Contacts of the helix formed by residues 110 - 141 (chain A) in PDB entry 1QAP
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 ALA 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.5 24.9 - - + -
50A PRO 5.7 0.4 - - - +
53A THR* 2.8 34.8 + - + +
55A ALA* 3.7 23.3 - - + +
108A GLY 3.4 2.2 + - - -
109A PRO* 1.3 68.4 - - - +
111A ARG* 1.3 68.4 + - + +
112A VAL 3.0 1.4 + - - -
113A LEU* 3.1 14.8 + - - +
114A LEU* 3.3 13.1 + - + +
295A PHE* 6.1 0.4 - - - -
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.4 28.4 + - + +
47A GLN* 3.0 45.6 + - - +
49A LEU* 2.9 40.4 + - + +
50A PRO 4.8 1.8 - - - +
51A ALA* 3.4 35.1 - - - +
109A PRO* 5.0 4.3 - - + +
110A ALA* 1.3 78.5 - - - +
112A VAL* 1.3 66.1 + - + +
114A LEU* 3.3 6.0 + - - +
115A THR* 3.1 24.9 + - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA* 4.9 15.7 - - + -
77A PHE* 3.8 24.2 - - + -
80A LEU* 4.9 11.4 - - + +
81A ALA* 4.1 19.5 - - + -
85A VAL* 3.9 17.0 - - + -
109A PRO* 3.3 25.5 + - + +
110A ALA 3.0 1.6 + - - -
111A ARG* 1.3 79.3 - - + +
113A LEU* 1.3 59.6 + - + +
115A THR* 2.9 6.6 + - - -
116A GLY* 2.7 32.7 + - - -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA* 3.5 32.5 - - + +
56A HIS* 4.1 4.5 - - - +
57A ALA* 4.7 3.8 - - + +
77A PHE* 4.0 12.0 - - + -
85A VAL* 3.5 32.3 - - + -
106A LEU* 4.2 17.5 - - + -
108A GLY* 3.4 25.4 - - - +
109A PRO 3.4 10.5 - - - +
110A ALA* 3.1 3.3 + - - +
112A VAL* 1.3 73.7 - - + +
114A LEU* 1.3 56.8 + - - +
116A GLY 3.7 0.7 - - - -
117A GLU* 2.9 30.1 + - - +
293A MET* 3.5 19.7 - - + +
295A PHE* 4.5 10.3 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP* 4.4 5.7 - - - +
46A ALA* 5.0 4.7 - - + -
49A LEU* 3.6 31.4 - - + -
110A ALA* 3.3 10.0 + - + +
111A ARG* 3.3 8.5 + - - +
112A VAL 3.1 0.4 - - - -
113A LEU* 1.3 74.5 - - - +
115A THR* 1.3 66.2 + - - +
117A GLU* 3.4 24.2 + - - +
118A ARG 4.6 0.7 + - - -
295A PHE* 3.6 33.2 - - + -
152B ARG* 5.4 2.9 + - - -
178B LEU* 5.4 3.6 - - - +
187B ASN* 4.1 22.7 - - + +
188B HIS* 4.2 28.5 - - + +
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.8 2.9 - - + +
33A ASP* 4.6 5.4 - - - +
34A LEU* 3.9 20.9 - - + -
40A ALA* 4.1 10.8 + - - +
43A ASP* 2.6 31.1 + - + +
46A ALA* 4.2 1.6 - - - +
80A LEU* 4.3 15.5 - - + -
111A ARG 3.1 11.6 + - - -
112A VAL* 2.9 9.2 + - - -
114A LEU* 1.3 79.8 - - - +
116A GLY* 1.3 64.4 + - - +
117A GLU 3.0 1.6 + - - -
118A ARG* 3.9 6.4 + - - +
119A THR* 4.7 2.4 + - - -
152B ARG* 5.6 0.3 + - - -
178B LEU* 3.4 31.0 - - + +
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.3 2.5 - - - -
76A VAL* 4.5 6.1 - - - +
77A PHE* 3.9 16.3 - - - -
80A LEU* 3.9 19.4 - - - +
112A VAL 2.7 18.3 + - - -
113A LEU 3.7 1.1 - - - -
115A THR* 1.3 72.6 - - - +
117A GLU* 1.3 62.7 + - - +
119A THR* 3.7 2.5 + - - -
120A ALA* 3.0 25.8 + - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 5.0 0.4 - - - -
113A LEU 2.9 19.6 + - - +
114A LEU* 3.4 18.8 - - - +
115A THR 3.0 3.2 + - - -
116A GLY* 1.3 77.1 - - - +
118A ARG* 1.3 77.0 + - - +
120A ALA* 3.6 2.7 - - - +
121A LEU* 2.9 40.8 + - + +
292A SER* 5.6 0.5 - - - -
293A MET* 3.7 43.5 + - + +
295A PHE* 5.0 2.5 - - - -
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Residues in contact with ARG 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 4.3 2.0 - - - +
114A LEU 4.6 0.6 + - - -
115A THR 3.9 3.5 + - - +
116A GLY 3.6 0.6 - - - -
117A GLU* 1.3 90.0 + - - +
119A THR* 1.3 60.5 + - - +
