Contacts of the helix formed by residues 112 - 144 (chain B) in PDB entry 5IXM
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 THR 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ILE* 6.5 1.3 - - + -
305A THR 5.7 2.2 - - - +
306A THR* 4.6 6.9 + - - +
444A LYS* 5.5 6.5 - - + -
109B ASN* 3.0 37.7 + - - +
111B LEU* 1.3 86.9 - - + +
113B ALA* 1.3 64.3 + - - +
114B LEU 3.3 2.7 - - - -
115B ALA* 3.0 26.5 + - + +
116B LYS* 3.0 16.6 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.9 25.3 + - + -
151A PHE* 3.7 33.6 - - + -
153A VAL* 5.0 2.9 - - + -
162A ALA* 5.6 5.6 - - + +
109B ASN 3.3 7.5 + - - -
110B PRO 4.1 9.8 + - - +
111B LEU 3.7 1.4 - - - -
112B THR* 1.3 74.9 - - - +
114B LEU* 1.3 64.3 + - - +
116B LYS* 2.9 8.7 + - - +
117B GLU* 2.8 21.7 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS* 4.0 26.9 - - + +
151A PHE* 3.5 23.8 - - + -
163A TYR* 3.8 30.3 + - + +
164A ARG 4.1 2.9 - - - -
165A ALA* 4.1 11.0 - - + +
168A GLN* 5.2 2.5 - - - +
192A PHE* 3.9 32.1 - - + -
303A TYR 3.6 20.9 - - - +
304A ASP* 3.9 8.7 - - + -
112B THR 3.3 0.8 - - - -
113B ALA* 1.3 76.3 - - - +
115B ALA* 1.3 65.0 + - - +
117B GLU* 3.0 7.4 + - + +
118B ALA* 2.9 20.5 + - + +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ILE* 6.1 0.2 - - + -
303A TYR 4.6 1.9 + - - +
304A ASP* 3.4 33.2 - - - +
305A THR 3.6 18.2 - - - +
306A THR* 3.8 13.5 - - - -
322A SER* 3.6 4.7 + - - -
112B THR* 3.0 18.4 + - - +
114B LEU* 1.3 77.2 - - - +
116B LYS* 1.3 58.4 + - - +
118B ALA* 3.0 6.8 + - - +
119B GLU* 2.8 24.4 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 4.5 9.6 - - - +
306A THR* 4.2 15.4 + - + +
307A LEU 4.7 3.6 + - - -
442A VAL* 3.6 17.2 - - - +
106B PHE* 4.1 13.0 - - + -
107B PHE* 2.8 31.8 + - - +
108B ASP* 4.3 3.8 - - - +
109B ASN* 3.8 34.3 - - - +
112B THR* 3.0 16.7 + - - +
113B ALA* 2.9 12.2 + - - +
115B ALA* 1.3 76.9 - - - +
117B GLU* 1.3 51.5 + - - +
119B GLU* 2.8 34.6 + - - +
120B ALA* 2.8 35.3 + - - +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 5.8 0.2 - - + -
132A ILE* 3.7 27.2 - - + +
149A LYS* 3.0 32.7 + - + +
151A PHE* 3.8 17.0 - - + -
113B ALA 2.8 11.7 + - - +
114B LEU* 3.3 10.8 - - + +
116B LYS* 1.3 73.6 - - - +
118B ALA* 1.3 69.4 + - - +
120B ALA* 3.0 12.0 + - + +
121B GLU* 2.8 47.1 + - - +
124B ARG* 4.8 5.7 + - - +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASP* 3.8 24.2 - - + +
322A SER* 4.3 0.7 - - - -
323A GLY* 4.2 16.2 - - - +
114B LEU 2.9 10.5 + - - +
115B ALA 3.1 9.6 - - - +
117B GLU* 1.3 82.5 + - - +
119B GLU* 1.3 64.0 + - - +
121B GLU* 3.0 22.2 + - - +
122B VAL* 3.1 17.2 + - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A THR* 3.7 5.3 - - + +
307A LEU 4.0 8.8 - - - +
308A MET* 3.6 29.1 - - + +
309A GLN* 3.3 25.6 + - - +
322A SER* 4.0 5.7 - - - -
106B PHE* 3.6 24.0 - - + +
115B ALA 2.8 11.5 + - - +
116B LYS* 2.8 44.2 + - - +
