Contacts of the helix formed by residues 113 - 139 (chain H) in PDB entry 1F33
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 113 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ARG* 3.4 8.6 - - - +
56H GLY* 5.1 4.2 - - - -
57H ALA 5.6 1.4 + - - -
112H HIS* 1.3 81.4 - - - +
114H VAL* 1.3 66.5 + - - +
115H GLN* 2.8 48.1 - - - +
116H ASP* 3.2 34.0 + - - +
117H HIS* 3.2 11.4 + - - -
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Residues in contact with VAL 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H MET* 4.3 13.4 - - + +
55H ARG 3.0 37.9 + - - +
56H GLY* 3.8 5.6 - - - +
57H ALA 3.4 26.9 - - - +
58H ASN* 4.5 1.3 - - + +
59H PHE* 4.1 11.2 - - - -
62H VAL* 4.2 24.2 - - + -
112H HIS 3.3 1.5 + - - -
113H ASN* 1.3 73.1 - - - +
115H GLN* 1.3 63.8 + - + +
117H HIS* 3.2 4.4 + - - +
118H LEU* 2.8 45.9 + - + +
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Residues in contact with GLN 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ALA* 5.3 4.0 + - + +
58H ASN* 5.9 3.2 - - - +
113H ASN* 2.8 22.6 - - - +
114H VAL* 1.3 78.9 - - + +
116H ASP* 1.3 61.0 + - - +
118H LEU* 3.2 12.4 + - - +
119H LYS* 3.0 43.3 + - - +
165H ASN 3.2 21.6 + - - -
166H ILE* 3.3 13.6 - - - +
167H GLU* 2.8 53.3 + - + +
57L ALA* 5.8 0.6 - - - +
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Residues in contact with ASP 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H ILE* 4.1 29.1 - - + +
112H HIS 4.8 0.3 + - - -
113H ASN* 3.2 32.8 + - - +
115H GLN* 1.3 77.7 - - - +
117H HIS* 1.3 62.5 + - - +
119H LYS* 3.2 16.2 + - - +
120H GLU* 2.9 26.6 + - + +
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Residues in contact with HIS 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLN* 4.5 4.3 - - - -
50H ALA* 3.4 25.0 - - + -
53H ASN* 3.3 16.6 + - + -
54H MET* 3.7 27.1 - - + -
107H TYR* 2.6 33.0 + + - +
108H PRO 4.9 1.3 - - - -
111H ILE* 3.2 40.3 + - + +
112H HIS* 3.4 23.3 - - - -
113H ASN 3.2 7.1 + - - -
114H VAL 3.2 7.3 + - - +
116H ASP* 1.3 78.9 - - - +
118H LEU* 1.3 53.1 + - - +
120H GLU 3.2 0.3 + - - -
121H LEU* 2.7 42.5 + - - +
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Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H MET* 5.0 1.3 - - + -
58H ASN* 5.8 0.4 - - - +
62H VAL* 3.8 27.6 - - + -
65H MET* 5.1 4.0 - - + -
66H LEU* 5.5 0.2 - - + -
114H VAL* 2.8 28.5 + - + +
115H GLN* 3.4 20.9 - - - +
116H ASP 3.2 0.2 - - - -
117H HIS* 1.3 77.1 - - - +
119H LYS* 1.3 56.1 + - - +
121H LEU* 4.5 9.6 - - + -
122H ALA* 2.9 25.3 + - - +
162H ILE* 3.3 40.8 - - + +
165H ASN* 3.6 34.8 - - + +
166H ILE* 3.9 10.3 - - + +
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Residues in contact with LYS 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H GLN* 3.0 32.8 + - - +
116H ASP* 3.6 14.9 + - - +
118H LEU* 1.3 73.9 - - - +
120H GLU* 1.3 67.5 + - + +
122H ALA* 3.3 3.9 + - - +
123H ASP* 3.1 29.6 + - - +
166H ILE* 4.0 37.9 - - + -
167H GLU 5.7 0.7 - - - -
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H TYR* 3.4 26.5 - - + +
108H PRO* 3.9 11.1 - - + +
111H ILE* 3.7 21.4 - - + +
116H ASP* 2.9 18.7 + - + +
117H HIS 3.6 0.2 - - - +
119H LYS* 1.3 76.6 - - + +
121H LEU* 1.3 61.3 + - - +
123H ASP* 3.4 14.1 + - - +
124H ARG* 2.9 52.8 + - - +
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Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ILE* 3.9 27.4 - - + +
47H THR* 4.3 9.6 - - - -
50H ALA* 3.6 32.8 - - + -
54H MET* 4.7 1.1 - - + -
66H LEU* 3.7 31.2 - - + -
