Contacts of the helix formed by residues 113 - 144 (chain H) in PDB entry 3E1N
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 ASP 113 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 4.6 7.7 + - - +
128B GLU* 4.3 1.9 - - - +
1H MET* 6.4 0.4 - - - -
3H GLY* 5.8 0.3 - - - -
4H ASP* 5.5 4.2 + - + -
7H VAL* 3.4 24.3 - - + +
61H ARG* 2.9 24.3 + - - -
65H LEU* 3.8 10.6 - - - +
108H ALA* 2.9 21.0 + - + +
111H VAL* 3.3 5.8 + - + +
112H HIS* 1.3 73.6 - - - +
114H TYR* 1.3 57.9 + - - +
115H VAL 3.7 1.7 + - - -
116H SER* 2.6 29.5 + - - -
117H ARG* 2.9 26.0 + - - +
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Residues in contact with TYR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 3.5 11.6 - - - +
105B ILE* 3.5 32.3 - - + -
106B GLY* 3.4 14.7 - - - -
117B ARG* 3.6 21.3 + - - -
121B ILE* 4.1 19.7 - - + +
124B LEU* 4.1 16.6 - - + +
302B SO4 5.4 0.2 - - - -
109H ASP* 3.3 38.7 + - - -
112H HIS* 2.8 62.1 + + + -
113H ASP* 1.3 73.2 + - - +
115H VAL* 1.3 58.3 + - - +
117H ARG* 3.4 8.9 - - - +
118H ASP* 2.8 29.3 + - - +
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 4.7 0.9 - - - +
121B ILE* 5.1 2.9 - - + +
124B LEU* 3.8 22.2 - - + -
125B ARG* 4.1 33.0 - - + +
128B GLU* 3.2 30.3 - - + +
61H ARG* 3.1 30.7 - - - +
113H ASP* 3.3 1.6 + - - -
114H TYR* 1.3 73.3 - - - +
116H SER* 1.3 65.2 + - - +
118H ASP* 3.7 6.1 - - + +
119H MET* 3.0 25.8 + - + +
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 4.0 11.9 - - - +
11H LEU* 4.3 6.2 - - - +
61H ARG* 2.9 31.0 + - - +
65H LEU* 3.7 5.5 - - - +
108H ALA* 4.7 0.7 - - - -
113H ASP* 2.6 37.1 + - - -
115H VAL* 1.3 75.1 - - - +
117H ARG* 1.3 63.9 + - - +
119H MET* 3.4 5.9 + - - +
120H MET* 2.9 35.7 + - - +
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Residues in contact with ARG 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 4.5 1.8 - - - +
302B SO4 2.8 39.1 + - - +
109C ASP* 2.7 25.9 + - - -
114C TYR* 3.6 19.6 + - - -
117C ARG* 3.9 2.8 - - - +
105H ILE* 3.3 40.9 + - + +
106H GLY* 4.3 1.0 - - - -
108H ALA* 4.1 6.1 - - + -
109H ASP* 3.1 43.0 + - - +
113H ASP 2.9 15.7 + - - +
114H TYR* 3.4 12.8 - - - +
115H VAL 3.2 0.2 - - - -
116H SER* 1.3 76.6 - - - +
118H ASP* 1.3 63.6 + - - +
120H MET* 2.9 14.4 + - - +
121H ILE* 2.9 29.1 + - + +
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Residues in contact with ASP 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 5.5 2.9 - - - +
121B ILE* 4.1 24.0 - - + +
122B GLU* 6.0 2.6 - - - +
125B ARG* 3.8 22.3 + - - -
302B SO4 5.3 5.6 + - - +
118C ASP* 5.5 2.8 - - - +
114H TYR 2.8 20.6 + - - +
115H VAL* 3.3 6.9 + - + +
117H ARG* 1.3 71.5 - - - +
119H MET* 1.3 64.6 + - - +
120H MET 3.2 0.2 + - - -
121H ILE* 3.3 12.0 + - - +
122H GLU* 3.1 42.4 + - - +
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Residues in contact with MET 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU* 5.8 1.8 - - - -
57H ARG* 3.4 67.6 + - + +
58H TYR* 4.6 14.1 - - - -
60H GLU* 6.2 0.2 - - + -
61H ARG* 3.7 32.3 - - + -
115H VAL* 3.0 18.1 + - + +
116H SER* 3.7 5.2 - - - +
118H ASP* 1.3 77.9 + - - +
120H MET* 1.3 63.5 + - - +
122H GLU* 3.4 3.2 + - - +
123H ILE* 3.2 31.4 + - + +
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Residues in contact with MET 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 5.5 1.6 - - + -
10H TYR* 6.2 0.2 - - + -
11H LEU* 3.9 14.8 - - + -
