
3130B TYR* 3.5 31.9 - - - +
3133B LEU* 3.7 26.9 - - + +
3141B GLU 2.9 12.7 + - - +
3142B ALA* 3.2 11.4 + - - +
3144B VAL* 1.3 77.5 - - - +
3146B SER* 1.3 57.7 + - - +
3148B VAL* 3.2 7.1 + - - +
3149B PHE* 2.9 27.0 + - - +
3535B HIS* 4.2 9.4 + - - -
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Residues in contact with SER3146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3142B ALA 2.9 9.2 + - - -
3143B ILE 3.5 8.3 - - - -
3145B ASN* 1.3 77.1 - - - +
3147B CYS* 1.3 55.8 + - - +
3149B PHE* 3.2 4.0 + - - +
3150B VAL* 2.9 35.5 + - - +
3508B LEU* 3.8 19.7 - - - -
3535B HIS* 3.7 22.5 + - - -
3536B LEU* 3.7 12.2 - - - +
3539B ALA* 4.1 7.3 - - - +
3541B ILE* 3.2 22.9 - - - +
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Residues in contact with CYS3147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3106B GLY* 6.0 1.6 - - - -
3143B ILE 2.9 26.4 + - - -
3144B VAL* 3.2 14.6 - - - +
3146B SER* 1.3 74.3 - - - +
3148B VAL* 1.3 60.2 + - - +
3150B VAL* 3.2 7.0 + - - +
3151B HIS* 2.9 28.2 + - - +
3176B TYR* 3.6 16.5 - - - +
3179B PHE* 3.7 33.8 - - + -
3180B ILE* 4.8 7.2 - - - -
3183B TYR* 4.4 18.6 - - - -
3508B LEU* 4.1 10.9 - - - +
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Residues in contact with VAL3148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3099B THR* 4.6 8.1 - - - +
3102B LEU* 3.6 31.2 - - + -
3103B TYR* 3.7 20.6 - - + +
3129B VAL* 4.2 20.6 - - + -
3130B TYR* 4.7 9.0 - - + +
3144B VAL 2.9 11.1 + - - +
3145B ASN* 3.2 10.7 + - - +
3147B CYS* 1.3 80.4 - - - +
3149B PHE* 1.3 57.1 + - - +
3151B HIS* 3.2 6.7 + - - +
3152B GLN* 2.9 35.0 + - + +
3176B TYR* 3.2 22.0 - - - +
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Residues in contact with PHE3149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3129B VAL* 3.9 21.1 - - + -
3145B ASN 2.9 8.2 + - - +
3146B SER 3.2 4.7 + - - +
3148B VAL* 1.3 75.3 - - - +
3150B VAL* 1.3 62.6 + - + +
3152B GLN* 3.2 6.9 + - + +
3153B THR* 2.9 56.0 + - + +
3156B GLN* 6.0 1.1 - - - -
3531B THR* 3.9 18.8 - - + -
3532B TRP* 4.1 8.1 - + - -
3535B HIS* 3.1 67.5 - + + +
----------------------------------------------------------
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Residues in contact with VAL3150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3146B SER 2.9 19.6 + - - +
3147B CYS* 3.3 10.8 - - - +
3149B PHE* 1.3 77.2 - - + +
3151B HIS* 1.3 63.6 + - - +
3153B THR* 2.2 21.5 + - - -
3154B LEU* 3.3 6.4 + - - +
3179B PHE* 4.1 10.8 - - + -
3508B LEU* 4.6 15.3 - - + -
3509B LEU* 5.5 0.2 - - + -
3512B ALA* 3.6 22.9 - - + -
3516B TYR* 4.8 7.2 - - + -
3532B TRP* 3.3 55.1 + - + +
3535B HIS* 5.9 0.7 - - + -
3536B LEU* 6.2 0.4 - - + -
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Residues in contact with HIS3151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3097B TRP 6.0 0.4 + - - -
3102B LEU* 3.6 24.6 - - + +
3147B CYS 2.9 6.1 + - - -
3148B VAL* 3.4 8.7 - - - +
3150B VAL* 1.3 79.3 - - - +
3152B GLN* 1.3 67.9 + - + +
3154B LEU* 3.5 1.4 + - - +
3155B HIS* 3.4 10.7 + - - -
3171B ILE* 3.1 49.7 - - + +
3172B THR 3.8 12.1 - - - -
3173B PRO* 4.7 3.2 - - + +
3176B TYR* 3.1 43.4 - + + -
3516B TYR* 2.3 36.8 + - - +
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Residues in contact with GLN3152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3099B THR* 2.5 38.3 - - - +
3102B LEU* 4.4 9.8 - - + +
3129B VAL* 3.3 27.1 - - + +
3148B VAL* 2.9 20.8 + - + +
3149B PHE* 3.2 10.7 + - + +
3151B HIS* 1.3 82.0 - - + +
3153B THR* 1.3 57.8 + - - +
3155B HIS* 3.2 8.3 + - - +
3156B GLN* 2.9 29.8 + - - +
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Residues in contact with THR3153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3149B PHE* 2.9 51.0 + - + +
3150B VAL 2.2 28.6 + - - -
3152B GLN* 1.3 78.1 - - + +
3154B LEU* 1.3 50.0 + - - +
3156B GLN* 3.2 15.3 + - - +
3157B ALA* 2.6 37.7 + - - +
3528B LEU* 5.5 5.2 - - - -
3531B THR* 4.0 14.4 - - + -
3532B TRP* 2.7 19.6 + - - +
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Residues in contact with LEU3154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3150B VAL 3.3 1.5 + - - +
3151B HIS 3.8 4.5 - - - +
3152B GLN 3.3 0.4 - - - -
3153B THR* 1.3 81.1 + - - +
3155B HIS* 1.3 63.8 + - - +
3157B ALA* 3.2 6.8 + - + +
3158B ASN* 3.1 27.6 + - - +
3169B MET 6.0 0.7 - - - +
3171B ILE* 4.0 20.9 - - + +
3175B HIS* 5.7 4.9 - - + -
3516B TYR* 3.1 57.2 - - + +
