Contacts of the helix formed by residues 113 - 144 (chain X) in PDB entry 2JD6
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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X MET 4.1 18.0 - - - +
2X LEU* 4.1 1.7 - - - +
3X SER 5.5 0.3 + - - -
6X MET* 3.5 17.0 - - + +
60X TYR* 4.4 0.2 + - - -
64X ARG* 4.9 2.9 + - - -
108X ALA* 2.9 21.6 + - - +
111X GLU* 3.1 12.4 - - + +
112X LYS* 1.3 75.2 - - - +
114X TYR* 1.3 61.2 + - - +
115X SER* 3.5 9.0 + - - -
116X THR* 2.6 35.8 + - - -
117X ARG* 3.0 23.0 + - - +
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Residues in contact with TYR 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S TYR* 3.6 51.4 - + + -
105S ALA* 3.7 22.2 - - + -
106S ALA* 3.5 18.4 - - + +
109S GLU* 3.0 32.5 + - - -
117S ARG* 3.8 19.3 + - - +
124S ILE* 3.8 12.0 - - + +
112X LYS* 3.3 32.8 + - + +
113X ASP* 1.3 72.2 - - - +
115X SER* 1.3 64.6 + - - +
117X ARG* 3.2 6.7 + - + +
118X ALA* 2.8 25.8 + - - +
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Residues in contact with SER 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S TYR* 3.0 18.0 + - - -
124S ILE* 3.7 13.5 + - - +
125S ASN* 4.9 1.0 - - - +
127S GLN* 6.2 0.2 - - - +
128S VAL* 3.7 17.5 - - - +
60X TYR* 3.2 11.5 - - - -
64X ARG* 2.9 36.8 + - - -
113X ASP* 3.3 4.3 + - - -
114X TYR* 1.3 77.3 - - - +
116X THR* 1.3 57.5 + - - +
118X ALA* 3.2 2.9 + - - +
119X PHE* 3.0 27.5 + - - +
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Residues in contact with THR 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X LEU* 3.7 7.3 - - - +
6X MET* 3.8 26.5 - - + -
10X LEU* 4.1 13.9 - - + -
60X TYR* 2.6 34.8 + - + -
108X ALA* 4.3 2.2 - - + -
113X ASP* 2.6 32.1 + - - -
115X SER* 1.3 73.1 - - - +
117X ARG* 1.3 67.4 + - - +
119X PHE* 3.2 3.4 + - + +
120X LEU* 3.0 30.7 + - + +
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Residues in contact with ARG 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117S ARG* 5.7 7.6 - - - +
121S GLU* 5.6 0.8 + - - +
114W TYR* 3.9 13.1 + - - +
117W ARG* 5.5 8.1 - - - +
118W ALA* 5.9 0.4 - - - +
105X ALA* 3.8 26.3 - - - +
108X ALA* 3.7 14.3 - - + +
109X GLU* 2.8 36.8 + - + +
113X ASP 3.0 17.1 + - - +
114X TYR* 3.8 7.2 - - + +
116X THR* 1.3 75.5 - - - +
118X ALA* 1.3 62.3 + - - +
120X LEU* 3.1 12.6 + - - +
121X GLU* 2.6 34.9 + - - +
124X ILE* 3.7 24.4 - - - +
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Residues in contact with ALA 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117S ARG* 6.1 0.2 - - - +
121S GLU* 3.7 26.5 - - - +
124S ILE* 3.8 15.7 - - + -
125S ASN* 3.4 26.3 + - - +
114X TYR 2.8 17.5 + - - +
115X SER 3.4 4.3 - - - +
117X ARG* 1.3 75.4 - - - +
119X PHE* 1.3 66.2 + - - +
121X GLU* 3.0 20.4 + - - +
122X TRP 4.4 1.0 + - - -
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Residues in contact with PHE 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125S ASN* 4.1 6.1 + - - +
10X LEU* 4.5 2.0 - - + -
56X ARG* 3.6 18.4 - - + -
57X PHE* 3.6 34.1 - + - -
60X TYR* 3.3 58.8 - + + -
115X SER 3.0 13.0 + - - +
116X THR* 3.2 12.1 + - + +
118X ALA* 1.3 78.0 - - - +
120X LEU* 1.3 69.9 + - + +
121X GLU 3.2 1.4 + - - -
122X TRP* 3.5 13.2 + - - +
123X PHE* 3.4 34.9 - + - -
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Residues in contact with LEU 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X LEU* 4.9 0.4 - - + -
57X PHE* 4.3 15.9 - - + -
101X ILE* 4.6 14.8 - - + +
104X LEU* 3.5 31.9 - - + +
