Contacts of the helix formed by residues 95 - 120 (chain F) in PDB entry 5GOU
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 SER 95 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.7 7.3 - - - -
46F VAL* 6.4 0.7 - - - -
93F TRP 2.9 12.4 + - - +
94F GLU* 1.3 82.3 + - - +
96F GLY* 1.3 60.1 + - - +
97F LEU 3.5 0.7 + - - -
98F ASN* 3.2 20.8 + - - +
99F ALA* 3.2 17.2 + - - +
168F PRO* 3.2 31.0 - - - +
174F GLU* 3.2 15.5 - - - -
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Residues in contact with GLY 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.6 22.5 - - - -
48F LEU* 5.3 1.0 - - - +
51F PHE* 3.6 22.9 - - - -
95F SER* 1.3 71.6 - - - +
97F LEU* 1.3 57.5 + - - -
99F ALA* 4.0 0.7 - - - +
100F MET* 3.0 29.1 + - - +
162F LEU* 4.3 1.8 - - - -
174F GLU* 2.7 20.6 + - - -
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F SER* 4.0 3.6 - - - +
96F GLY* 1.3 76.6 - - - +
98F ASN* 1.3 58.7 + - - +
100F MET* 3.3 1.6 + - - +
101F GLU* 2.9 42.3 + - - +
159F VAL* 3.9 14.4 - - + +
162F LEU* 3.8 25.9 - - + +
163F ARG* 3.7 31.4 - - + -
167F ALA* 3.3 46.7 - - + +
168F PRO* 3.7 12.1 - - + -
174F GLU* 2.9 7.1 + - - +
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Residues in contact with ASN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F TRP* 3.1 27.7 - - - +
94F GLU* 3.6 30.1 + - - +
95F SER* 3.2 16.2 + - - +
97F LEU* 1.3 80.1 - - - +
99F ALA* 1.3 56.5 + - - +
101F GLU* 3.1 10.5 + - - +
102F CYS* 2.8 49.1 + - - -
168F PRO* 5.9 1.6 - - + -
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F MET* 3.5 18.8 - - + +
41F PHE* 3.5 37.7 - - + -
55F PHE* 3.7 8.8 - - + -
93F TRP* 4.0 16.4 - - + -
95F SER 3.2 6.0 + - - +
96F GLY 4.2 0.4 - - - +
98F ASN* 1.3 81.7 + - - +
100F MET* 1.3 60.7 + - - +
102F CYS* 3.5 5.3 + - - -
103F ALA* 3.1 20.6 + - - +
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Residues in contact with MET 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F PHE* 3.5 30.7 - - + -
54F TYR* 4.0 11.9 - - + -
55F PHE* 3.7 18.8 - - + -
96F GLY 3.0 16.3 + - - +
97F LEU 3.6 4.5 - - - +
99F ALA* 1.3 77.4 - - - +
101F GLU* 1.3 62.1 + - - +
103F ALA* 3.4 4.3 + - - +
104F LEU* 3.3 20.4 + - - +
155F LEU* 3.5 28.2 - - + +
158F HIS* 3.6 39.7 - - + -
159F VAL* 4.0 15.3 - - + +
162F LEU* 4.2 6.7 - - + -
177F PHE* 4.6 5.8 - - + -
182F LEU 5.1 2.5 - - - +
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Residues in contact with GLU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU* 2.9 30.5 + - - +
98F ASN* 3.6 9.6 + - - +
100F MET* 1.3 75.9 - - - +
102F CYS* 1.3 64.9 + - - +
104F LEU* 3.4 8.8 + - + +
105F HIS* 3.3 19.6 + - - +
159F VAL* 3.7 24.6 - - + +
163F ARG* 3.5 25.8 + - - -
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Residues in contact with CYS 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F MET* 3.7 20.2 - - + -
90F CYS* 6.0 1.1 - - - -
93F TRP* 3.9 20.9 - - + -
98F ASN* 2.8 44.1 + - - +
101F GLU* 1.3 77.1 - - - +
103F ALA* 1.3 61.4 + - - +
105F HIS* 3.1 10.2 + - - +
106F LEU* 3.0 23.0 + - - +
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TYR* 3.4 39.6 + - + +
37F MET* 4.0 4.6 - - - +
55F PHE* 3.9 7.6 - - + -
99F ALA 3.1 17.0 + - - +