121A LEU* 3.0 36.5 + - - +
122A ASN* 2.5 66.4 + - - +
125A GLN* 4.2 11.3 + - - +
291A LEU 5.6 1.6 + - - -
152B ARG* 2.9 62.1 - - + +
153B LYS* 3.3 27.3 - - - +
159B ARG* 5.0 1.3 - - - +
301B NTM 3.3 25.2 + - - -
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 5.1 0.4 - - + +
29A ALA* 3.8 25.8 + - + +
30A LEU* 3.8 24.9 - - + +
33A ASP* 4.0 12.5 + - - +
76A VAL* 3.9 17.7 - - + -
115A THR 4.7 1.8 + - - -
116A GLY 3.7 3.9 + - - -
117A GLU 3.4 0.4 - - - -
118A ARG* 1.3 76.6 - - - +
120A ALA* 1.3 64.0 + - - +
122A ASN* 3.3 8.9 + - - +
123A PHE* 3.2 49.1 + - + -
156B PRO* 6.2 0.2 - - + -
159B ARG* 5.6 1.9 + - - -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.6 12.9 - - + +
76A VAL* 4.0 14.1 - - + +
77A PHE* 3.8 24.9 - - + -
104A PHE* 5.8 5.6 - - + -
106A LEU* 5.9 0.7 - - + -
116A GLY 3.0 20.9 + - - +
117A GLU* 3.6 3.8 - - - +
119A THR* 1.3 77.7 - - - +
121A LEU* 1.3 66.9 + - + +
123A PHE* 3.5 5.4 + - - +
124A VAL* 3.4 23.7 + - - +
293A MET* 6.5 0.4 - - - -
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Residues in contact with LEU 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 3.8 24.5 - - + -
104A PHE* 5.9 2.7 - - + -
117A GLU* 2.9 42.3 + - + +
118A ARG* 3.0 27.6 - - - +
120A ALA* 1.3 80.3 - - + +
122A ASN* 1.3 57.1 + - - +
124A VAL* 3.4 3.2 + - + +
125A GLN* 2.8 39.6 + - + +
291A LEU* 3.7 37.5 - - + -
292A SER* 4.2 9.6 - - - +
293A MET* 4.1 18.6 - - + +
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Residues in contact with ASN 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ARG* 2.5 47.5 + - - +
119A THR* 3.3 8.8 + - + +
121A LEU* 1.3 70.8 - - - +
123A PHE* 1.3 60.7 + - - +
125A GLN* 3.9 9.9 + - - +
126A THR* 2.5 32.4 + - - -
152B ARG 3.4 21.4 + - - -
153B LYS* 3.8 6.8 - - - -
154B THR 3.2 28.8 + - - +
156B PRO* 4.0 11.2 - - + +
159B ARG* 4.5 7.7 - - - +
284B LYS* 5.8 0.5 - - - +
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Residues in contact with PHE 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 4.1 10.1 - - + -
26A VAL* 3.7 38.6 - - + -
29A ALA* 3.7 10.8 - - + -
69A GLY* 6.0 0.2 - - - -
72A TRP* 3.6 48.0 - + + -
73A VAL* 5.6 0.4 - - + +
76A VAL* 5.6 1.1 - - + -
119A THR* 3.2 42.3 + - + +
120A ALA* 3.9 5.2 - - - +
122A ASN* 1.3 82.2 - - - +
124A VAL* 1.3 64.9 + - + +
126A THR* 3.1 3.0 + - - -
127A LEU* 3.0 34.1 + - + +
158A LEU* 4.7 8.5 - - + -
161A ALA* 6.3 0.9 - - + -
156B PRO* 3.5 32.3 - - + -
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Residues in contact with VAL 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 3.9 18.4 - - + -
68A CYS 3.9 12.8 - - - +
69A GLY* 3.8 12.8 - - - +
73A VAL* 3.5 31.0 - - + -
104A PHE* 5.4 5.2 - - + -
120A ALA 3.4 9.5 + - - +
121A LEU* 3.4 6.1 + - + +
123A PHE* 1.3 77.9 - - + +
125A GLN* 1.3 66.8 + - - +
127A LEU* 4.9 0.7 - - - -
128A SER* 2.8 43.4 + - - +
291A LEU* 3.4 28.3 - - + -
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Residues in contact with GLN 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ARG* 4.2 13.6 + - - +
121A LEU* 2.8 29.4 + - + +
122A ASN* 3.9 22.2 + - - +
124A VAL* 1.3 72.6 - - - +
126A THR* 1.3 58.8 + - - +
129A GLY* 2.8 23.4 + - - -
288A ALA* 3.5 9.8 - - + -
289A LEU* 3.2 36.8 + - - +
290A ASP* 4.6 1.2 - - - +
291A LEU* 3.4 41.3 + - + +
153B LYS* 5.3 3.1 - - - +
284B LYS* 3.3 29.5 + - - +