105X ALA* 3.5 38.1 - - + +
116X THR* 3.0 23.1 + - + +
117X ARG* 3.4 19.5 - - - +
118X ALA 3.1 0.8 - - - -
119X PHE* 1.3 93.6 - - + +
121X GLU* 1.3 65.4 + - - +
122X TRP 3.2 0.4 - - - -
123X PHE* 3.1 16.5 + - + +
124X ILE* 3.1 15.3 + - + +
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Residues in contact with GLU 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S GLU* 4.6 14.6 - - + +
117W ARG* 5.6 0.7 + - - +
118W ALA* 3.5 30.8 - - - +
121W GLU* 3.8 19.3 - - + +
117X ARG* 2.6 46.1 + - - +
118X ALA 3.0 17.1 + - - +
120X LEU* 1.3 78.3 - - - +
122X TRP* 1.3 63.8 + - - +
124X ILE* 3.4 6.5 + - - +
125X ASN* 3.1 40.3 + - - +
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Residues in contact with TRP 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X HIS* 3.8 22.7 - + - -
56X ARG* 3.3 55.9 - - - +
118X ALA 4.4 1.0 + - - -
119X PHE* 3.5 11.5 + - + +
120X LEU 3.2 0.6 - - - -
121X GLU* 1.3 79.2 - - - +
123X PHE* 1.3 89.8 + + + +
125X ASN* 3.3 8.5 + - + +
126X GLU* 2.8 50.3 + - + +
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Residues in contact with PHE 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X GLU* 4.4 7.9 - - - -
53X HIS* 3.9 22.9 - + + -
56X ARG* 3.6 29.6 - - + -
57X PHE* 3.4 35.0 - + - -
101X ILE* 4.0 23.1 - - + -
119X PHE* 3.4 42.6 - + - -
120X LEU* 3.1 10.5 + - + +
122X TRP* 1.3 98.1 - + + +
124X ILE* 1.3 60.6 + - - +
126X GLU* 3.8 3.0 - - + +
127X GLN* 2.8 40.1 + - + +
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Residues in contact with ILE 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114W TYR* 3.6 47.1 - - + +
115W SER* 3.8 18.2 + - - +
118W ALA* 3.8 10.8 - - + -
101X ILE* 3.7 18.2 - - + -
102X TYR* 4.6 6.5 - - + -
105X ALA* 4.6 7.6 - - + -
117X ARG* 3.7 34.1 - - - +
120X LEU 3.1 12.4 + - - +
121X GLU* 3.8 9.2 - - - +
122X TRP 3.3 0.4 - - - -
123X PHE* 1.3 76.2 - - - +
125X ASN* 1.3 63.2 + - - +
127X GLN* 3.9 5.2 - - - +
128X VAL* 3.5 19.9 + - + +
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Residues in contact with ASN 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115W SER 5.0 0.5 - - - +
118W ALA* 3.4 30.9 + - - +
119W PHE* 4.1 3.6 + - - -
121X GLU* 3.1 31.7 + - - +
122X TRP* 3.7 7.9 - - + +
124X ILE* 1.3 75.1 - - - +
126X GLU* 1.3 64.3 + - - +
128X VAL* 3.1 24.0 + - - +
129X GLU* 3.4 12.7 + - - +
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Residues in contact with GLU 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X GLU* 2.6 25.2 - - - +
53X HIS* 3.7 17.9 + - + +
122X TRP* 2.8 47.9 + - + +
123X PHE* 3.2 4.9 + - + +
125X ASN* 1.3 72.0 - - - +
127X GLN* 1.3 58.9 + - + +
129X GLU* 3.0 35.1 + - - +
130X GLU* 2.9 38.5 + - - +
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Residues in contact with GLN 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64W ARG* 5.3 0.4 - - - -
115W SER* 6.0 0.7 - - - +
53X HIS* 4.7 2.2 - - - -
94X GLU* 3.0 33.2 + - - +
97X ILE* 3.6 20.0 - - + +
98X SER* 2.9 30.8 + - - +
101X ILE* 4.5 11.9 - - + -
102X TYR* 5.9 2.7 - - + +
123X PHE* 2.8 25.5 + - + +
124X ILE* 3.9 6.1 - - - +
126X GLU* 1.3 79.5 - - + +
128X VAL* 1.3 56.7 + - + +
130X GLU* 3.7 11.3 + - - +
131X GLU* 2.8 37.4 + - - +
201X FE 3.6 22.0 - - - -
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Residues in contact with VAL 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60W TYR* 4.3 13.5 - - + -
63W ASP* 3.9 29.3 - - + +
64W ARG* 4.0 25.9 + - - +
115W SER* 3.5 31.6 - - - +