100F MET 3.7 5.6 - - - +
101F GLU 3.3 0.4 - - - -
102F CYS* 1.3 76.6 - - - +
104F LEU* 1.3 56.7 + - - +
106F LEU* 3.3 4.5 + - - +
107F GLU* 3.0 27.4 + - - +
155F LEU* 3.6 17.7 - - + -
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Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F MET 3.3 10.1 + - - +
101F GLU* 3.7 13.2 - - + +
102F CYS 3.2 0.6 - - - -
103F ALA* 1.3 79.2 - - - +
105F HIS* 1.3 62.5 + - - +
107F GLU* 3.3 1.2 + - - +
108F LYS* 3.0 41.1 + - + +
152F ILE* 3.7 44.0 - - + +
155F LEU* 3.7 17.4 - - + +
156F GLY* 4.3 4.9 - - - +
159F VAL* 4.6 7.2 - - + -
7G GLN* 3.2 45.5 - - + +
8G VAL* 4.6 1.1 - - + -
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Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F GLU 3.3 8.5 + - - +
102F CYS* 3.1 12.2 + - - +
104F LEU* 1.3 78.5 - - - +
106F LEU* 1.3 64.0 + - - +
108F LYS* 3.5 10.7 + - - +
109F ASN* 3.1 52.5 + - - -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 5.1 3.8 - - + -
29F TYR* 3.9 32.3 - - + -
30F ALA* 3.6 36.8 - - + +
33F VAL* 4.1 18.8 - - + -
34F TYR* 3.9 22.9 - - + -
102F CYS 3.0 12.3 + - - +
103F ALA* 3.6 8.1 - - - +
104F LEU 3.2 0.2 - - - -
105F HIS* 1.3 80.2 - - - +
107F GLU* 1.3 57.3 + - - +
109F ASN* 3.0 12.7 + - + +
110F VAL* 2.8 35.6 + - + +
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ALA* 4.9 1.2 - - - +
34F TYR* 2.8 32.3 + - - +
58F GLN* 5.5 1.3 - - - +
62F GLU* 2.9 37.1 - - - +
103F ALA 3.0 13.4 + - - +
104F LEU 3.9 2.5 - - - +
106F LEU* 1.3 79.1 - - - +
108F LYS* 1.3 52.6 + - - +
110F VAL* 3.6 5.4 - - - +
111F ASN* 2.7 36.7 + - - +
148F GLN* 3.5 20.6 - - - +
151F ALA* 4.2 17.6 - - + +
152F ILE* 3.7 20.3 - - + +
155F LEU* 3.6 15.5 - - + -
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F LEU* 3.0 31.5 + - + +
105F HIS* 3.9 9.9 - - - +
107F GLU* 1.3 76.3 - - - +
109F ASN* 1.3 60.1 + - - +
112F GLN* 3.0 11.3 + - - +
152F ILE* 3.8 20.0 - - + -
7G GLN 3.3 27.3 + - - +
8G VAL 3.8 4.9 + - - -
9G ARG 3.5 22.4 + - - -
10G GLN* 2.5 48.8 + - - +
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Residues in contact with ASN 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 4.0 9.6 - - + +
105F HIS* 3.1 48.1 + - - -
106F LEU* 3.0 15.8 + - + +
108F LYS* 1.3 76.2 - - - +
110F VAL* 1.3 66.2 + - + +
112F GLN* 3.3 14.4 + - - +
113F SER* 3.2 27.2 + - - -
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Residues in contact with VAL 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLN* 2.8 29.1 + - - +
26F LEU* 3.9 26.0 - - + +
27F GLU* 3.2 35.4 - - + +
30F ALA* 4.1 24.5 - - + -
62F GLU* 4.2 4.5 - - - +
106F LEU* 2.8 27.3 + - + +
107F GLU* 3.7 9.2 - - - +
109F ASN* 1.3 70.7 - - - +
111F ASN* 1.3 63.2 + - - +
114F LEU* 3.0 7.0 + - + +
148F GLN* 3.8 15.7 - - - +
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Residues in contact with ASN 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU 2.7 21.2 + - - +
108F LYS 3.9 0.2 - - - +
110F VAL* 1.3 74.0 - - - +
112F GLN* 1.3 61.6 + - - +
114F LEU* 3.1 8.2 + - - +
115F LEU* 3.0 45.6 + - - +
145F ALA 4.9 1.9 - - - +
148F GLN* 3.5 33.3 + - + +
149F VAL* 4.7 13.1 - - - +
152F ILE* 3.7 10.5 - - + +
10G GLN* 2.6 32.4 + - - +
