Contacts of the helix formed by residues 113 - 139 (chain D) in PDB entry 1F33
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 ASN 113 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ARG 3.4 8.6 - - - +
56D GLY* 5.0 5.0 - - - -
57D ALA 5.5 0.9 + - - -
112D HIS* 1.3 81.2 - - - +
114D VAL* 1.3 66.8 + - - +
115D GLN* 2.8 47.7 - - - +
116D ASP* 3.1 33.1 + - - +
117D HIS* 3.2 12.3 + - - -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D MET* 4.4 13.0 - - + -
55D ARG 2.9 37.0 + - - +
56D GLY 3.8 6.3 - - - +
57D ALA 3.4 28.9 - - - +
58D ASN* 4.3 1.6 - - + +
59D PHE* 4.2 10.8 - - - -
62D VAL* 4.3 22.9 - - + -
112D HIS 4.1 1.8 - - - -
113D ASN* 1.3 73.8 - - - +
115D GLN* 1.3 64.0 + - + +
117D HIS* 3.2 4.6 + - - +
118D LEU* 2.8 45.9 + - + +
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA* 5.3 4.5 + - + -
58D ASN* 5.9 2.6 - - - +
113D ASN* 2.8 22.8 - - - +
114D VAL* 1.3 78.5 - - + +
116D ASP* 1.3 62.1 + - - +
118D LEU* 3.3 12.4 + - - +
119D LYS* 3.0 41.9 + - - +
165D ASN 3.2 22.2 + - - -
166D ILE* 3.3 13.1 - - - +
167D GLU* 2.8 54.4 + - + +
57E ALA* 5.8 0.6 - - - +
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Residues in contact with ASP 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 4.2 28.5 - - + +
112D HIS 4.8 0.5 + - - -
113D ASN* 3.1 32.7 + - - +
115D GLN* 1.3 77.6 - - - +
117D HIS* 1.3 58.6 + - - +
119D LYS* 3.2 16.1 + - - +
120D GLU* 2.9 32.2 + - + +
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Residues in contact with HIS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLN* 4.5 2.0 - - - -
50D ALA* 3.4 23.9 - - + -
53D ASN* 3.4 19.0 + - + -
54D MET* 3.7 27.8 - - + -
107D TYR* 2.6 32.4 + + - +
108D PRO 5.0 1.6 - - - -
111D ILE* 3.3 40.6 + - + +
112D HIS* 3.4 23.1 - - - -
113D ASN 3.2 9.1 + - - -
114D VAL 3.6 6.1 - - - +
116D ASP* 1.3 75.7 - - - +
118D LEU* 1.3 56.2 + - - +
120D GLU 3.2 0.5 + - - -
121D LEU* 2.7 41.5 + - - +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D MET* 5.1 1.1 - - + -
58D ASN* 5.8 0.4 - - - +
62D VAL* 3.8 26.7 - - + -
65D MET* 5.1 3.6 - - + -
66D LEU* 5.5 0.4 - - + -
114D VAL* 2.8 34.0 + - + +
115D GLN* 3.5 15.0 - - - +
116D ASP 3.2 0.2 - - - -
117D HIS* 1.3 76.9 - - - +
119D LYS* 1.3 57.3 + - - +
121D LEU* 4.5 10.3 - - + -
122D ALA* 2.8 30.1 + - - +
162D ILE* 3.3 37.8 - - + +
165D ASN* 3.7 34.1 - - + +
166D ILE* 3.9 10.1 - - + -
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLN* 3.0 34.7 + - - +
116D ASP* 3.7 12.8 + - - +
118D LEU* 1.3 74.4 - - - +
120D GLU* 1.3 67.1 + - + +
122D ALA* 3.3 7.0 + - - +
123D ASP* 3.1 31.0 + - - +
166D ILE* 4.0 32.5 - - + -
167D GLU 5.7 0.7 - - - -
18F ARG* 4.4 8.9 + - - +
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D TYR* 3.5 26.0 - - + +
108D PRO* 3.9 11.1 - - + +
111D ILE* 3.7 21.1 - - + +
116D ASP* 2.9 19.8 + - + +
119D LYS* 1.3 78.4 - - - +
121D LEU* 1.3 62.1 + - - +
123D ASP* 3.4 12.6 + - - +
124D ARG* 2.9 52.8 + - - +
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 3.8 27.6 - - + +
47D THR* 4.2 9.0 - - - -
50D ALA* 3.6 31.2 - - + -
54D MET* 4.7 0.9 - - + -
66D LEU* 3.7 32.3 - - + -
107D TYR* 4.0 2.9 - - + +
117D HIS 2.7 31.5 + - - +
118D LEU* 3.7 11.9 - - + +
120D GLU* 1.3 71.4 - - - +