14H LEU* 3.6 26.5 - - - -
58H TYR* 4.4 13.2 - - + -
101H LEU* 3.8 13.2 - - + +
104H ALA* 3.7 24.9 - - + +
105H ILE* 3.6 14.4 - - + -
108H ALA* 3.7 29.4 - - + -
116H SER* 2.9 26.8 + - - +
117H ARG* 2.9 8.9 + - - +
119H MET* 1.3 79.0 - - + +
121H ILE* 1.3 58.4 + - - +
123H ILE* 3.2 8.0 + - - +
124H LEU* 2.8 28.4 + - - +
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Residues in contact with ILE 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B SO4 3.9 20.9 - - - +
114C TYR* 4.1 23.3 - - + +
115C VAL* 5.0 1.9 - - + +
118C ASP* 4.1 34.3 - - + +
105H ILE* 4.0 22.2 - - + -
117H ARG* 2.9 46.3 + - + +
118H ASP* 3.3 9.8 + - - +
120H MET* 1.3 73.1 - - - +
122H GLU* 1.3 65.9 + - + +
124H LEU* 3.3 4.1 + - + +
125H ARG* 3.0 23.2 + - + +
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Residues in contact with GLU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG* 3.6 22.7 + - - -
118C ASP* 6.0 2.2 - - - +
57H ARG* 3.3 29.1 + - - +
118H ASP* 3.1 29.2 + - - +
119H MET* 3.8 7.4 - - - +
120H MET 3.3 0.2 - - - -
121H ILE* 1.3 75.4 - - + +
123H ILE* 1.3 63.6 + - - +
125H ARG* 3.3 15.8 + - - +
126H ASP* 3.2 23.5 + - - +
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Residues in contact with ILE 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU* 4.0 1.6 - - - +
54H HIS* 3.7 38.4 - - + +
57H ARG* 4.0 15.0 - - + +
58H TYR* 3.6 41.7 - - + +
101H LEU* 4.0 7.4 - - + -
119H MET* 3.2 33.1 + - + +
120H MET* 3.2 6.9 + - - +
122H GLU* 1.3 75.5 - - - +
124H LEU* 1.3 57.9 + - - +
126H ASP* 2.8 21.9 + - - +
127H GLU* 2.9 31.3 + - - +
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Residues in contact with LEU 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TYR* 4.0 19.7 - - + -
115C VAL* 3.8 19.7 - - + -
98H ALA* 4.0 26.7 - - + +
101H LEU* 3.7 22.4 - - + -
102H ARG* 4.1 17.5 - - + +
105H ILE* 3.8 22.2 - - + -
120H MET 2.8 16.3 + - - +
121H ILE* 3.3 6.5 + - - +
123H ILE* 1.3 74.5 - - - +
125H ARG* 1.3 53.1 + - - +
127H GLU* 2.9 6.6 + - + +
128H GLU* 2.8 48.9 + - + +
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Residues in contact with ARG 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ARG* 5.0 10.3 - - - +
115C VAL* 4.1 28.1 - - + +
118C ASP* 3.8 17.6 + - - -
122C GLU* 3.6 26.8 + - - -
121H ILE* 3.0 13.4 + - + +
122H GLU* 3.3 17.0 - - - +
123H ILE 3.2 0.2 - - - -
124H LEU* 1.3 76.3 - - - +
126H ASP* 1.3 64.6 + - - +
128H GLU* 3.5 4.0 + - - +
129H GLY* 3.2 16.8 + - - -
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Residues in contact with ASP 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ASP* 4.9 7.8 - - - +
54H HIS* 3.0 30.9 + - + +
57H ARG* 5.4 3.5 + - - -
122H GLU 3.2 13.1 + - - +
123H ILE* 2.8 10.0 + - - +
125H ARG* 1.3 77.5 - - - +
127H GLU* 1.3 66.9 + - - +
129H GLY* 3.1 4.1 + - - -
130H HIS* 3.0 31.1 + - + +
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Residues in contact with GLU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU* 3.2 6.9 - - - +
54H HIS* 3.1 11.8 + - - -
94H GLU* 3.6 8.2 - - - +
97H GLY 5.7 1.3 - - - -
98H ALA* 5.1 6.7 - - + +
101H LEU* 3.7 22.5 - - + +
123H ILE* 2.9 19.0 + - - +
124H LEU* 2.9 11.6 + - + +
126H ASP* 1.3 74.4 - - - +
128H GLU* 1.3 58.7 + - - +
130H HIS* 2.8 20.0 + - - +
131H ILE* 2.8 36.8 + - + +
300H FE2 1.9 29.7 - - - -
301H FE2 2.0 30.0 - - - -
400H UNK 3.9 3.8 + - - -