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Residues in contact with GLN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F LYS 3.0 17.8 + - - +
109F ASN* 3.7 16.1 - - - +
110F VAL 3.3 0.2 - - - -
111F ASN* 1.3 75.0 - - - +
113F SER* 1.3 67.2 + - - +
115F LEU* 3.2 19.1 + - - +
116F GLU* 3.3 28.4 + - - +
10G GLN* 3.4 17.0 + - + +
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Residues in contact with SER 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ALA 5.5 0.2 - - - +
22F ARG* 5.7 10.8 + - - -
23F GLN* 3.5 21.5 + - - +
26F LEU* 3.8 14.8 - - - +
109F ASN 3.2 13.2 + - - -
112F GLN* 1.3 79.7 + - - +
114F LEU* 1.3 60.6 + - - +
116F GLU* 3.5 14.9 + - - +
117F LEU* 3.2 20.4 + - - +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLN* 3.0 24.0 - - - +
27F GLU* 4.4 3.6 - - - +
69F LEU* 5.9 3.6 - - + -
110F VAL 3.0 19.1 + - - +
111F ASN* 3.1 19.7 + - - +
113F SER* 1.3 78.5 - - - +
115F LEU* 1.3 73.5 + - + +
117F LEU* 3.2 8.4 + - + +
118F HIS* 3.1 20.4 + - + +
143F VAL* 3.3 42.9 - - + +
145F ALA* 4.4 11.9 - - + -
148F GLN* 3.4 26.7 - - + +
127G PRO* 6.3 0.2 - - + -
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ASN* 3.0 41.8 + - - +
112F GLN* 3.2 8.9 + - - +
114F LEU* 1.3 84.6 - - + +
116F GLU* 1.3 61.9 + - - +
118F HIS* 3.2 6.3 + - - +
119F LYS* 3.0 25.6 + - - +
145F ALA* 5.3 4.5 - - + -
10G GLN* 5.0 3.6 - - + +
11G ASN* 3.5 34.8 - - + +
125G ASN* 3.8 15.2 + - - +
126G ASP* 6.0 0.2 - - - +
127G PRO* 3.9 29.2 - - + -
128G HIS* 5.5 4.0 - - + +
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Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ALA* 5.5 0.7 - - - -
22F ARG* 5.7 4.2 + - - +
112F GLN* 3.3 24.9 + - - +
113F SER* 3.8 18.1 + - - +
114F LEU 3.3 0.2 - - - -
115F LEU* 1.3 74.4 - - + +
117F LEU* 1.3 64.2 + - - +
119F LYS* 3.3 13.9 + - + +
120F LEU* 3.3 31.8 + - + +
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F SER* 5.0 3.4 - - - +
19F ALA* 3.4 40.3 - - + +
20F ILE* 3.6 33.0 - - + -
23F GLN* 3.6 20.0 - - + -
69F LEU* 4.6 10.3 - - + -
72F LEU* 5.2 4.0 - - + -
113F SER 3.2 11.1 + - - +
114F LEU* 3.2 11.5 + - + +
116F GLU* 1.3 78.9 - - - +
118F HIS* 1.3 60.7 + - - +
120F LEU* 3.7 14.3 + - - +
143F VAL* 3.8 26.0 - - + -
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Residues in contact with HIS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LEU* 3.1 12.7 + - + +
115F LEU* 3.2 9.1 + - + +
117F LEU* 1.3 77.8 - - - +
119F LYS* 1.3 64.5 + - - +
120F LEU 3.3 7.1 - - - +
141F GLU* 4.5 14.8 + - + +
143F VAL* 4.3 26.0 - - + -
125G ASN* 4.3 6.4 + - - -
127G PRO* 3.4 43.1 - - + +
130G CYS* 6.4 0.2 - - + -
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LEU 3.0 13.7 + - - +
116F GLU* 3.7 16.2 - - + +
117F LEU 3.3 0.4 - - - -
118F HIS* 1.3 74.5 - - - +
120F LEU* 1.3 70.4 + - + +
125G ASN* 3.5 36.5 + - + +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ASP* 4.2 23.1 - - + +
16F SER* 4.3 21.1 - - - -
19F ALA* 4.1 22.9 - - + -
22F ARG* 5.9 0.9 - - - +
116F GLU* 3.3 18.4 + - + +
117F LEU* 4.1 9.7 - - - +
118F HIS 3.3 10.7 - - - +
119F LYS* 1.3 87.7 - - + +
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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