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Residues in contact with THR 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASN 2.5 24.1 + - - -
123A PHE 3.5 4.7 - - - -
124A VAL 3.1 0.6 - - - -
125A GLN* 1.3 75.3 - - - +
127A LEU* 1.3 72.0 + - + +
129A GLY* 2.8 13.3 + - - -
130A VAL* 2.9 19.7 + - + +
155A LEU* 4.7 5.4 - - + -
158A LEU* 5.8 5.4 - - + -
162A LEU* 5.4 3.4 - - + -
286A VAL* 3.7 21.9 - - + +
288A ALA* 4.7 3.0 - - - +
155B LEU* 3.6 33.0 - - + +
156B PRO* 4.0 11.3 - - + +
284B LYS 5.4 1.5 + - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A CYS* 4.0 23.3 - - - +
69A GLY* 4.0 7.9 - - - +
72A TRP* 3.6 52.9 - - + +
123A PHE* 3.0 24.2 + - + +
126A THR* 1.3 82.0 - - + +
128A SER* 1.3 57.5 + - - +
130A VAL* 3.5 1.9 + - - -
131A ALA* 2.9 25.1 + - - +
158A LEU* 5.6 5.8 - - + -
161A ALA* 3.8 32.1 - - + +
162A LEU* 4.5 10.8 - - + +
165A ALA* 3.3 16.3 - - + +
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Residues in contact with SER 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL 3.5 10.5 - - - +
67A PHE* 3.8 4.0 - - - -
68A CYS* 2.7 34.2 + - - -
124A VAL* 2.8 26.8 + - - +
125A GLN 4.2 0.4 - - - -
127A LEU* 1.3 73.6 - - - +
129A GLY* 1.3 57.3 + - - +
131A ALA* 4.2 2.9 - - - -
132A SER* 2.6 39.4 + - - -
289A LEU* 3.4 24.5 - - - -
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Residues in contact with GLY 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN 2.8 21.0 + - - -
126A THR 2.8 2.0 + - - -
128A SER* 1.3 77.4 - - - +
130A VAL* 1.3 61.5 + - - +
132A SER* 3.5 3.7 + - - -
133A GLU* 3.2 22.6 + - - +
286A VAL* 5.2 1.8 - - - -
287A ARG* 3.7 27.5 + - - +
288A ALA* 4.3 1.8 - - - -
289A LEU* 3.8 10.5 - - - +
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Residues in contact with VAL 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR* 2.9 17.1 + - + +
127A LEU 3.7 5.8 - - - +
129A GLY* 1.3 73.8 - - - +
131A ALA* 1.3 59.8 + - - +
133A GLU* 2.9 9.0 + - - +
134A VAL* 2.8 40.7 + - + +
162A LEU* 3.6 29.2 - - + -
165A ALA* 4.2 13.2 - - + -
166A VAL* 4.7 2.2 - - + -
282A LEU 3.5 24.7 - - - +
283A THR* 4.4 8.3 - - + -
285A HIS 4.8 3.1 - - - +
286A VAL* 4.1 22.0 - - + +
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Residues in contact with ALA 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.0 19.5 - - + +
68A CYS* 4.0 18.2 - - + -
127A LEU 2.9 19.8 + - - +
128A SER* 3.3 5.1 + - - +
130A VAL* 1.3 74.4 - - - +
132A SER* 1.3 60.8 - - - +
134A VAL* 4.1 0.7 - - - -
135A ARG* 3.2 20.4 + - - +
165A ALA* 3.5 24.4 - - - +
168A CYS* 4.4 0.9 - - + -
169A GLY* 3.3 13.7 - - - +
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Residues in contact with SER 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP 5.3 0.4 - - - -
65A GLY* 3.6 10.9 - - - -
66A VAL* 2.9 33.6 + - - -
128A SER 2.6 25.6 + - - -
129A GLY* 3.6 6.5 - - - -
131A ALA* 1.3 74.7 - - - +
133A GLU* 1.3 64.4 + - - +
135A ARG* 3.7 2.8 + - - +
136A ARG* 3.4 31.9 + - - -
289A LEU* 3.8 11.4 - - - +
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Residues in contact with GLU 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY 3.2 12.2 + - - +
130A VAL* 2.9 11.8 + - - +
132A SER* 1.3 74.5 - - - +
134A VAL* 1.3 69.1 + - + +
136A ARG* 2.9 39.7 + - - +
137A TYR* 3.1 47.8 + - + -
281A ALA 5.8 2.2 - - - +
282A LEU* 5.2 12.8 - - + +
285A HIS 6.0 1.3 - - - +
287A ARG* 4.4 24.0 + - + +
