Contacts of the helix formed by residues 113 - 144 (chain K) in PDB entry 3E1O
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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ARG* 4.7 8.0 + - - +
128F GLU* 4.3 1.9 - - - +
1K MET* 6.5 0.2 - - - -
3K GLY* 5.7 0.2 - - - -
4K ASP* 5.4 4.6 + - + -
7K VAL* 3.5 17.6 - - + +
61K ARG* 2.9 24.3 + - - -
65K LEU* 3.8 12.4 - - - +
108K ALA* 2.9 19.2 + - + +
111K VAL* 3.2 14.2 + - + +
112K HIS* 1.3 70.9 - - - +
114K TYR* 1.3 56.0 + - - +
115K VAL* 3.6 1.9 + - - +
116K SER* 2.6 27.5 + - - -
117K ARG* 3.0 26.2 + - - +
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Residues in contact with TYR 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ARG* 3.5 25.8 - - - +
105F ILE* 3.5 28.9 - - + -
106F GLY* 3.4 15.6 - - - -
117F ARG* 3.5 19.8 + - - -
121F ILE* 4.1 23.5 - - + +
124F LEU* 4.2 12.1 - - + +
109K ASP* 3.3 39.3 + - - -
112K HIS* 2.9 58.9 + + + -
113K ASP* 1.3 72.3 - - - +
115K VAL* 1.3 59.0 + - - +
117K ARG* 3.4 7.8 - - - +
118K ASP* 2.9 26.3 + - - +
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Residues in contact with VAL 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ARG* 4.5 1.3 - - - +
121F ILE* 5.2 2.9 - - + +
124F LEU* 4.0 22.2 - - + -
125F ARG* 4.3 31.6 - - + +
128F GLU* 3.1 31.6 - - + +
61K ARG* 3.3 27.8 - - - +
113K ASP 3.3 0.8 - - - -
114K TYR* 1.3 74.1 - - - +
116K SER* 1.3 64.7 + - - +
117K ARG 3.1 1.1 - - - -
118K ASP* 3.0 7.9 + - + +
119K MET* 2.9 25.1 + - + +
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Residues in contact with SER 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 4.1 11.1 - - - +
11K LEU* 4.3 7.6 - - - +
61K ARG* 2.9 27.9 + - - +
65K LEU* 3.8 6.1 - - - +
108K ALA* 4.8 0.4 - - - -
113K ASP* 2.6 39.4 + - - -
115K VAL* 1.3 73.3 - - - +
117K ARG* 1.3 65.1 + - - +
119K MET* 3.2 7.0 + - - +
120K MET* 2.8 35.9 + - - +
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Residues in contact with ARG 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ARG* 4.1 3.1 - - - +
302F SO4 2.7 40.3 + - - +
109I ASP* 2.8 25.1 + - - -
114I TYR* 3.6 17.4 + - - -
117I ARG* 4.0 1.0 - - - +
105K ILE* 3.3 37.9 + - + +
106K GLY* 4.3 0.8 - - - -
108K ALA* 3.9 6.5 - - + -
109K ASP* 3.2 42.4 + - - +
113K ASP 3.0 15.3 + - - +
114K TYR* 3.4 13.7 - - - +
116K SER* 1.3 76.3 - - - +
118K ASP* 1.3 57.7 + - - +
120K MET* 3.1 14.6 + - - +
121K ILE* 2.8 38.4 + - + +
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Residues in contact with ASP 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ASP* 5.4 3.3 - - - +
121F ILE* 4.0 17.1 - - + +
122F GLU* 3.2 28.0 - - - +
125F ARG* 4.4 15.4 + - - -
302F SO4 4.8 10.7 + - - -
118I ASP* 5.5 2.6 - - - +
114K TYR 2.9 17.9 + - - +
115K VAL* 3.0 10.9 + - + +
117K ARG* 1.3 77.0 - - - +
119K MET* 1.3 62.2 + - - +
121K ILE* 3.3 10.3 + - - +
122K GLU* 3.2 34.3 + - - +
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Residues in contact with MET 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LEU* 5.6 2.0 - - - -
57K ARG* 3.5 64.5 + - + +
58K TYR* 4.5 15.0 - - - -
61K ARG* 3.7 32.8 - - + -
115K VAL* 2.9 14.3 + - + +
116K SER* 3.7 8.5 - - - +
118K ASP* 1.3 77.3 + - - +
120K MET* 1.3 65.6 + - - +
122K GLU* 3.4 2.8 + - - +
123K ILE* 3.1 31.7 + - + +
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Residues in contact with MET 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 5.6 2.0 - - + -
10K TYR* 6.1 0.9 - - + -
11K LEU* 3.8 16.4 - - + -
14K LEU* 3.6 25.4 - - - -