118B ALA* 1.3 73.8 - - - +
120B ALA* 1.3 65.2 + - - +
122B VAL* 3.0 7.6 + - - +
123B LEU* 2.9 29.2 + - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 5.9 0.4 - - - +
80B LEU* 4.1 14.8 - - + +
106B PHE* 4.6 12.8 - - + -
116B LYS 2.8 15.0 + - - +
117B GLU* 3.0 13.9 + - + +
119B GLU* 1.3 73.7 - - - +
121B GLU* 1.3 51.6 + - - +
123B LEU* 3.0 9.5 + - - +
124B ARG* 2.8 61.0 + - - +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS* 2.8 25.5 + - - -
168A GLN* 5.0 0.9 - - - +
170A ASP* 5.2 4.2 - - - +
117B GLU* 2.8 37.6 + - - +
118B ALA* 3.0 12.2 + - - +
120B ALA* 1.3 76.2 - - - +
122B VAL* 1.3 64.3 + - + +
124B ARG* 3.0 19.4 + - - +
125B GLN* 2.9 22.7 + - - +
128B ARG* 4.5 3.0 + - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 3.6 30.7 - - + -
317A ARG* 4.4 7.4 - - - -
321A TYR 6.0 0.2 - - - +
322A SER* 5.2 6.3 - - - -
323A GLY 5.7 1.6 - - - +
118B ALA 3.1 13.0 + - - +
119B GLU 3.0 7.9 + - - +
121B GLU* 1.3 77.0 - - + +
123B LEU* 1.3 64.0 + - - +
125B GLN* 3.0 20.2 + - + +
126B GLU* 3.0 30.4 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A MET* 4.3 15.9 - - + -
309A GLN* 4.9 8.1 - - + +
317A ARG* 4.6 4.0 - - - +
80B LEU* 4.0 15.5 - - + -
104B ARG* 4.4 28.0 - - + +
105B THR 4.8 4.0 - - - +
106B PHE* 3.6 41.5 - - + -
119B GLU* 2.9 24.1 + - + +
120B ALA* 3.3 7.9 - - - +
122B VAL* 1.3 74.8 - - - +
124B ARG* 1.3 59.1 + - - +
126B GLU* 3.0 20.5 + - - +
127B MET* 2.8 32.5 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.5 33.7 + - - +
64B GLN* 3.8 20.2 + - - -
80B LEU* 4.3 18.7 - - + +
117B GLU* 4.8 5.1 + - - +
120B ALA* 2.8 47.2 + - - +
121B GLU* 3.0 21.7 + - - +
123B LEU* 1.3 71.1 - - - +
125B GLN* 1.3 64.5 + - - +
127B MET* 3.0 14.1 + - - +
128B ARG* 2.9 44.4 + - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PRO* 5.0 5.2 - - - +
31B SER* 4.5 6.6 + - - -
34B GLN* 5.8 0.8 + - - -
121B GLU 2.9 11.2 + - - +
122B VAL* 3.1 14.6 - - + +
124B ARG* 1.3 77.7 - - - +
126B GLU* 1.3 66.2 + - + +
128B ARG* 3.0 34.5 + - - +
129B GLU* 2.6 46.4 + - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASP* 4.9 0.9 - - - +
313A SER* 4.8 7.1 - - - -
314A GLY* 5.0 1.0 + - - -
317A ARG* 2.4 51.6 + - - +
104B ARG* 3.9 29.3 + - - +
122B VAL* 3.0 24.0 + - + +
123B LEU* 3.0 14.0 + - - +
125B GLN* 1.3 76.6 - - + +
127B MET* 1.3 64.5 + - - +
129B GLU* 3.0 19.7 + - - +
130B GLN* 2.8 22.2 + - - +
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Residues in contact with MET 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.5 31.9 - - + +
81B VAL 3.6 3.4 - - - -
82B LEU* 3.4 30.6 - - + +
102B VAL* 3.2 46.6 - - + +
103B PHE 4.3 0.4 - - - +
104B ARG* 3.5 30.7 - - + +
123B LEU 2.8 23.4 + - - +
124B ARG* 3.4 12.3 - - - +
126B GLU* 1.3 75.6 - - - +
128B ARG* 1.3 64.0 + - - +
130B GLN* 3.0 4.9 + - - +
131B ALA* 2.8 22.9 + - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PRO* 3.5 26.5 - - - +
