Contacts of the helix formed by residues 84 - 111 (chain H) in PDB entry 1ZMC
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 ASN 84 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G GLY* 2.9 20.1 + - - +
77G GLU* 2.6 38.2 + - - +
82H ARG 3.6 0.4 + - - -
83H LEU* 1.3 72.6 - - - +
85H LEU* 1.3 62.5 + - - +
86H ASP* 3.0 14.4 + - - +
87H LYS* 3.0 36.6 + - - +
88H MET* 3.0 12.8 + - - +
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Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 6.0 0.2 - - + -
83H LEU* 3.5 20.3 + - + +
84H ASN* 1.3 73.8 - - - +
86H ASP* 1.3 60.7 - - - +
88H MET* 3.9 10.8 - - + -
89H MET* 3.1 39.8 + - + +
174H LEU 3.9 9.4 - - - +
175H LYS 4.0 4.5 - - - +
176H LYS* 3.5 43.5 - - - +
177H VAL* 3.9 6.3 - - + +
197H TRP* 4.0 24.5 - - + -
200H LEU* 4.3 13.9 - - + -
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Residues in contact with ASP 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ASN* 3.0 10.6 + - - +
85H LEU* 1.3 77.0 - - - +
87H LYS* 1.3 65.0 + - - +
89H MET* 3.4 5.7 + - - +
90H GLU* 3.2 21.0 + - - +
175H LYS* 5.1 8.3 + - - -
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Residues in contact with LYS 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ALA* 3.5 21.0 + - - +
73G SER* 3.4 37.4 - - - +
75G GLY* 3.7 8.7 - - - +
77G GLU* 5.6 0.9 - - - +
84H ASN* 3.0 30.6 + - - +
86H ASP* 1.3 74.9 - - - +
88H MET* 1.3 65.1 + - - +
90H GLU* 3.1 41.4 + - - +
91H GLN 3.2 11.0 + - - +
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Residues in contact with MET 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ARG* 2.9 27.7 + - - +
75G GLY* 4.2 0.9 - - - +
76G ILE* 5.4 1.3 - - - -
56H LEU* 4.1 19.3 - - + +
59H ASN* 3.4 35.4 + - + +
60H SER* 3.6 25.1 - - - +
63H TYR* 5.1 2.7 - - - -
83H LEU* 3.9 18.2 - - + -
84H ASN 3.0 15.5 + - - +
85H LEU* 3.9 10.8 - - + +
87H LYS* 1.3 80.2 - - - +
89H MET* 1.3 60.1 + - - +
90H GLU 3.5 0.2 + - - -
91H GLN 3.7 0.3 + - - -
92H LYS* 3.6 9.5 + - - +
196H VAL* 5.5 0.2 - - + -
200H LEU* 3.6 35.2 - - + -
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Residues in contact with MET 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 3.9 15.7 - - + -
85H LEU* 3.1 32.4 + - + +
86H ASP* 3.9 5.8 - - - +
87H LYS 3.2 0.2 - - - -
88H MET* 1.3 74.0 - - - +
90H GLU* 1.3 61.4 + - - +
92H LYS* 3.3 37.2 + - - +
93H SER* 3.0 31.6 + - - +
172H LEU 3.4 13.0 - - - +
173H SER* 3.9 14.1 - - - -
174H LEU 3.9 8.1 - - - +
197H TRP* 3.7 34.8 - - + -
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Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H ASP 3.2 12.1 + - - +
87H LYS* 3.1 39.3 + - - +
89H MET* 1.3 75.3 - - - +
91H GLN* 1.3 65.5 + - - +
93H SER* 2.9 8.2 + - - +
94H THR* 2.8 35.9 + - - +
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Residues in contact with GLN 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G SER* 3.6 26.2 + - - +
74G ARG* 4.2 11.0 - - + +
395G LYS 4.7 0.8 + - - -
396G THR 3.0 24.3 + - - +
398G ALA* 3.8 21.2 - - + +
55H ALA* 3.7 12.3 - - - +
59H ASN* 2.8 42.6 + - - +
87H LYS* 3.2 7.9 + - - +
88H MET 3.9 2.5 - - - +
90H GLU* 1.3 75.3 - - - +
92H LYS* 1.3 63.6 + - - +
94H THR* 3.5 7.9 + - - -
95H ALA* 3.2 21.2 + - - +
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Residues in contact with LYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H PRO* 3.8 39.1 - - + +
55H ALA* 4.0 13.0 - - + +
56H LEU* 3.7 24.9 - - + -
88H MET 3.6 9.3 + - - +
89H MET* 3.3 32.6 + - - +