122D ALA* 1.3 56.6 + - - +
124D ARG* 3.2 3.9 + - - +
125D TYR* 2.7 50.9 + - + -
162D ILE* 4.1 12.3 - - + -
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU 2.8 18.3 + - - +
119D LYS* 3.5 5.2 - - - +
121D LEU* 1.3 74.4 - - - +
123D ASP* 1.3 56.6 + - - +
125D TYR* 4.6 0.7 - - - -
126D ALA* 2.8 32.7 + - - +
159D LEU* 3.5 9.1 - - - +
162D ILE* 3.9 14.8 - - + +
163D GLU* 4.3 5.2 - - + -
166D ILE* 4.3 5.2 - - + -
18F ARG* 3.4 35.6 - - - +
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LYS* 3.1 15.1 + - - +
120D GLU* 3.5 16.2 - - - +
121D LEU 3.1 0.2 - - - -
122D ALA* 1.3 77.5 - - - +
124D ARG* 1.3 69.6 + - - +
126D ALA* 3.3 4.8 + - - +
127D ILE* 3.1 30.6 + - + +
18F ARG* 2.7 36.7 + - - +
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.8 18.4 - - + -
46D ILE* 4.2 11.9 - - + +
104D LEU* 3.8 18.5 - - + +
105D LYS* 2.9 55.2 + - - +
106D SER 3.7 4.2 + - - -
107D TYR* 2.9 35.9 - - - +
108D PRO* 3.6 14.3 - - - +
120D GLU* 2.9 40.9 + - - +
121D LEU* 3.2 7.1 + - - +
123D ASP* 1.3 76.9 - - - +
125D TYR* 1.3 65.8 + - - +
127D ILE* 3.2 10.5 + - - +
128D VAL* 3.1 25.8 + - - +
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Residues in contact with TYR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.5 36.1 - - + -
47D THR* 2.6 32.0 + - + +
66D LEU* 5.5 0.4 - - + -
69D PHE* 3.6 17.2 - + - +
73D LEU* 3.4 11.9 - - + +
121D LEU* 2.7 42.0 + - + +
122D ALA 3.8 2.9 - - - +
124D ARG* 1.3 73.7 - - - +
126D ALA* 1.3 51.8 + - - +
128D VAL* 3.3 1.4 + - - +
129D ALA* 2.6 39.9 + - - +
155D LEU* 4.2 9.3 - - + +
158D PHE* 3.8 36.3 - + + -
159D LEU* 4.2 13.7 - - + -
162D ILE* 3.5 26.7 - - + -
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ALA 2.8 19.4 + - - +
123D ASP 3.4 5.8 - - - +
125D TYR* 1.3 76.5 - - - +
127D ILE* 1.3 58.2 + - + +
129D ALA* 4.2 0.4 - - - -
130D ASN* 2.8 45.4 + - - +
159D LEU* 3.9 14.1 - - + +
18F ARG* 3.3 33.9 - - + +
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLN* 4.2 10.8 - - - +
103D PRO* 4.5 17.9 - - + +
104D LEU* 3.8 24.5 - - + -
105D LYS* 5.5 2.9 - - + +
123D ASP* 3.1 18.4 + - + +
124D ARG* 3.2 13.2 + - - +
126D ALA* 1.3 76.1 - - + +
128D VAL* 1.3 63.4 + - - +
130D ASN* 4.2 4.0 - - - +
131D ASP* 3.1 27.4 + - + +
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLN* 3.3 38.8 - - + +
40D PHE* 3.6 27.8 - - + -
43D LEU* 4.0 13.2 - - + -
104D LEU* 3.8 20.0 - - + -
124D ARG 3.1 14.1 + - - +
125D TYR 3.9 2.5 - - - +
127D ILE* 1.3 73.7 - - - +
129D ALA* 1.3 66.5 + - - +
131D ASP* 3.8 0.3 - - - +
132D VAL* 2.9 24.3 + - - +
155D LEU* 3.5 23.1 - - + -
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D TYR 2.6 24.3 + - - +
126D ALA* 3.7 5.6 - - - +
128D VAL* 1.3 72.3 - - - +
130D ASN* 1.3 62.0 + - - +
132D VAL* 3.2 9.9 - - - +
133D ARG* 3.0 31.2 + - - +
155D LEU* 3.8 23.1 - - + +
156D ASP* 3.6 17.7 - - - +
159D LEU* 4.4 9.6 - - + -
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Residues in contact with ASN 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA* 2.8 31.9 + - - +
127D ILE* 4.2 3.5 - - - +
129D ALA* 1.3 73.0 - - - +
131D ASP* 1.3 63.5 + - - +
133D ARG* 2.4 35.2 + - - +
134D LYS* 3.3 31.6 + - - +
18F ARG 2.9 22.4 + - - -
19F ASN* 3.4 4.2 - - - -
20F ASP* 2.6 37.9 + - - +