28B LEU* 3.7 40.7 - - + +
31B SER* 4.1 12.6 - - - +
62B GLU* 3.5 23.0 + - - +
82B LEU* 3.9 20.6 - - + -
121B GLU* 4.5 2.6 + - - +
124B ARG* 2.9 28.9 + - - +
125B GLN* 3.4 38.0 + - - +
127B MET* 1.3 74.4 - - - +
129B GLU* 1.3 65.2 + - - +
131B ALA* 3.0 13.9 + - - +
132B ALA* 3.1 13.2 + - - +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 3.8 22.0 + - - +
34B GLN* 5.0 9.0 - - - +
35B GLN* 4.6 5.6 - - - +
125B GLN* 2.6 40.3 + - - +
126B GLU* 3.0 19.3 + - - +
128B ARG* 1.3 75.4 - - - +
130B GLN* 1.3 63.6 + - - +
132B ALA* 3.0 14.7 + - - +
133B GLN* 3.1 23.4 + - - +
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A SER* 4.4 5.7 + - - -
102B VAL* 3.8 13.8 - - + +
104B ARG* 2.8 37.2 + - - +
126B GLU 2.8 11.9 + - - +
127B MET* 3.5 7.9 - - - +
129B GLU* 1.3 74.4 - - - +
131B ALA* 1.3 65.7 + - - +
133B GLN* 3.0 30.1 + - + +
134B GLN* 3.0 38.6 + - + +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.5 4.5 - - + -
82B LEU* 3.9 19.1 - - + -
84B VAL* 4.3 13.0 - - + -
100B VAL* 3.9 24.2 - - + +
102B VAL* 4.0 5.3 - - + +
127B MET 2.8 11.4 + - - +
128B ARG* 3.0 10.7 + - - +
130B GLN* 1.3 75.7 - - - +
132B ALA* 1.3 64.9 + - - +
134B GLN* 3.0 6.1 + - - +
135B LEU* 2.9 27.2 + - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 5.1 0.2 - - - +
31B SER* 3.6 23.1 - - - +
32B ILE* 3.8 20.0 - - + +
35B GLN* 3.6 21.3 - - + -
128B ARG 3.1 6.9 + - - +
129B GLU 3.0 10.6 + - - +
131B ALA* 1.3 78.3 - - - +
133B GLN* 1.3 64.1 + - - +
135B LEU* 3.0 11.2 + - - +
136B VAL* 3.0 23.9 + - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LYS* 5.4 4.7 + - - -
35B GLN* 3.7 34.2 - - - +
129B GLU* 3.5 18.3 + - - +
130B GLN* 3.0 22.3 + - + +
132B ALA* 1.3 74.6 - - - +
134B GLN* 1.3 66.5 + - + +
136B VAL* 3.0 8.5 + - - +
137B ARG* 3.0 43.6 + - + +
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.3 29.2 - - + +
101B ASN 4.4 10.0 + - - +
102B VAL* 4.1 7.9 - - - +
130B GLN* 3.0 41.3 + - + +
131B ALA 3.0 7.6 + - - +
133B GLN* 1.3 77.6 - - + +
135B LEU* 1.3 52.8 + - - +
137B ARG* 3.0 29.7 + - - +
138B GLN* 2.6 51.0 + - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 5.8 0.4 - - + -
32B ILE* 3.9 31.9 - - + -
55B LEU* 5.2 11.9 - - + -
57B ILE* 4.8 4.5 - - + -
84B VAL* 4.1 21.1 - - + +
86B ALA* 4.0 19.3 - - + -
98B LEU* 4.0 30.2 - - + +
100B VAL* 3.9 20.2 - - + +
131B ALA* 2.9 15.7 + - + +
132B ALA* 3.2 10.1 - - - +
134B GLN* 1.3 75.6 - - - +
136B VAL* 1.3 65.3 + - + +
138B GLN* 3.0 16.0 + - - +
139B LEU* 3.1 14.4 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 3.8 14.4 + - - +
32B ILE* 5.1 3.4 - - + +
35B GLN* 3.9 25.4 - - + +
36B LEU* 4.1 25.6 - - + +
39B ASN* 3.7 33.7 - - + +
41B VAL* 6.1 0.9 - - + -
132B ALA 3.0 16.9 + - - +
133B GLN* 3.0 7.6 + - - +
135B LEU* 1.3 74.6 - - + +
137B ARG* 1.3 67.3 + - + +