107H TYR* 4.0 2.9 - - + +
117H HIS 2.7 30.3 + - - +
118H LEU* 3.7 12.8 - - + +
120H GLU* 1.3 72.4 - - - +
122H ALA* 1.3 56.3 + - - +
124H ARG* 3.1 3.9 + - - -
125H TYR* 2.7 50.4 + - + -
162H ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H LEU 2.9 18.4 + - - +
119H LYS* 3.5 9.9 - - - +
121H LEU* 1.3 75.0 - - - +
123H ASP* 1.3 60.9 + - - +
125H TYR* 4.5 0.7 - - - -
126H ALA* 2.8 32.6 + - - +
159H LEU* 3.4 11.1 - - + +
162H ILE* 3.9 15.0 - - + +
163H GLU* 4.3 16.4 - - + +
166H ILE* 4.2 11.2 - - + -
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Residues in contact with ASP 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H LYS* 3.1 14.7 + - - +
120H GLU* 3.5 16.7 - - - +
121H LEU 3.1 0.8 - - - -
122H ALA* 1.3 79.9 - - - +
124H ARG* 1.3 69.7 + - - +
126H ALA* 3.2 8.0 + - - +
127H ILE* 3.1 30.8 + - + +
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Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.8 18.2 - - + -
46H ILE* 4.2 13.0 - - + +
104H LEU* 3.8 19.0 - - + +
105H LYS* 2.9 53.9 + - - +
106H SER 3.7 3.6 + - - -
107H TYR* 2.8 35.7 - - - +
108H PRO* 3.5 14.8 - - - +
120H GLU* 2.9 41.5 + - - +
121H LEU* 3.1 7.0 + - - +
123H ASP* 1.3 80.1 - - - +
125H TYR* 1.3 63.4 + - - +
127H ILE* 3.2 10.2 + - - +
128H VAL* 3.1 25.8 + - - +
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Residues in contact with TYR 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.5 39.5 - - + -
47H THR* 2.7 28.5 + - + +
66H LEU* 5.4 0.2 - - + -
69H PHE* 3.6 16.4 - + - +
73H LEU* 3.5 12.1 - - + +
121H LEU* 2.7 42.7 + - + +
122H ALA 3.8 2.9 - - - +
124H ARG* 1.3 72.6 - - - +
126H ALA* 1.3 52.4 + - - +
128H VAL* 3.4 0.7 + - - +
129H ALA* 2.6 40.4 + - - +
155H LEU* 4.2 9.7 - - + +
158H PHE* 3.7 36.3 - + + -
159H LEU* 4.1 15.5 - - + -
162H ILE* 3.5 25.8 - - + -
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Residues in contact with ALA 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H ALA 2.8 19.5 + - - +
123H ASP* 3.4 8.3 - - - +
124H ARG 3.2 0.2 - - - -
125H TYR* 1.3 77.1 - - - +
127H ILE* 1.3 57.7 + - + +
129H ALA* 4.2 0.2 - - - -
130H ASN* 2.8 47.9 + - - +
159H LEU* 3.9 23.1 - - + +
163H GLU* 5.6 1.3 - - - +
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Residues in contact with ILE 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 4.3 11.4 - - - +
103H PRO* 4.4 17.7 - - + +
104H LEU* 3.9 24.0 - - + -
105H LYS* 5.5 3.1 - - + +
123H ASP* 3.1 17.2 + - + +
124H ARG* 3.2 14.1 + - - +
126H ALA* 1.3 77.5 - - + +
128H VAL* 1.3 57.6 + - - +
130H ASN* 4.1 2.9 - - - +
131H ASP* 3.0 32.8 + - + +
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 3.4 38.1 - - + +
40H PHE* 3.6 27.8 - - + -
43H LEU* 4.0 15.7 - - + -
104H LEU* 3.9 18.2 - - + -
124H ARG 3.1 15.7 + - - +
125H TYR 3.9 0.7 - - - +
127H ILE* 1.3 71.7 - - - +
129H ALA* 1.3 67.1 + - - +
131H ASP* 3.8 0.3 - - - +
132H VAL* 2.9 24.4 + - - +
155H LEU* 3.5 23.1 - - + -
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Residues in contact with ALA 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR 2.6 25.6 + - - +
126H ALA* 3.7 5.8 - - - +
128H VAL* 1.3 73.0 - - - +
130H ASN* 1.3 63.6 + - - +
132H VAL* 3.2 9.7 - - - +
133H ARG* 3.0 30.7 + - - +
155H LEU* 3.8 23.3 - - + +
156H ASP* 3.7 17.8 - - - +
159H LEU* 4.3 10.1 - - + -
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Residues in contact with ASN 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H ALA* 2.8 39.1 + - - +
127H ILE* 4.1 3.3 - - - +
