Contacts of the helix formed by residues 105 - 136 (chain C) in PDB entry 2WLM
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 ILE 105 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASP 4.8 5.8 - - - +
74C VAL* 2.8 38.5 + - + +
75C ILE 3.9 4.9 - - - -
76C GLU* 3.4 47.6 - - + +
104C PRO* 1.3 80.6 - - - +
106C GLY* 1.3 64.6 + - - +
109C ALA* 3.1 15.1 - - - +
110C ASN* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE* 1.3 81.8 - - - +
107C PRO* 1.3 74.6 - - - +
108C LEU 3.4 2.0 - - - -
109C ALA 3.3 0.3 + - - -
110C ASN* 2.6 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY* 1.3 83.3 - - - +
108C LEU* 1.3 69.5 + - + +
110C ASN* 3.3 5.8 + - + +
111C THR* 2.8 35.5 + - - +
84D THR* 5.8 6.1 - - + -
88D PHE* 4.2 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C CYS* 3.8 32.0 - - + -
74C VAL* 5.4 3.4 - - + -
106C GLY 3.4 0.6 - - - -
107C PRO* 1.3 83.7 - - + +
109C ALA* 1.3 66.8 + - - +
111C THR* 3.4 6.5 + - - +
112C LEU* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.4 13.9 - - + -
71C CYS* 4.9 0.6 - - - -
74C VAL* 3.6 23.3 - - + +
104C PRO* 3.9 4.7 - - + -
105C ILE 3.1 42.7 + - - +
106C GLY 3.3 2.0 + - - +
108C LEU* 1.3 81.5 - - - +
110C ASN* 1.3 60.5 + - - +
112C LEU* 3.3 6.6 - - - +
113C VAL* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C PRO* 2.8 35.9 + - - +
105C ILE* 4.4 0.4 - - - +
106C GLY 2.6 39.5 + - - +
107C PRO* 3.9 1.0 - - - +
109C ALA* 1.3 71.9 - - - +
111C THR* 1.3 68.7 + - - +
113C VAL* 2.8 19.5 + - + +
114C THR* 2.8 16.6 + - - +
88D PHE* 3.3 35.1 - - + +
92D GLN* 4.1 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PRO* 2.8 25.6 + - - +
108C LEU* 3.9 7.2 - - - +
110C ASN* 1.3 75.1 - - - +
112C LEU* 1.3 65.2 + - - +
114C THR* 3.1 8.9 + - - +
115C LEU* 2.9 30.9 + - + +
88D PHE* 3.6 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.5 16.0 - - + -
67C ALA* 3.5 49.8 - - + +
68C TYR* 3.5 25.4 - - + +
71C CYS* 4.3 10.1 - - - -
108C LEU 3.2 12.0 + - - +
109C ALA 3.3 10.1 - - - +
111C THR* 1.3 78.7 - - - +
113C VAL* 1.3 56.4 + - - +
115C LEU* 3.4 14.9 + - + +
116C GLU* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.3 18.4 - - + +
89C PHE* 4.4 2.2 - - + -
93C THR* 3.6 7.8 + - - +
104C PRO* 3.8 18.8 - - + -
109C ALA 3.1 16.0 + - - +
110C ASN* 2.8 20.8 + - + +
112C LEU* 1.3 71.6 - - - +
114C THR* 1.3 63.8 + - + +
115C LEU 2.9 5.6 + - - -
116C GLU* 3.0 5.3 + - - +
117C ALA* 2.9 22.2 + - - +
91D VAL* 5.6 1.6 - - + -
92D GLN* 5.3 3.6 - - - +
97D ILE* 4.1 14.6 - - + -
99D TYR* 3.6 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASN 2.8 17.9 + - - +
111C THR* 3.4 8.9 + - - +
113C VAL* 1.3 74.3 - - + +
115C LEU* 1.3 62.3 + - - +
117C ALA* 4.2 5.4 - - - -
118C LEU* 3.7 5.7 + - - +
57D TYR* 3.3 34.1 + - - -
58D LEU* 5.0 8.2 - - - +
87D PHE* 4.9 4.6 - - + -
88D PHE* 3.3 31.4 - - + -
91D VAL* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.3 17.5 - - + -
111C THR* 2.9 22.0 + - + +
112C LEU* 3.4 16.4 - - + +
113C VAL 2.9 0.6 + - - -
114C THR* 1.3 79.1 + - - +
116C GLU* 1.3 67.2 + - - +
118C LEU* 3.5 15.0 + - + +
119C CYS* 3.0 27.8 + - - +
54D THR* 6.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASN* 3.6 5.0 - - - +
64C PHE* 3.2 42.6 - - + +
68C TYR* 3.2 18.0 + - - -
90C SER* 2.6 28.1 + - - +