124X ILE 3.5 15.2 + - - +
125X ASN* 3.1 13.1 + - - +
127X GLN* 1.3 77.4 - - - +
129X GLU* 1.3 64.5 + - + +
131X GLU* 4.0 1.0 - - - +
132X ALA* 3.0 22.9 + - - +
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Residues in contact with GLU 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63W ASP* 5.8 3.4 - - - +
125X ASN* 3.4 11.2 + - - +
126X GLU* 3.0 35.7 + - - +
128X VAL* 1.3 79.3 - - + +
130X GLU* 1.3 59.1 + - - +
132X ALA* 3.2 8.4 + - - +
133X SER* 2.9 31.2 + - - -
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Residues in contact with GLU 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X GLN* 3.7 17.3 - - - +
49X GLU* 2.7 30.4 - - - +
50X GLU* 2.7 25.8 - - - +
53X HIS* 3.4 16.4 - - - -
94X GLU* 3.4 24.3 - - - +
126X GLU* 2.9 23.4 + - - +
127X GLN* 3.7 13.1 + - - +
129X GLU* 1.3 75.3 - - - +
131X GLU* 1.3 68.9 + - - +
133X SER* 3.2 9.5 + - - +
134X VAL* 3.2 25.6 + - + +
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Residues in contact with GLU 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 3.4 37.6 - - + +
64W ARG* 3.7 16.5 + - - +
91X TYR* 4.0 7.8 - - + -
94X GLU* 3.8 25.5 - - + +
95X LYS* 4.0 21.0 - - - +
98X SER* 2.5 33.2 + - - +
102X TYR* 4.9 0.9 + - - -
127X GLN* 2.8 23.1 + - - +
128X VAL 4.1 2.0 - - - +
130X GLU* 1.3 73.5 - - - +
132X ALA* 1.3 54.7 + - - +
134X VAL* 3.2 1.4 + - - +
135X LYS* 2.8 36.4 + - - +
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Residues in contact with ALA 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 5.5 0.2 - - - -
63W ASP* 3.7 44.0 + - + +
128X VAL 3.0 19.1 + - - +
129X GLU* 3.4 5.6 - - - +
131X GLU* 1.3 75.8 - - - +
133X SER* 1.3 57.9 + - - +
135X LYS* 3.6 7.0 + - - +
136X LYS* 2.9 30.2 + - - +
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Residues in contact with SER 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X TRP* 4.3 15.0 - - - -
46X GLN* 4.9 3.1 + - - -
129X GLU 2.9 14.3 + - - -
130X GLU* 3.3 14.6 + - - +
131X GLU 3.1 0.4 - - - -
132X ALA* 1.3 74.7 - - - +
134X VAL* 1.3 68.5 + - - +
136X LYS* 3.6 11.0 + - - +
137X ILE* 3.5 28.0 + - - +
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Residues in contact with VAL 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24X TYR* 5.4 1.8 - - + +
42X TRP* 3.9 24.5 - - + -
46X GLN* 5.6 4.5 - - + +
87X PHE* 3.9 17.7 - - + +
90X ALA* 3.8 15.5 - - + -
91X TYR* 3.5 37.0 - - + +
94X GLU* 4.2 17.5 - - + +
130X GLU* 3.2 14.2 + - + +
131X GLU 3.8 4.9 - - - +
133X SER* 1.3 73.2 + - - +
135X LYS* 1.3 66.3 + - - +
137X ILE* 3.2 3.3 + - - +
138X LEU* 2.9 21.3 + - - +
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Residues in contact with LYS 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 5.3 1.6 - - + -
63W ASP 6.0 0.4 - - - +
65W ASN* 3.7 32.2 + - + +
91X TYR* 3.4 49.4 - - + +
131X GLU 2.8 20.9 + - - +
132X ALA* 3.8 7.4 - - - +
134X VAL* 1.3 73.6 - - - +
136X LYS* 1.3 62.2 + - - +
138X LEU* 3.3 9.8 + - + +
139X ASP* 2.7 60.9 + - - +
142X LYS* 5.0 7.9 - - - +
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Residues in contact with LYS 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E GLY 6.1 1.3 - - - +
37E GLU* 3.1 33.8 + - - +
132X ALA 2.9 21.9 + - - +
133X SER* 3.7 10.5 - - - +
134X VAL 3.3 0.4 - - - -
135X LYS* 1.3 74.2 - - - +
137X ILE* 1.3 65.3 + - + +
139X ASP* 3.6 6.1 + - - +
140X LYS* 3.3 49.0 + - + +
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Residues in contact with ILE 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X PHE* 4.3 7.0 - - + -