129H ALA* 1.3 73.6 - - - +
131H ASP* 1.3 64.0 + - - +
133H ARG* 2.4 36.6 + - - +
134H LYS* 3.3 45.2 + - - +
159H LEU* 5.2 4.8 - - - +
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Residues in contact with ASP 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ARG* 2.9 41.0 + - - -
36H GLN* 3.6 2.4 - - - +
39H GLN* 3.0 26.6 + - - +
103H PRO* 5.4 0.7 - - - +
127H ILE* 3.0 22.0 + - + +
128H VAL 3.8 2.5 - - - +
130H ASN* 1.3 73.9 - - - +
132H VAL* 1.3 66.5 + - - +
134H LYS* 3.0 13.4 + - - +
135H ALA 3.0 16.3 + - - -
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Residues in contact with VAL 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLN* 3.6 29.6 - - - +
40H PHE* 4.3 19.5 - - + -
128H VAL 2.9 19.0 + - - +
129H ALA* 3.2 16.6 - - - +
131H ASP* 1.3 74.7 - - - +
133H ARG* 1.3 67.7 + - - +
135H ALA* 3.1 10.3 + - - +
136H ILE* 3.3 13.2 + - - +
148H LEU* 3.8 35.8 - - + +
151H ALA* 4.7 1.8 - - + -
152H SER* 4.0 20.6 - - - +
155H LEU* 4.8 2.9 - - + -
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Residues in contact with ARG 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H ALA* 3.0 21.1 + - - +
130H ASN* 2.4 37.7 + - - +
131H ASP 3.1 0.2 - - - -
132H VAL* 1.3 77.2 - - - +
134H LYS* 1.3 66.9 + - + +
136H ILE* 3.4 25.0 - - + +
137H GLY 4.4 0.7 + - - -
152H SER* 3.7 17.0 - - - +
156H ASP* 2.6 44.6 + - - -
159H LEU* 6.2 0.8 - - - +
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Residues in contact with LYS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H ASN* 3.3 36.1 + - - +
131H ASP* 3.0 9.5 + - - +
133H ARG* 1.3 81.9 - - + +
135H ALA* 1.3 64.9 + - - +
136H ILE 3.0 3.7 + - - -
137H GLY* 3.1 12.0 + - - +
138H GLU* 3.2 15.0 + - - +
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Residues in contact with ALA 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.9 19.8 - - + +
35H ARG* 4.3 3.6 - - - +
36H GLN* 3.6 23.3 - - - +
131H ASP* 3.0 9.3 + - - +
132H VAL* 3.1 9.4 + - - +
134H LYS* 1.3 76.1 - - - +
136H ILE* 1.3 57.1 - - - +
138H GLU* 3.5 13.1 - - - +
139H ALA* 2.8 31.5 + - - +
148H LEU* 3.7 13.2 - - + +
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H VAL 3.4 8.7 - - - +
133H ARG* 3.4 21.3 - - + +
134H LYS 3.0 0.4 - - - -
135H ALA* 1.3 78.1 - - - +
137H GLY* 1.3 63.4 + - - +
139H ALA* 3.2 21.1 + - - +
145H ALA* 4.0 14.4 - - + +
148H LEU* 3.9 22.0 - - + +
149H THR* 3.5 41.5 - - + +
152H SER* 3.7 20.0 - - - +
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Residues in contact with GLY 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ARG 4.4 0.8 + - - -
134H LYS 3.1 6.8 + - - -
136H ILE* 1.3 81.0 - - - +
138H GLU* 1.3 60.4 - - - +
139H ALA 3.4 5.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 138 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.6 30.9 - - + +
35H ARG* 3.9 12.3 + - - -
134H LYS* 3.2 13.1 + - - +
135H ALA* 3.5 11.8 + - - +
137H GLY* 1.3 77.0 - - - +
139H ALA* 1.3 61.5 + - - +
140H LYS* 3.5 11.6 + - - +
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Residues in contact with ALA 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 4.0 15.0 - - + -
135H ALA 2.8 10.8 + - - +
136H ILE 3.4 17.3 - - - +
137H GLY 3.2 5.0 - - - +
138H GLU* 1.3 77.2 - - - +
140H LYS* 1.3 64.0 + - - +
141H ASP 4.4 1.3 - - - +
144H THR* 4.4 6.7 - - + -
145H ALA* 4.0 30.2 - - - +
148H LEU* 4.1 5.6 - - + -
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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