58K TYR* 4.4 12.6 - - + -
101K LEU* 3.7 12.4 - - + +
104K ALA* 3.8 24.5 - - + +
105K ILE* 3.5 16.6 - - + +
108K ALA* 3.7 31.6 - - + -
116K SER* 2.8 26.3 + - - +
117K ARG* 3.5 7.2 - - - +
119K MET* 1.3 77.6 - - + +
121K ILE* 1.3 56.8 + - - +
123K ILE* 3.2 7.0 + - - +
124K LEU* 2.9 29.6 + - - +
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Residues in contact with ILE 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F SO4 4.0 22.0 - - - +
114I TYR* 4.2 21.1 - - + +
115I VAL* 5.2 3.4 - - + +
118I ASP* 4.0 33.9 - - + +
105K ILE* 4.0 22.7 - - + -
117K ARG* 2.8 50.8 + - + +
118K ASP* 3.7 9.0 - - - +
120K MET* 1.3 70.7 - - - +
122K GLU* 1.3 66.4 + - - +
124K LEU* 3.1 5.4 + - + +
125K ARG* 3.0 21.8 + - + +
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Residues in contact with GLU 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ARG* 6.3 1.3 - - - +
118I ASP* 3.3 27.8 - - - +
57K ARG* 4.2 18.8 - - - +
118K ASP* 3.2 25.2 + - - +
119K MET 3.9 6.5 - - - +
120K MET 3.3 0.2 - - - -
121K ILE* 1.3 79.1 - - - +
123K ILE* 1.3 62.4 + - - +
125K ARG* 3.3 32.2 + - - +
126K ASP* 3.2 25.6 + - - +
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Residues in contact with ILE 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K GLU* 3.8 17.5 - - - +
54K HIS* 3.8 32.1 - - + +
57K ARG* 3.8 20.2 - - + +
58K TYR* 3.5 45.1 - - + +
101K LEU* 4.2 7.2 - - + -
119K MET* 3.1 28.4 + - + +
120K MET* 3.2 7.4 + - - +
122K GLU* 1.3 75.9 - - - +
124K LEU* 1.3 58.9 + - - +
126K ASP* 2.8 21.9 + - - +
127K GLU* 2.9 14.5 + - - +
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Residues in contact with LEU 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I TYR* 4.2 14.1 - - + -
115I VAL* 4.0 22.0 - - + -
98K ALA* 3.9 22.4 - - + +
101K LEU* 3.8 30.5 - - + +
102K ARG* 4.1 22.2 - - + +
105K ILE* 4.0 19.5 - - + -
120K MET 2.9 16.9 + - - +
121K ILE* 3.1 5.6 + - + +
123K ILE* 1.3 76.2 - - - +
125K ARG* 1.3 55.5 + - - +
127K GLU* 3.1 4.8 + - + +
128K GLU* 2.8 44.2 + - - +
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Residues in contact with ARG 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ARG* 5.3 10.5 - - - +
115I VAL* 4.4 25.0 - - + +
118I ASP* 4.4 16.0 + - - +
122I GLU* 6.2 1.8 - - - +
121K ILE* 3.0 12.6 + - + +
122K GLU* 3.4 34.5 + - - +
124K LEU* 1.3 76.6 - - - +
126K ASP* 1.3 65.0 + - - +
128K GLU* 3.5 7.6 - - - +
129K GLY* 3.1 17.3 + - - -
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Residues in contact with ASP 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K ASP* 4.0 14.1 - - - +
54K HIS* 3.1 30.5 + - + +
57K ARG* 5.0 5.2 + - - -
122K GLU 3.2 13.1 + - - +
123K ILE* 2.8 14.3 + - - +
125K ARG* 1.3 77.1 - - - +
127K GLU* 1.3 61.2 + - - +
129K GLY* 3.1 4.4 + - - -
130K HIS* 3.1 26.2 + - + +
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Residues in contact with GLU 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K GLU* 2.6 7.6 - - - +
54K HIS* 3.1 4.6 + - - -
94K GLU* 2.5 10.8 - - - +
97K GLY 5.9 0.9 - - - -
98K ALA* 5.3 4.5 - - + +
101K LEU* 3.8 22.0 - - + -
123K ILE* 2.9 16.9 + - - +
124K LEU* 3.1 11.4 + - + +
126K ASP* 1.3 71.1 - - - +
128K GLU* 1.3 56.8 + - - +
130K HIS* 2.8 13.0 + - - +
131K ILE* 2.7 43.1 + - + +
300K ZN 1.8 37.5 - - - -
301K ZN 1.7 37.9 - - - -
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Residues in contact with GLU 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 3.7 13.8 - - + +
61I ARG* 2.8 34.7 + - - +
64I PHE* 3.3 30.9 - - + -
115I VAL* 3.0 18.2 - - + +