90H GLU 3.0 0.2 - - - -
91H GLN* 1.3 88.1 + - - +
93H SER* 1.3 70.5 + - - +
95H ALA* 3.2 6.1 + - - +
96H VAL* 3.1 26.2 + - + +
172H LEU* 2.6 27.5 + - - +
173H SER* 3.3 13.7 + - - -
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Residues in contact with SER 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H MET* 3.0 14.1 + - - +
90H GLU* 2.9 12.1 + - - -
92H LYS* 1.3 83.2 + - - +
94H THR* 1.3 60.8 + - - +
96H VAL* 3.2 8.4 + - - +
97H LYS* 2.8 34.6 + - - +
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Residues in contact with THR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G LYS* 6.5 0.4 - - - -
90H GLU* 2.8 29.1 + - - +
91H GLN* 3.7 8.8 - - - -
93H SER* 1.3 78.3 - - - +
95H ALA* 1.3 56.4 + - - +
97H LYS* 3.6 9.4 - - + +
98H ALA* 2.9 31.2 + - + +
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Residues in contact with ALA 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G LYS* 4.0 24.4 - - - +
396G THR* 4.0 24.5 - - + +
51H ILE* 4.7 4.3 - - + -
91H GLN* 3.2 12.2 + - - +
92H LYS* 3.2 11.3 + - - +
94H THR* 1.3 80.6 - - - +
96H VAL* 1.3 62.6 + - - +
98H ALA* 3.3 5.9 + - - +
99H LEU* 2.9 30.7 + - + +
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Residues in contact with VAL 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H LEU* 3.3 37.2 - - + +
47H ASN* 4.0 24.0 - - - +
51H ILE* 4.1 11.0 - - + -
52H PRO* 4.3 17.7 - - + -
92H LYS* 3.1 19.9 + - + +
93H SER* 3.2 8.7 + - - +
95H ALA* 1.3 73.8 - - - +
97H LYS* 1.3 55.9 + - - +
99H LEU* 3.1 3.3 + - - +
100H THR* 2.8 40.2 + - + +
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Residues in contact with LYS 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER* 4.6 8.3 + - - -
263A GLY* 3.0 43.6 + - - +
265A LYS* 5.2 4.2 - - - +
93H SER* 2.8 18.9 + - - +
94H THR* 3.6 9.4 - - + +
96H VAL* 1.3 77.0 - - - +
98H ALA* 1.3 63.2 + - - +
100H THR* 2.8 22.9 + - - +
101H GLY* 2.9 9.5 + - - -
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Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G LYS* 3.7 29.4 - - - -
94H THR* 2.9 21.6 + - + +
95H ALA 3.7 4.3 - - - +
97H LYS* 1.3 78.7 - - - +
99H LEU* 1.3 58.0 + - - +
101H GLY* 3.2 3.0 + - - -
102H GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390G ALA* 5.2 8.5 - - - +
391G ASN 5.2 0.2 - - - +
392G SER* 4.1 27.1 - - - +
395G LYS* 4.0 28.9 - - + -
396G THR* 4.1 12.1 - - - +
46H LEU* 3.4 22.6 - - + +
51H ILE* 4.0 23.6 - - + -
95H ALA 2.9 18.3 + - - +
98H ALA* 1.3 75.0 - - - +
100H THR* 1.3 65.2 + - - +
102H GLY* 3.3 4.4 + - - +
103H ILE* 3.2 25.5 + - - +
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Residues in contact with THR 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H THR* 3.9 19.6 - - + +
41H LEU* 3.4 25.4 - - - +
46H LEU* 3.6 15.5 - - + -
47H ASN* 3.5 20.0 - - - +
96H VAL* 2.8 25.7 + - + +
97H LYS* 2.8 27.0 + - - +
99H LEU* 1.3 68.6 - - - +
101H GLY* 1.3 65.4 + - - +
103H ILE* 3.0 17.2 + - - +
104H ALA* 3.2 10.9 + - - +
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Residues in contact with GLY 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H LYS 2.9 15.1 + - - -
98H ALA* 3.6 4.3 - - - -
100H THR* 1.3 78.6 + - - +
102H GLY* 1.3 56.0 + - - +
104H ALA* 3.2 10.5 + - - +
105H HIS* 3.0 28.0 + - - +
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Residues in contact with GLY 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H ALA 2.9 13.9 + - - -
99H LEU* 3.3 7.8 + - - -
100H THR 3.1 0.4 - - - -