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.7 12.5 - - + +
61C ARG* 2.7 37.5 + - - +
64C PHE* 3.4 33.8 - - + -
115C VAL* 3.2 19.5 - - + +
98H ALA* 5.3 0.9 - - - +
102H ARG* 2.5 32.4 + - - -
124H LEU* 2.8 18.7 + - - +
125H ARG* 3.7 7.9 - - - +
127H GLU* 1.3 78.7 - - - +
129H GLY* 1.3 55.7 + - - +
131H ILE* 3.3 10.9 + - + +
132H ASP* 2.9 25.1 + - - +
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Residues in contact with GLY 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG 3.2 11.0 + - - -
126H ASP* 3.1 8.5 + - - -
128H GLU* 1.3 71.1 - - - +
130H HIS* 1.3 65.1 + - - +
132H ASP* 3.1 9.0 + - - +
133H TRP* 3.0 22.3 + - - +
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Residues in contact with HIS 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TYR* 4.0 4.9 + - - +
47H GLU* 3.1 37.3 + - + +
50H ASP* 2.9 34.7 + - + +
51H GLU* 3.1 26.0 - - - -
54H HIS* 4.2 5.6 - + - -
94H GLU* 2.9 17.3 + - - +
126H ASP 3.0 17.0 + - - -
127H GLU* 2.8 17.0 + - - +
129H GLY* 1.3 76.0 - - - +
131H ILE* 1.3 62.8 + - - +
133H TRP* 3.2 3.4 + - - +
134H LEU* 3.0 30.1 + - - +
301H FE2 2.4 22.9 - - - -
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Residues in contact with ILE 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 4.2 21.3 - - + -
64C PHE* 4.6 1.1 - - + -
91H LEU* 3.9 15.3 - - + -
94H GLU* 3.6 32.5 - - + +
95H LEU* 3.8 25.4 - - + -
98H ALA* 4.2 12.3 - - + -
127H GLU* 2.8 24.4 + - + +
128H GLU* 3.4 12.1 - - + +
130H HIS* 1.3 77.0 - - - +
132H ASP* 1.3 63.5 + - - +
134H LEU* 3.3 3.0 + - - +
135H GLU* 2.9 46.9 + - - +
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Residues in contact with ASP 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.7 31.2 - - + +
34D ASN* 4.3 15.2 + - - +
128H GLU 2.9 14.6 + - - +
129H GLY* 3.4 12.3 - - - +
131H ILE* 1.3 74.8 - - - +
133H TRP* 1.3 63.0 + - - +
135H GLU* 3.3 4.9 + - - +
136H THR* 2.8 41.4 + - - -
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Residues in contact with TRP 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ARG* 4.1 12.5 - - - +
40H LEU* 4.0 17.5 - - + -
43H VAL* 3.4 40.9 - - + +
44H GLU* 3.7 20.2 - - + -
47H GLU* 4.1 18.6 - - - +
87H LEU* 4.9 4.7 - - + -
129H GLY 3.0 12.4 + - - +
130H HIS 3.7 6.5 - - - +
131H ILE 3.1 0.4 - - - -
132H ASP* 1.3 79.9 - - - +
134H LEU* 1.3 90.5 + - + +
136H THR* 3.4 6.0 + - + -
137H GLU* 3.0 59.7 + - + +
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H TYR* 3.6 22.9 - - - +
44H GLU* 4.2 4.5 - - - +
47H GLU* 4.6 2.7 - - - +
87H LEU* 4.0 26.0 - - + +
90H ASP* 4.1 8.7 - - + -
91H LEU* 3.9 32.5 - - + +
94H GLU* 4.0 13.2 - - + -
130H HIS 3.0 29.2 + - - +
131H ILE* 3.9 4.0 - - - +
133H TRP* 1.3 102.2 - - + +
135H GLU* 1.3 63.8 + - - +
137H GLU* 3.2 3.5 + - - +
138H LEU* 2.9 30.5 + - + +
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Residues in contact with GLU 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 2.7 42.4 + - - +
64C PHE* 3.9 13.2 - - - -
66C GLU* 4.2 4.1 - - - +
91H LEU* 4.2 23.9 - - + +
95H LEU* 5.3 2.9 - - - +
131H ILE* 2.9 30.2 + - - +
132H ASP* 3.8 5.0 - - - +
134H LEU* 1.3 77.3 - - - +
136H THR* 1.3 63.2 + - - +
138H LEU* 3.5 5.1 + - - +
139H ASP* 3.0 32.2 + - - +
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Residues in contact with THR 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN* 3.3 13.6 + - - +