93C THR* 2.7 31.1 - - + +
94C MET* 3.4 21.9 - - + +
112C LEU 2.9 11.8 + - - +
113C VAL 3.4 7.4 - - - +
115C LEU* 1.3 73.1 - - - +
117C ALA* 1.3 68.5 + - - +
119C CYS* 2.7 5.9 + - - +
120C GLY* 2.6 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR 4.8 9.1 + - - +
94C MET* 4.7 3.1 - - - +
96C THR* 5.0 8.7 - - + +
113C VAL 2.9 15.4 + - - +
114C THR* 4.0 8.1 - - - +
116C GLU* 1.3 76.5 - - - +
118C LEU* 1.3 65.8 + - - +
120C GLY* 2.7 10.4 + - - -
121C MET* 3.0 13.2 + - - +
57D TYR* 4.1 9.0 - - - +
91D VAL* 6.2 0.4 - - + -
95D ALA* 4.2 21.1 - - + -
97D ILE* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR 3.7 11.0 + - - +
115C LEU* 3.5 18.5 + - + +
117C ALA* 1.3 78.5 - - - +
119C CYS* 1.3 67.8 + - - +
121C MET* 3.3 5.9 + - - +
122C LEU* 3.0 47.0 + - + +
50D ILE* 5.6 2.7 - - + -
53D ILE* 4.2 24.2 - - + -
54D THR* 4.2 24.0 - - + +
57D TYR* 3.8 36.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.2 22.7 - - + -
94C MET* 5.2 3.8 - - + -
115C LEU* 3.0 21.1 + - - +
116C GLU* 2.7 21.1 + - + +
118C LEU* 1.3 77.8 - - - +
120C GLY* 1.3 60.5 + - - +
122C LEU* 3.3 9.9 + - - +
123C GLY* 2.9 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C MET* 3.4 38.0 - - - +
116C GLU 2.6 14.3 + - - -
117C ALA 2.7 6.6 + - - -
119C CYS* 1.3 73.6 - - - +
121C MET* 1.3 61.3 + - - -
123C GLY* 3.1 2.4 + - - -
124C LEU* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C MET 5.0 0.4 + - - -
96C THR* 6.3 0.4 - - - +
117C ALA 3.0 10.3 + - - +
118C LEU* 3.9 7.9 - - + +
120C GLY* 1.3 72.3 - - - +
122C LEU* 1.3 61.9 + - + +
124C LEU* 2.9 12.7 + - + +
125C ALA* 2.8 28.5 + - - +
124D LEU* 3.6 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.0 47.4 + - + +
119C CYS* 3.6 9.6 - - - +
121C MET* 1.3 76.5 - - + +
123C GLY* 1.3 64.3 + - - +
125C ALA* 3.0 9.1 + - + +
126C VAL* 2.9 29.2 + - + +
50D ILE* 4.5 24.0 - - + -
53D ILE* 4.7 17.5 - - + -
124D LEU* 6.4 0.9 - - + -
127D ALA* 5.2 8.5 - - + -
131D ILE* 4.7 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C CYS 2.9 14.0 + - - -
120C GLY 3.1 5.4 + - - -
122C LEU* 1.3 75.8 - - - +
124C LEU* 1.3 49.9 + - - +
126C VAL* 3.0 7.8 + - - +
127C ALA* 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B MET* 3.6 39.0 - - + +
122B LEU* 6.4 1.3 - - + -
124B LEU* 4.4 20.2 - - + -
125B ALA* 5.4 6.3 - - + -
120C GLY 3.0 10.8 + - - +
121C MET* 2.9 14.0 + - + +
123C GLY* 1.3 76.0 - - - +
125C ALA* 1.3 55.2 + - - +
127C ALA* 3.7 7.8 - - + +
128C ALA* 2.8 41.4 + - + +
124D LEU* 4.4 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C MET 2.8 15.0 + - - +
122C LEU* 3.0 13.2 + - + +
124C LEU* 1.3 74.9 - - - +
126C VAL* 1.3 54.6 + - - +
128C ALA* 3.7 5.4 + - - +
129C SER* 2.5 34.8 + - - -
124D LEU* 5.4 5.6 - - + +
127D ALA* 5.1 1.3 - - + -
128D ALA* 4.0 24.6 - - + +
131D ILE* 4.0 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 2.9 19.5 + - + +
123C GLY* 3.5 9.2 - - - +
125C ALA* 1.3 74.4 - - - +
127C ALA* 1.3 65.2 + - - +
129C SER* 3.5 7.1 + - - -
130C LEU* 3.2 38.3 + - + +
46D TRP* 6.2 1.1 - - + -
131D ILE* 3.8 22.7 - - + -
135D PHE* 4.1 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 5.2 9.4 - - + -
125B ALA* 5.8 1.6 - - + -
53C ILE* 4.5 22.2 - - + -
123C GLY 2.7 20.2 + - - +
124C LEU* 3.7 10.8 - - + +
126C VAL* 1.3 72.5 - - - +