101H GLY* 1.3 74.5 - - - +
103H ILE* 1.3 64.5 + - - +
105H HIS* 3.4 7.2 + - - +
106H LEU* 3.0 34.2 + - - +
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Residues in contact with ILE 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473G ASN* 5.1 0.4 - - - +
19H TYR* 3.6 63.9 - - + +
41H LEU* 3.6 30.7 - - + -
42H GLY* 4.4 2.7 - - - -
46H LEU* 4.0 18.4 - - + -
99H LEU 3.2 15.6 + - - +
100H THR* 3.0 9.2 + - - +
102H GLY* 1.3 75.6 - - - +
104H ALA* 1.3 65.2 + - - +
106H LEU* 3.0 11.5 + - + +
107H PHE* 2.9 29.9 + - + +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H LEU* 3.7 17.9 - - + +
100H THR 3.2 7.6 + - - +
101H GLY* 3.2 13.0 + - - +
103H ILE* 1.3 79.7 - - - +
105H HIS* 1.3 57.7 + - - +
107H PHE* 3.3 5.1 + - - +
108H LYS* 3.0 29.9 + - - +
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Residues in contact with HIS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H GLY 3.0 16.1 + - - +
102H GLY* 3.8 8.3 - - - +
103H ILE 3.2 0.2 - - - -
104H ALA* 1.3 78.1 - - - +
106H LEU* 1.3 60.3 + - - +
108H LYS* 3.5 26.7 + - + +
109H GLN* 2.9 54.6 + - + +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472G ILE 4.1 7.4 - - - +
473G ASN* 3.5 55.6 - - + +
474G PHE* 3.7 15.3 - - + +
19H TYR* 4.9 1.8 - - + -
23H ILE* 4.2 18.8 - - + -
102H GLY* 3.0 25.4 + - - +
103H ILE* 3.0 10.1 + - + +
105H HIS* 1.3 76.5 - - + +
107H PHE* 1.3 62.5 + - - +
109H GLN* 3.7 14.8 - - - +
110H ASN* 2.8 38.4 + - - +
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Residues in contact with PHE 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H SER* 4.8 0.4 - - - -
19H TYR* 3.4 49.6 - - + -
22H ALA* 4.0 8.5 - - + -
23H ILE* 4.0 12.3 - - + -
34H CYS* 3.9 32.5 - - + -
41H LEU* 4.0 31.6 - - + -
103H ILE* 2.9 14.5 + - + +
104H ALA* 3.5 9.6 - - - +
106H LEU* 1.3 73.4 - - - +
108H LYS* 1.3 65.5 + - - +
110H ASN 3.0 1.9 + - - -
111H LYS 2.9 4.3 + - - -
112H VAL* 2.8 53.3 + - + +
114H HIS* 4.4 16.8 - + + -
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Residues in contact with LYS 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ALA 3.0 16.0 + - - +
105H HIS* 3.7 26.9 + - + +
107H PHE* 1.3 76.9 - - - +
109H GLN* 1.3 65.7 + - - +
111H LYS* 3.1 20.5 + - - +
112H VAL 4.6 3.6 + - - +
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Residues in contact with GLN 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G PHE* 3.2 34.8 + - - +
27H GLN* 6.1 0.2 - - - +
105H HIS* 2.9 41.5 + - + +
106H LEU* 3.7 10.8 - - - +
108H LYS* 1.3 82.5 - - - +
110H ASN* 1.3 72.1 + - - +
111H LYS* 3.7 8.6 + - - +
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Residues in contact with ASN 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470G LYS* 5.0 5.2 + - - +
472G ILE 5.0 0.6 + - - -
474G PHE 5.6 0.8 + - - -
23H ILE* 3.8 24.2 - - + +
26H ALA* 3.3 21.9 - - + +
27H GLN* 3.4 28.8 + - - +
106H LEU* 2.8 34.2 + - - +
107H PHE* 3.0 2.6 + - - +
109H GLN* 1.3 95.9 + - - +
111H LYS* 1.3 72.2 - - - +
112H VAL* 3.2 11.9 - - + -
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Residues in contact with LYS 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 5.0 1.8 - - + +
31H LYS* 5.8 0.3 - - - -
32H THR 4.0 8.3 + - - +
107H PHE 2.9 3.5 + - - -
108H LYS* 3.1 17.5 + - - +
109H GLN 4.1 8.1 - - - +
110H ASN* 1.3 82.2 - - - +
112H VAL* 1.3 63.2 + - - +
113H VAL* 3.4 8.3 + - - +
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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