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Residues in contact with VAL 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 2.8 34.1 + - + +
131A ALA* 3.8 1.8 - - - +
133A GLU* 1.3 74.6 - - - +
135A ARG* 1.3 59.0 + - - +
137A TYR* 2.8 25.7 + - - +
138A VAL* 2.8 11.9 + - + +
148A LEU* 4.5 4.0 - - + -
166A VAL* 3.6 43.5 - - + +
169A GLY* 3.7 16.2 - - - -
170A GLY 4.6 0.7 - - - -
171A GLY* 3.9 12.6 - - - +
282A LEU* 4.3 27.3 - - + +
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Residues in contact with ARG 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.6 29.4 - - + +
96A ALA* 5.2 10.8 - - - +
131A ALA 3.2 13.4 + - - +
132A SER 4.0 3.8 - - - +
133A GLU 3.3 0.4 - - - -
134A VAL* 1.3 78.6 - - - +
136A ARG* 1.3 55.2 + - - +
138A VAL* 2.8 13.9 + - + +
139A GLY* 2.7 40.2 + - - -
168A CYS 5.6 0.9 - - - -
169A GLY 3.2 20.1 + - - +
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Residues in contact with ARG 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 3.4 17.9 + - - +
133A GLU* 2.9 47.5 + - - +
135A ARG* 1.3 80.9 - - - +
137A TYR* 1.3 63.0 + - + +
139A GLY* 3.5 10.0 + - - +
140A LEU* 4.1 12.2 - - + +
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Residues in contact with TYR 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLU* 3.1 37.0 + - + +
134A VAL 2.8 13.2 + - - +
136A ARG* 1.3 79.4 - - + +
138A VAL* 1.3 57.3 + - - +
139A GLY 3.1 0.2 - - - -
140A LEU* 3.2 29.6 - - + +
141A LEU* 3.7 6.6 - - - +
148A LEU* 3.7 19.5 - - + -
260A ASN 5.4 0.9 + - - -
261A VAL 4.6 10.1 + - - -
263A ALA* 5.6 7.7 + - + +
266A LEU* 4.4 27.6 - - + -
279A VAL* 4.3 20.4 - - + +
281A ALA* 4.7 10.5 - - + +
282A LEU* 3.4 26.7 - - + -
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Residues in contact with VAL 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL 2.8 8.9 + - - +
135A ARG* 2.8 32.9 + - + +
137A TYR* 1.3 75.1 - - - +
139A GLY* 1.3 65.6 + - - +
140A LEU 3.2 0.2 - - - -
141A LEU* 3.3 22.7 + - + +
142A ALA* 4.2 2.8 + - - +
147A GLN* 6.3 1.3 - - + -
148A LEU* 4.3 22.6 - - + +
169A GLY 3.8 10.3 - - - +
170A GLY* 3.7 25.8 - - - +
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Residues in contact with GLY 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 2.7 20.2 + - - -
136A ARG* 3.5 6.2 + - - -
137A TYR 3.1 1.4 - - - -
138A VAL* 1.3 81.7 - - - +
140A LEU* 1.3 58.3 + - - +
141A LEU 3.5 0.3 + - - -
142A ALA* 3.6 18.5 - - - +
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Residues in contact with LEU 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ARG* 4.1 9.4 + - + +
137A TYR* 3.2 27.6 - - + +
138A VAL 3.2 0.2 - - - -
139A GLY* 1.3 72.7 - - - +
141A LEU* 1.3 72.5 + - + +
142A ALA* 3.1 8.8 + - - -
263A ALA* 4.3 20.0 - - + +
264A GLU* 5.1 8.3 - - - +
266A LEU* 3.9 26.2 - - + -
267A ARG* 3.0 44.3 + - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR 3.7 19.5 - - - +
138A VAL* 3.3 17.1 + - + +
140A LEU* 1.3 84.0 - - + +
142A ALA* 1.3 59.5 + - - +
144A THR* 2.9 31.5 + - - +
146A THR* 3.8 43.6 - - + +
147A GLN 4.3 0.2 - - - -
148A LEU* 4.2 26.9 - - + +
266A LEU* 3.7 25.4 - - + +
267A ARG* 5.0 0.2 - - - -
270A ALA* 4.0 16.2 - - + -
277A ILE* 4.4 4.0 - - + -
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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) + - + + + + + -
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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