35D TRP* 3.6 33.4 - - - +
36D GLY* 3.6 11.9 - - - -
132H ASP* 2.8 27.2 + - - -
133H TRP* 3.7 7.0 - - + -
135H GLU* 1.3 75.1 - - - +
137H GLU* 1.3 64.5 + - - +
139H ASP* 3.2 7.9 + - + +
140H LEU* 2.9 34.0 + - + +
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Residues in contact with GLU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ARG* 3.0 32.1 + - - -
87H LEU* 4.3 10.5 - - + -
133H TRP* 3.0 56.4 + - + +
134H LEU* 3.7 4.9 - - - +
136H THR* 1.3 77.8 - - - +
138H LEU* 1.3 62.6 + - - +
140H LEU* 3.0 20.7 + - - +
141H ILE* 3.0 27.5 + - - +
149H TYR* 2.6 38.6 + - - +
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H GLU* 3.9 29.7 - - + +
87H LEU* 3.7 32.1 - - + -
88H ARG* 3.8 41.0 + - + +
91H LEU* 3.8 30.1 - - + -
134H LEU 2.9 19.4 + - - +
135H GLU* 3.8 5.2 - - - +
137H GLU* 1.3 75.5 - - - +
139H ASP* 1.3 65.0 + - - +
141H ILE* 3.4 19.1 + - + +
142H GLN* 3.5 13.6 + - - +
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Residues in contact with ASP 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TRP* 5.4 4.5 - - - -
135H GLU* 3.0 24.0 + - - +
136H THR* 3.6 6.1 - - - +
138H LEU* 1.3 76.9 - - - +
140H LEU* 1.3 68.2 + - - +
142H GLN* 3.0 9.4 + - - +
143H LYS* 2.9 48.9 + - + +
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TRP 3.4 21.1 - - - +
36D GLY* 4.8 4.7 - - - +
37D LEU* 3.8 20.2 - - + -
150D LEU* 5.9 0.9 - - + -
154D ILE* 4.2 22.4 - - + -
39H ARG* 5.0 2.7 - - - +
136H THR* 2.9 25.3 + - + +
137H GLU* 3.0 32.7 + - - +
139H ASP* 1.3 75.8 - - - +
141H ILE* 1.3 63.3 + - - +
143H LYS* 4.4 11.2 - - + +
144H MET* 2.9 49.2 + - + +
149H TYR* 4.3 7.6 - - + -
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Residues in contact with ILE 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H VAL* 4.6 3.6 - - + -
84H GLU* 4.2 31.4 - - + +
87H LEU* 4.3 15.9 - - + -
137H GLU 3.0 15.0 + - - +
138H LEU* 3.5 11.7 - - + +
139H ASP 3.1 0.2 - - - -
140H LEU* 1.3 76.1 - - - +
142H GLN* 1.3 69.7 + - - +
145H GLY* 2.9 30.1 + - - -
146H LEU* 3.8 27.1 + - + -
149H TYR* 3.6 41.3 - - + -
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Residues in contact with GLN 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D GLN* 4.4 4.5 + - - -
84H GLU* 3.8 26.9 + - - -
88H ARG* 4.9 8.0 - - - +
138H LEU 3.5 10.8 + - - +
139H ASP* 3.0 10.1 + - - +
141H ILE* 1.3 88.4 - - - +
143H LYS* 1.3 69.4 + - + +
144H MET 3.5 0.2 + - - -
145H GLY* 3.7 5.9 + - - -
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Residues in contact with LYS 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TRP* 4.0 47.5 + - + +
37D LEU* 5.8 4.7 - - + +
146D LEU* 5.6 2.3 - - - +
147D GLN* 3.7 15.1 + - - +
150D LEU* 4.0 32.6 - - + +
139H ASP* 2.9 44.1 + - + +
140H LEU* 3.2 10.8 + - + +
142H GLN* 1.3 80.1 - - + +
144H MET* 1.3 59.1 + - + +
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Residues in contact with MET 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D GLN* 3.5 41.7 - - - +
150D LEU* 4.4 6.5 - - + -
151D GLN* 3.6 32.3 - - - +
154D ILE* 3.3 31.2 - - + -
140H LEU* 2.9 43.0 + - + +
143H LYS* 1.3 76.7 - - - +
145H GLY* 1.3 69.1 + - - +
148H ASN* 3.4 16.2 + - + +
149H TYR* 3.7 27.4 - - + +
152H ALA* 4.8 0.2 - - - -
250H SO4 4.6 0.7 + - - -
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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