102K ARG* 2.7 31.2 + - - -
124K LEU* 2.8 22.0 + - - +
125K ARG* 3.5 9.0 - - - +
127K GLU* 1.3 76.4 - - - +
129K GLY* 1.3 55.9 + - - +
131K ILE* 3.2 13.3 + - - +
132K ASP* 2.8 28.4 + - - +
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Residues in contact with GLY 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K ARG 3.1 10.8 + - - -
126K ASP* 3.1 9.8 + - - -
128K GLU* 1.3 76.3 - - - +
130K HIS* 1.4 61.8 + - - +
132K ASP* 3.1 10.9 + - - +
133K TRP* 3.1 20.4 + - - +
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Residues in contact with HIS 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 4.0 6.0 + - - +
47K GLU* 3.3 42.2 - - + +
50K ASP* 3.6 28.7 + - + -
51K GLU* 3.3 15.7 - - + -
54K HIS* 4.3 4.0 - + - -
94K GLU* 2.8 14.3 + - - +
126K ASP* 3.1 14.0 + - - +
127K GLU* 2.8 15.1 + - - +
129K GLY* 1.4 68.6 - - - -
131K ILE* 1.3 67.5 + - - +
133K TRP* 3.1 3.3 + - - +
134K LEU* 3.0 29.3 + - - +
301K ZN 2.0 34.9 - - - -
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Residues in contact with ILE 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 4.1 22.7 - - - -
64I PHE* 4.3 3.1 - - + -
91K LEU* 4.2 13.2 - - + -
94K GLU* 3.6 31.6 - - + +
95K LEU* 3.9 23.1 - - + -
98K ALA* 4.2 13.5 - - + -
127K GLU* 2.7 26.0 + - + +
128K GLU* 3.2 17.2 + - - +
130K HIS* 1.3 72.9 - - - +
132K ASP* 1.3 64.8 + - - +
134K LEU* 3.2 3.3 + - - +
135K GLU* 2.9 46.8 + - - +
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Residues in contact with ASP 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I PHE* 3.7 31.8 - - + +
34J ASN* 4.0 16.6 + - - +
128K GLU 2.8 15.4 + - - +
129K GLY* 3.2 14.6 - - - +
131K ILE* 1.3 73.7 - - - +
133K TRP* 1.3 58.8 + - - +
135K GLU* 3.3 5.9 + - - +
136K THR* 2.6 41.9 + - - -
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Residues in contact with TRP 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ARG* 4.2 7.4 - - - +
40K LEU* 4.1 20.4 - - + -
43K VAL* 3.4 42.1 - - + +
44K GLU* 3.7 28.3 - - + -
47K GLU* 4.0 20.6 - - - +
87K LEU* 4.9 4.9 - - + -
129K GLY 3.1 9.5 + - - +
130K HIS 3.1 6.7 + - - +
132K ASP* 1.3 78.8 - - - +
134K LEU* 1.3 91.5 + - + +
136K THR* 3.1 7.8 + - - -
137K GLU* 3.0 59.1 + - + +
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Residues in contact with LEU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 3.7 23.8 - - + +
44K GLU* 4.0 6.5 - - - +
47K GLU* 5.0 0.2 - - - +
87K LEU* 3.9 24.5 - - + +
90K ASP* 4.0 15.3 - - + -
91K LEU* 4.0 35.2 - - + +
94K GLU* 4.3 4.0 - - + -
130K HIS* 3.0 28.7 + - + +
131K ILE* 3.7 3.8 - - - +
133K TRP* 1.3 106.0 - - + +
135K GLU* 1.3 61.8 + - - +
136K THR 3.3 0.2 + - - -
137K GLU* 3.3 3.3 + - - +
138K LEU* 3.0 28.5 + - + +
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Residues in contact with GLU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 2.8 41.1 + - - +
64I PHE* 3.8 15.4 - - - -
66I GLU* 4.3 3.8 - - - +
91K LEU* 4.2 23.3 - - + +
95K LEU* 5.4 2.9 - - - +
131K ILE* 2.9 29.3 + - - +
132K ASP* 3.7 4.8 - - - +
134K LEU* 1.3 75.2 - - - +
136K THR* 1.3 59.1 + - - +
138K LEU* 3.3 6.9 + - - +
139K ASP* 2.9 38.8 + - - +
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Residues in contact with THR 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J ASN 3.6 12.4 + - - +
35J TRP* 3.4 33.8 - - - +
36J GLY* 3.7 10.1 - - - -
132K ASP* 2.6 33.7 + - - -
133K TRP* 3.1 8.0 + - + -
135K GLU* 1.3 77.5 - - - +
137K GLU* 1.3 65.3 + - - +
139K ASP* 3.2 7.9 + - + +
140K LEU* 2.9 28.5 + - + +