42X TRP* 3.7 38.6 - - + +
87X PHE* 3.5 37.5 - - + -
133X SER* 3.5 10.1 + - - +
134X VAL 3.2 3.2 + - - +
136X LYS* 1.3 80.0 - - + +
138X LEU* 1.3 68.6 + - - +
139X ASP 3.1 1.3 - - - -
140X LYS* 2.9 13.9 + - + +
141X LEU* 2.8 24.4 + - + +
154X LEU* 5.1 5.6 - - + -
158X LEU* 3.7 35.4 - - + -
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Residues in contact with LEU 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X LEU* 3.9 16.9 - - + +
87X PHE* 4.1 21.2 - - + +
88X GLU* 4.0 22.7 - - + -
91X TYR* 3.7 42.0 - - + -
134X VAL 2.9 17.2 + - - +
135X LYS* 3.6 11.7 - - + +
137X ILE* 1.3 76.8 - - - +
139X ASP* 1.3 67.8 + - - +
141X LEU* 3.1 7.5 + - - +
142X LYS* 3.0 41.9 + - + +
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Residues in contact with ASP 139 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU 6.2 0.4 - - - +
35E GLY* 6.2 4.0 - - - -
65W ASN* 4.7 4.2 - - - +
135X LYS* 2.7 55.3 + - - +
136X LYS* 4.0 6.6 - - - +
138X LEU* 1.3 84.2 - - - +
140X LYS* 1.3 62.0 + - - +
142X LYS* 3.4 15.4 + - - +
143X PHE* 3.0 26.0 + - - +
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Residues in contact with LYS 140 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E GLY* 4.7 16.2 + - - +
37E GLU* 4.9 2.8 + - - +
152E PHE* 4.6 13.7 - - + -
155E ASP* 5.9 2.2 - - - -
136X LYS* 3.3 46.5 + - - +
137X ILE* 2.9 15.1 + - + +
139X ASP* 1.3 77.9 - - + +
141X LEU* 1.3 62.3 + - - +
143X PHE* 3.2 15.8 + - + +
144X ALA* 3.1 23.4 + - - +
150X ILE* 5.0 0.2 - - - +
154X LEU* 4.0 31.2 - - + +
157X GLU* 3.8 24.5 + - - -
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Residues in contact with LEU 141 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X PHE* 4.1 9.6 - - + -
83X PRO* 3.5 33.9 - - + +
84X LEU* 3.8 21.6 - - + +
87X PHE* 3.6 29.4 - - + -
137X ILE* 2.8 14.3 + - + +
138X LEU 3.1 9.2 + - - +
140X LYS* 1.3 75.6 - - - +
142X LYS* 1.3 65.7 + - - +
144X ALA* 3.1 21.7 + - + +
145X LYS* 3.8 2.1 + - - -
151X LEU* 3.7 30.1 - - + -
154X LEU* 3.8 14.8 - - + -
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Residues in contact with LYS 142 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X LEU* 3.9 21.5 - - + +
88X GLU* 4.3 11.9 + - - -
135X LYS* 5.0 5.9 - - - +
138X LEU* 3.0 36.1 + - + +
139X ASP* 3.6 17.6 + - - +
140X LYS 3.3 0.2 - - - -
141X LEU* 1.3 74.0 - - - +
143X PHE* 1.3 64.0 - - - +
144X ALA 2.9 1.7 + - - -
145X LYS* 3.2 29.6 + - - +
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Residues in contact with PHE 143 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU 5.8 4.5 - - - -
36E LEU* 5.2 9.4 - - + -
148E PRO* 3.6 38.7 - - + +
151E LEU* 4.2 21.3 - - + -
152E PHE* 3.9 27.1 - + + -
139X ASP 3.0 19.0 + - - +
140X LYS* 3.3 19.1 - - + +
141X LEU 3.1 0.2 - - - -
142X LYS* 1.3 78.3 - - - +
144X ALA* 1.3 54.5 + - - +
145X LYS* 3.5 5.5 + - - +
150X ILE* 3.8 27.0 - - + +
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Residues in contact with ALA 144 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140X LYS 3.1 15.0 + - - +
141X LEU* 3.6 12.7 - - + +
142X LYS 2.9 1.4 + - - -
143X PHE* 1.3 76.2 - - - +
145X LYS* 1.3 69.2 + - - +
146X ASP 3.7 1.1 - - - -
147X SER* 3.3 18.2 + - - +
150X ILE* 3.5 39.5 - - + -
151X LEU* 4.5 8.5 - - + +
154X LEU* 5.2 2.0 - - + -
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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