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Residues in contact with ASP 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 2.8 40.4 + - - -
36D GLN* 3.6 2.7 - - - +
39D GLN* 3.1 26.5 + - - +
127D ILE* 3.1 20.7 + - + +
128D VAL 3.8 2.5 - - - +
129D ALA 3.3 0.2 - - - -
130D ASN* 1.3 74.3 - - - +
132D VAL* 1.3 66.6 + - - +
134D LYS* 3.0 11.7 + - - +
135D ALA* 3.0 16.3 + - - +
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLN* 3.6 28.0 + - - +
40D PHE* 4.3 19.7 - - + -
128D VAL 2.9 16.5 + - - +
129D ALA* 3.2 17.0 - - - +
131D ASP* 1.3 76.8 - - - +
133D ARG* 1.3 67.1 + - - +
135D ALA* 3.1 10.7 + - - +
136D ILE* 3.3 13.2 + - - +
148D LEU* 3.9 35.7 - - + +
151D ALA* 4.7 0.7 - - + -
152D SER* 4.0 20.0 - - - +
155D LEU* 4.8 2.7 - - + -
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ALA* 3.0 23.7 + - - +
130D ASN* 2.4 34.1 + - - +
131D ASP 3.2 0.4 - - - -
132D VAL* 1.3 82.0 - - - +
134D LYS* 1.3 63.6 + - + +
136D ILE* 3.3 23.9 - - + +
137D GLY 4.3 1.0 + - - -
152D SER* 3.7 14.1 - - - +
156D ASP* 2.6 43.4 + - - -
19F ASN* 2.9 23.6 + - - +
20F ASP* 3.2 13.7 + - - -
21F VAL* 3.2 20.0 - - - +
83F ARG* 3.9 10.1 - - - +
141F ASP* 4.2 7.9 - - - +
142F ASP* 4.3 7.1 - - + +
143F ASP* 3.9 8.7 - - - +
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASN* 3.3 17.6 + - - +
131D ASP* 3.0 10.5 + - - +
133D ARG* 1.3 75.8 - - + +
135D ALA* 1.3 67.1 + - - +
136D ILE 3.0 3.5 + - - -
137D GLY* 3.1 12.0 + - - +
138D GLU* 3.2 14.8 + - - +
20F ASP* 2.2 47.5 + - - -
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.9 19.8 - - + +
35D ARG* 4.3 3.8 - - - +
36D GLN* 3.6 23.1 - - - +
131D ASP 3.0 8.5 + - - +
132D VAL* 3.1 10.7 + - - +
134D LYS* 1.3 76.6 - - - +
136D ILE* 1.3 56.9 + - - +
138D GLU* 3.1 14.1 + - - +
139D ALA* 2.8 31.2 + - - +
148D LEU* 3.7 12.4 - - + +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D VAL 3.3 9.7 + - - +
133D ARG* 3.3 17.3 - - + +
134D LYS 3.0 0.2 - - - -
135D ALA* 1.3 76.5 - - - +
137D GLY* 1.3 63.5 + - - +
139D ALA* 3.2 20.7 + - - +
145D ALA* 4.0 14.8 - - + +
148D LEU* 3.9 21.5 - - + +
149D THR* 3.4 29.2 - - - +
152D SER* 3.6 13.0 - - - +
142F ASP* 3.7 28.3 - - + +
143F ASP* 3.3 26.9 - - - +
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Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ARG 4.3 0.4 + - - -
134D LYS 3.1 6.8 + - - -
136D ILE* 1.3 81.4 - - - +
138D GLU* 1.3 60.3 + - - +
139D ALA 3.4 4.3 + - - +
142F ASP* 4.1 10.5 + - - -
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Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.6 28.0 - - + +
35D ARG* 3.8 13.8 + - - -
134D LYS* 3.2 13.5 + - - +
135D ALA* 3.1 13.8 + - - +
137D GLY* 1.3 76.2 - - - +
139D ALA* 1.3 61.3 + - - +
140D LYS* 3.5 11.6 + - - +
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 4.1 10.8 - - + -
135D ALA 2.8 11.3 + - - +
136D ILE 3.4 16.1 - - - +
137D GLY 3.2 5.3 - - - +
138D GLU* 1.3 76.9 - - - +
140D LYS* 1.3 65.2 + - - +
141D ASP 4.4 0.9 - - - +
144D THR* 4.4 6.7 - - + -
145D ALA* 3.9 31.9 - - - +
148D LEU* 4.1 10.5 - - + -
----------------------------------------------------------
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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