3520B PHE* 3.5 29.2 - - + -
3528B LEU* 3.4 31.2 - - + -
3532B TRP* 5.3 0.4 - - + -
----------------------------------------------------------
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Residues in contact with HIS3155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2938B VAL* 6.4 0.9 - - + -
3096B ASP* 4.2 25.1 + - + -
3151B HIS* 3.4 10.6 + - + +
3152B GLN* 3.2 13.2 + - - +
3154B LEU* 1.3 80.7 - - - +
3156B GLN* 1.3 60.5 + - - +
3158B ASN* 3.5 14.9 + - - +
3159B ALA* 3.7 5.5 + - - +
3171B ILE* 3.2 43.2 - - + +
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Residues in contact with GLN3156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3149B PHE* 6.0 0.9 - - - -
3152B GLN 2.9 13.3 + - - +
3153B THR* 3.5 17.5 - - - +
3155B HIS* 1.3 74.1 - - - +
3157B ALA* 1.3 64.9 + - - +
3159B ALA* 3.0 19.3 + - + +
3160B ARG* 3.1 18.3 + - + +
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Residues in contact with ALA3157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3153B THR 2.6 20.5 + - - +
3154B LEU* 3.2 15.2 + - + +
3156B GLN* 1.3 73.3 - - - +
3158B ASN* 1.3 58.2 + - - +
3160B ARG* 3.2 10.7 + - - +
3161B LEU* 2.9 28.8 + - - +
3520B PHE* 5.2 7.0 - - + -
3528B LEU* 4.2 22.0 - - + -
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Residues in contact with ASN3158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3154B LEU* 3.1 19.5 + - - +
3155B HIS* 3.6 8.9 + - + +
3156B GLN 3.2 0.4 - - - -
3157B ALA* 1.3 75.5 - - - +
3159B ALA* 1.3 57.6 + - - +
3161B LEU* 3.2 8.5 + - - +
3162B ALA* 2.9 28.8 + - - +
3168B THR* 3.2 27.7 + - + +
3169B MET 3.3 25.1 + - - +
3170B ALA* 4.3 2.2 - - - +
3171B ILE* 3.7 22.2 - - - +
3520B PHE* 3.9 23.6 - - - -
----------------------------------------------------------
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Residues in contact with ALA3159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3155B HIS 3.7 4.8 + - - +
3156B GLN* 3.0 16.5 + - + +
3158B ASN* 1.3 78.8 - - - +
3160B ARG* 1.3 60.8 + - - +
3162B ALA* 3.2 17.8 + - - +
3163B LYS* 3.3 27.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG3160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3156B GLN* 3.1 16.8 + - + +
3157B ALA* 3.2 13.7 + - - +
3159B ALA* 1.3 77.4 - - - +
3161B LEU* 1.3 63.2 + - - +
3163B LYS* 3.3 41.3 + - - +
3164B ARG* 3.7 29.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU3161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157B ALA 2.9 13.9 + - - +
3158B ASN* 3.3 7.9 - - - +
3160B ARG* 1.3 76.0 - - - +
3162B ALA* 1.3 62.1 + - - +
3164B ARG* 3.1 32.9 + - + +
3165B GLY 3.2 8.3 + - - -
3166B GLY* 3.8 14.2 + - - +
3167B ARG 3.2 27.4 - - - +
3168B THR* 3.9 18.2 - - - +
3519B TYR* 5.4 3.6 - - + -
3520B PHE* 4.7 19.3 - - + -
3524B MET* 3.8 30.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA3162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3158B ASN 2.9 13.2 + - - +
3159B ALA* 3.2 14.3 + - - +
3161B LEU* 1.3 74.4 - - - +
3163B LYS* 1.3 62.2 + - - +
3164B ARG 3.4 0.2 - - - -
3165B GLY* 3.3 16.9 + - - +
3166B GLY 4.8 6.7 - - - +
3168B THR* 5.2 11.4 - - + -
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Residues in contact with LYS3163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3159B ALA* 3.7 27.6 + - - +
3160B ARG* 3.3 27.6 + - - +
3161B LEU 3.2 0.6 - - - -
3162B ALA* 1.3 75.6 - - - +
3164B ARG* 1.3 66.0 + - + +
3165B GLY* 3.5 0.9 + - - -
----------------------------------------------------------
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Residues in contact with ARG3164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3160B ARG* 3.7 39.4 + - - +
3161B LEU* 3.1 21.4 + - + +
3163B LYS* 1.3 77.1 - - + +
3165B GLY* 1.3 60.8 + - - +
3166B GLY 5.0 1.8 - - - +
3524B MET* 6.4 1.1 - - - -
3820B GLN* 5.3 7.8 + - - +
4348B MET 5.5 4.6 + - - -
4349B LEU* 5.9 11.8 - - + +
----------------------------------------------------------
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Residues in contact with GLY3165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3161B LEU 3.2 5.3 + - - -
3162B ALA 3.3 13.4 + - - -
3163B LYS 3.2 3.1 - - - -
3164B ARG* 1.3 79.2 - - - +
3166B GLY* 1.3 62.8 + - - +
3167B ARG* 5.8 1.0 + - - -
3820B GLN* 5.3 4.2 - - - +
----------------------------------------------------------
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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