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Residues in contact with GLU 137 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ARG* 3.2 29.8 + - - -
40K LEU* 4.1 0.5 - - - +
87K LEU* 4.1 11.0 - - + -
133K TRP* 3.0 56.9 + - + +
134K LEU* 3.8 4.0 - - - +
136K THR* 1.3 79.1 - - - +
138K LEU* 1.3 65.0 + - - +
140K LEU* 3.0 30.1 + - - +
141K ILE* 3.0 19.4 + - - +
149K TYR* 2.5 37.9 + - - +
153K GLN* 4.1 0.5 + - - -
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Residues in contact with LEU 138 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K GLU* 3.8 32.7 - - + +
87K LEU* 3.8 26.0 - - + -
88K ARG* 3.8 42.7 + - + +
91K LEU* 3.8 28.5 - - + -
134K LEU 3.0 17.3 + - - +
135K GLU* 3.7 5.2 - - - +
137K GLU* 1.3 77.4 - - - +
139K ASP* 1.3 65.8 + - - +
141K ILE* 3.5 16.4 + - + +
142K GLN* 3.6 17.5 + - - +
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Residues in contact with ASP 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J TRP* 5.7 4.9 - - + +
135K GLU* 2.9 24.8 + - - +
136K THR* 3.7 6.0 - - - +
137K GLU 3.1 0.2 - - - -
138K LEU* 1.3 80.3 - - - +
140K LEU* 1.3 65.7 + - - +
142K GLN* 3.2 9.8 + - - +
143K LYS* 3.0 45.2 + - - +
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Residues in contact with LEU 140 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J TRP 3.4 23.6 - - - +
36J GLY* 4.7 5.6 - - - +
37J LEU* 3.6 22.2 - - + -
150J LEU* 5.9 0.2 - - + -
154J ILE* 4.3 21.3 - - + -
39K ARG* 5.2 2.9 - - - +
136K THR* 2.9 20.7 + - + +
137K GLU* 3.0 33.1 + - - +
139K ASP* 1.3 76.7 - - - +
141K ILE* 1.3 64.4 + - - +
143K LYS* 3.1 10.8 + - + +
144K MET* 2.9 51.5 + - + +
149K TYR* 4.2 6.7 - - + -
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Residues in contact with ILE 141 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K VAL* 4.3 8.3 - - + -
84K GLU* 4.3 26.5 - - + +
87K LEU* 4.2 16.6 - - + -
137K GLU 3.0 19.0 + - - +
138K LEU* 3.6 11.4 - - + +
139K ASP 3.2 0.2 - - - -
140K LEU* 1.3 77.1 - - - +
142K GLN* 1.3 70.0 + - - +
145K GLY* 3.0 27.9 + - - -
146K LEU* 3.7 28.9 + - + +
149K TYR* 3.5 41.5 - - + -
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Residues in contact with GLN 142 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLN* 4.6 3.3 + - - -
84K GLU* 3.8 27.1 + - - -
88K ARG* 4.8 7.5 - - - +
138K LEU 3.6 11.9 + - - +
139K ASP* 3.2 10.2 + - - +
140K LEU 3.1 0.8 - - - -
141K ILE* 1.3 88.2 + - - +
143K LYS* 1.3 68.2 + - + +
144K MET 3.5 0.3 + - - -
145K GLY* 3.7 5.1 + - - -
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Residues in contact with LYS 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J TRP* 3.8 51.9 + - + +
37J LEU* 5.6 4.0 - - + +
146J LEU* 5.6 2.3 - - - +
147J GLN* 3.4 17.2 + - - +
150J LEU* 4.0 29.6 - - + +
139K ASP* 3.0 33.7 + - - +
140K LEU* 3.9 10.0 - - + +
142K GLN* 1.3 80.9 - - + +
144K MET* 1.3 60.8 + - + +
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Residues in contact with MET 144 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLN* 3.5 41.2 - - - +
150J LEU* 4.0 9.0 - - + -
151J GLN* 3.6 30.5 - - - +
154J ILE* 3.3 32.8 - - + -
140K LEU* 2.9 38.9 + - + +
143K LYS* 1.3 75.9 - - + +
145K GLY* 1.3 70.3 + - - +
148K ASN* 3.4 16.2 + - + +
149K TYR* 3.8 28.0 - - + +
250K SO4 4.5 1.2 + - - -
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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) + - + + + + + -
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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