128C ALA* 1.3 65.8 + - - +
130C LEU* 3.2 10.5 + - - +
131C ILE* 2.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ALA* 4.1 27.3 - - + +
128B ALA* 6.3 1.3 - - + -
129B SER* 4.9 0.7 + - - -
124C LEU* 2.8 25.9 + - + +
125C ALA* 3.8 6.7 - - - +
127C ALA* 1.3 72.0 - - - +
129C SER* 1.3 53.8 + - - +
131C ILE* 3.1 3.5 + - - +
132C TYR* 2.7 37.2 + - - +
128D ALA* 6.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ALA 2.5 24.9 + - - -
126C VAL* 3.7 6.5 + - - -
127C ALA 3.3 0.2 - - - -
128C ALA* 1.3 75.9 - - - +
130C LEU* 1.3 52.6 + - - +
132C TYR* 3.3 3.1 + - - +
133C ALA* 2.6 39.2 + - - +
128D ALA 4.8 0.2 + - - -
131D ILE* 4.6 1.2 - - - +
132D TYR* 3.4 50.9 + - - +
135D PHE* 4.6 13.0 - - - -
136D THR* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C TYR* 4.2 15.0 - - + -
41C LEU* 4.1 38.8 - - + -
42C LEU* 4.2 6.5 - - + -
49C PHE* 3.8 22.7 - - + -
53C ILE* 5.7 2.7 - - + -
126C VAL* 3.2 25.0 + - + +
127C ALA* 3.4 9.6 - - - +
129C SER* 1.3 76.4 - - - +
131C ILE* 1.3 64.5 + - - +
133C ALA* 2.9 5.7 + - - +
134C ARG* 2.8 30.2 + - + +
135D PHE* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.8 14.1 - - + +
125B ALA* 4.1 21.5 - - + +
126B VAL* 3.9 30.1 - - + +
129B SER* 4.6 0.7 - - - +
46C TRP* 4.2 15.1 - - + -
49C PHE* 3.3 29.8 - - + -
53C ILE* 4.5 5.6 - - + -
127C ALA* 2.8 35.3 + - + +
128C ALA* 3.3 5.8 - - - +
130C LEU* 1.3 72.4 - - - +
132C TYR* 1.3 52.5 + - - +
134C ARG* 3.2 7.2 + - - +
135C PHE* 2.6 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 3.5 38.8 + - - +
132B TYR* 3.7 38.3 - + + -
133B ALA* 5.0 1.9 - - + +
128C ALA 2.7 19.8 + - - +
129C SER* 3.7 5.4 - - - +
131C ILE* 1.3 73.2 - - - +
133C ALA* 1.3 59.0 + - - +
135C PHE* 4.2 1.6 - - - -
136C THR* 2.6 72.4 + - + +
1299C K 3.9 10.7 - - - -
132D TYR* 3.6 32.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C TYR* 4.0 16.2 - - + +
42C LEU* 3.7 21.7 - - + +
129C SER 2.6 23.0 + - - +
130C LEU* 3.4 5.4 - - - +
132C TYR* 1.3 82.3 - - - +
134C ARG* 1.3 62.2 + - - +
136C THR* 3.9 7.3 + - - +
137C ARG* 3.8 15.0 + - - +
132D TYR* 4.9 1.3 - - + +
136D THR* 4.3 9.6 - - + -
250D PHE 5.3 3.6 - - - +
251D ALA* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 2.5 37.9 + - - -
42C LEU* 3.9 24.6 + - + +
44C VAL* 2.9 30.1 + - - +
46C TRP* 3.4 61.0 + - + +
49C PHE* 3.5 36.0 - - - +
130C LEU 2.8 25.8 + - - +
131C ILE 3.5 4.9 - - - +
133C ALA* 1.3 73.9 - - - +
135C PHE* 1.3 63.1 + - - +
137C ARG* 3.6 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 4.4 24.7 - + - -
38B TYR* 4.0 26.9 - + - +
41B LEU* 4.9 4.9 - - + -
126B VAL* 4.3 22.0 - - + -
129B SER* 4.6 12.8 - - - -
130B LEU* 3.5 38.4 - - + -
46C TRP* 4.2 20.0 - + + -
131C ILE* 2.6 34.2 + - + +
132C TYR* 4.0 4.7 - - - +
134C ARG* 1.3 75.7 - - - +
136C THR* 1.3 58.7 + - + +
137C ARG 2.9 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.4 27.6 - - + +
129B SER* 4.8 6.5 - - - -
133B ALA* 4.4 10.1 - - + -
132C TYR* 2.6 69.1 + - + +
133C ALA* 3.9 4.7 + - - +
134C ARG 3.5 0.6 - - - -
135C PHE* 1.3 75.0 - - + +
137C ARG* 1.3 64.2 + - - +
138C PRO* 4.0 1.1 - - - +
252C GLN* 3.9 19.8 + - - -
251D ALA* 5.2 2.1 - - - +
----------------------------------------------------------
Back to top of page
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