139B LEU* 3.0 30.0 + - + +
140B LEU 4.0 0.2 + - - -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LYS* 5.4 5.5 - - - +
284A GLU* 5.7 0.4 - - - -
340A ARG* 3.3 45.8 - - - +
342A TYR* 4.1 20.2 + - + +
348A GLU* 4.2 13.3 + - - -
9B GLN* 6.2 0.4 - - - +
133B GLN* 3.0 35.1 + - - +
134B GLN* 3.5 35.3 - - - +
136B VAL* 1.3 78.6 - - + +
138B GLN* 1.3 60.2 + - + +
140B LEU* 2.9 31.6 + - - +
141B THR* 4.0 1.9 + - - +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.4 31.3 - - + +
99B GLN 3.4 25.9 + - - +
100B VAL* 3.6 16.0 - - - +
134B GLN* 2.6 32.0 + - + +
135B LEU 3.0 6.7 + - - +
137B ARG* 1.3 70.4 - - + +
139B LEU* 1.3 64.9 + - - +
140B LEU 3.0 0.4 - - - -
141B THR* 2.4 42.4 + - + +
142B VAL* 3.2 7.5 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.8 26.0 - - + +
17B LEU* 4.1 26.0 - - + -
36B LEU* 4.6 11.7 - - + -
41B VAL* 6.0 2.2 - - + -
55B LEU* 5.0 12.1 - - + -
88B VAL* 3.7 35.9 - - + -
98B LEU* 4.9 2.7 - - + -
135B LEU 3.1 10.0 + - - +
136B VAL* 3.0 24.9 + - + +
138B GLN* 1.3 78.8 - - - +
140B LEU* 1.3 60.5 + - - +
142B VAL* 3.0 12.2 + - + +
143B HIS* 2.9 21.9 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A TYR* 4.2 24.0 - - + -
346A ARG* 3.7 45.1 - - + +
9B GLN* 4.3 21.5 - - + +
12B THR* 4.4 26.4 + - - +
13B GLU 5.3 2.2 - - - +
136B VAL 4.0 0.8 + - - -
137B ARG* 2.9 14.8 + - - +
139B LEU* 1.3 78.0 - - - +
141B THR* 1.3 58.7 + - + +
143B HIS* 2.9 26.8 + - + +
144B ALA* 3.3 14.2 + - - -
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Residues in contact with THR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A TYR* 6.1 1.8 - - + -
345A ALA 4.7 4.7 - - - +
346A ARG* 3.1 32.3 - - - +
347A VAL* 4.7 9.0 - - + -
348A GLU 5.3 2.0 - - - +
96B TYR* 4.0 24.8 + - - -
98B LEU* 4.1 1.9 - - - +
137B ARG 4.6 2.0 - - - +
138B GLN* 2.4 44.4 + - + +
140B LEU* 1.3 76.8 - - + +
142B VAL* 1.3 64.7 + - - +
143B HIS 3.5 0.2 + - - -
144B ALA* 4.0 12.5 - - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.5 46.4 - - + -
90B ILE* 4.3 17.2 - - + +
93B HIS* 5.2 5.5 + - - +
96B TYR* 3.6 38.1 - - + -
98B LEU* 3.9 7.9 - - + -
138B GLN 3.4 13.9 - - - +
139B LEU* 3.0 17.9 + - + +
141B THR* 1.3 78.0 - - - +
143B HIS* 1.3 63.5 + - - +
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Residues in contact with HIS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 6.2 1.8 - - + -
13B GLU* 4.4 40.6 + - + +
14B LEU* 5.0 15.1 - - + +
90B ILE* 5.8 5.1 - - - +
139B LEU 2.9 10.6 + - - +
140B LEU* 2.9 18.5 + - + +
142B VAL* 1.3 80.6 - - - +
144B ALA* 1.3 89.3 + - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASP 6.1 0.2 - - - +
345A ALA* 4.9 10.8 - - - +
346A ARG* 4.6 18.4 - - + +
140B LEU 3.3 6.8 + - - +
141B THR 4.0 13.9 - - - +
143B HIS* 1.3 109.4 + - - +
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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