Contacts of the helix formed by residues 97 - 128 (chain A) in PDB entry 1X1O
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 LEU 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.0 17.5 - - + -
41A LEU* 3.1 23.8 + - + +
42A GLU 4.3 0.7 - - - -
43A GLY* 4.0 20.0 - - - +
95A GLY 3.1 6.1 + - - -
96A PRO* 1.3 70.5 - - - +
98A ARG* 1.3 62.9 - - - +
100A ILE* 3.0 13.2 + - + +
101A LEU* 2.9 47.5 + - + +
283A VAL* 4.3 18.8 - - + -
286A PRO* 3.7 28.5 - - + -
174B ASN* 5.1 3.1 - - + +
178B ALA* 3.9 17.7 - - + -
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Residues in contact with ARG 98 (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 ASP* 4.7 2.1 - - - +
33A SER* 4.0 14.2 + - - +
34A LEU* 3.2 49.5 + - + +
37A VAL* 2.6 44.9 + - + +
38A PRO* 4.3 3.9 - - - +
39A GLU* 3.4 44.6 + - - +
69A ASP* 5.9 0.9 - - - +
96A PRO* 3.1 5.3 - - + -
97A LEU* 1.3 78.4 - - - +
99A GLY* 1.3 57.7 + - - +
101A LEU* 3.3 6.3 + - - +
102A ALA* 2.9 31.2 + - - +
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Residues in contact with GLY 99 (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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65A PHE* 4.3 2.9 - - - -
68A ALA* 3.5 13.8 - - - +
69A ASP* 3.7 27.9 + - - -
72A THR* 4.2 6.2 + - - -
96A PRO* 3.0 11.2 + - - +
98A ARG* 1.3 79.3 - - - +
100A ILE* 1.3 62.7 + - - +
102A ALA* 3.4 5.7 + - - -
103A GLY* 3.1 17.7 + - - -
11C GLN* 5.7 0.7 - - - -
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Residues in contact with ILE 100 (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 GLY* 3.7 35.4 - - - +
44A GLU* 4.3 1.6 - - - +
45A ALA* 4.7 4.9 - - + +
65A PHE* 3.5 11.1 - - + -
72A THR* 4.1 8.5 - - + -
93A VAL* 3.8 39.5 - - + +
95A GLY 3.8 12.8 - - - +
96A PRO 3.2 8.6 + - - +
97A LEU* 3.0 16.7 + - + +
99A GLY* 1.3 76.8 - - - +
101A LEU* 1.3 59.6 + - + +
103A GLY 3.3 0.7 + - - -
104A GLU* 2.9 28.6 + - - +
281A LEU* 3.9 23.6 - - + -
283A VAL* 5.4 1.3 - - + -
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Residues in contact with LEU 101 (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 ASP* 4.2 2.7 - - - +
33A SER* 3.4 26.9 - - - +
37A VAL* 4.2 8.7 - - + -
97A LEU* 2.9 44.8 + - + +
98A ARG 3.8 3.4 - - - +
100A ILE* 1.3 78.8 - - + +
102A ALA* 1.3 61.2 + - - +
103A GLY 3.6 0.2 + - - -
104A GLU* 3.8 21.5 + - - +
105A ARG 4.7 2.1 + - - -
281A LEU* 5.7 0.2 - - + -
283A VAL* 4.8 4.5 - - + -
139B ARG* 5.3 1.7 + - - -
165B LEU* 4.3 9.9 - - - +
174B ASN* 3.9 37.5 - - + +
175B HIS* 3.9 20.6 - - + +
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Residues in contact with ALA 102 (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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22A LEU* 3.8 6.9 - - - +
25A ASP* 4.6 4.2 - - - +
26A LEU* 3.3 32.3 - - + +
30A ASP* 4.3 12.5 + - + +
68A ALA* 4.1 12.1 - - + -
98A ARG 2.9 17.6 + - - +
99A GLY* 3.7 7.2 - - - +
100A ILE 3.2 0.2 - - - -
101A LEU* 1.3 79.7 - - - +
103A GLY* 1.3 58.1 + - - +
105A ARG* 5.1 1.6 + - - +
106A LEU* 5.5 1.2 + - - +
139B ARG* 5.7 0.2 + - - -
165B LEU* 4.5 2.6 - - - +
11C GLN* 4.1 18.8 - - - +
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Residues in contact with GLY 103 (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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22A LEU* 4.5 7.9 - - - -
64A VAL* 4.4 6.0 - - - +
65A PHE* 3.8 13.5 - - - -
68A ALA* 3.8 12.5 - - - +
99A GLY 3.1 14.1 + - - -
100A ILE 3.9 0.9 - - - -
102A ALA* 1.3 77.9 - - - +
104A GLU* 1.3 65.2 + - - +
105A ARG 3.4 1.9 + - - -
106A LEU* 3.5 4.3 + - - +
107A ALA* 3.0 24.9 + - - +
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Residues in contact with GLU 104 (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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65A PHE* 3.6 10.5 - - - -
100A ILE 2.9 18.1 + - - +
101A LEU* 3.9 18.4 - - - +
102A ALA 3.6 1.0 - - - -
103A GLY* 1.3 75.7 - - - +
105A ARG* 1.3 74.8 + - + +
108A LEU* 2.9 33.9 + - + +
281A LEU* 3.4 44.9 + - + +
172B LYS* 6.0 1.8 - - - +
174B ASN* 3.6 22.1 + - - -
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Residues in contact with ARG 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP* 3.9 9.4 - - - +
101A LEU 4.7 2.2 + - - +
102A ALA 5.1 1.0 + - - +
103A GLY 3.5 0.4 - - - -
104A GLU* 1.3 88.9 + - + +
106A LEU* 1.3 59.2 + - - +
108A LEU* 3.8 18.5 - - - +
109A ASN* 2.9 34.7 + - + +
112A GLN* 3.7 22.4 + - - +
139B ARG* 3.1 71.4 + - + +
140B LYS* 4.0 33.6 - - - +
146B ARG* 4.8 1.3 - - - +
272B HIS* 6.0 0.6 - - - -
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Residues in contact with LEU 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 6.3 - - - +
21A TRP* 3.7 14.1 - - + +
22A LEU* 3.5 49.8 - - + +
25A ASP* 5.0 7.5 + - + +
64A VAL* 4.2 15.9 - - + -
102A ALA 5.5 0.6 + - - +
103A GLY 3.5 5.6 + - - +
104A GLU 3.4 0.4 - - - -
105A ARG* 1.3 76.0 - - - +
107A ALA* 1.3 67.0 + - - +
109A ASN* 3.3 2.6 + - + +
110A LEU* 3.0 37.8 + - + +
143B PRO* 3.7 34.5 - - + -
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Residues in contact with ALA 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 4.1 11.0 - - + +
64A VAL* 3.1 32.5 - - + +
65A PHE* 3.5 25.1 - - + -
103A GLY 3.0 16.4 + - - +
104A GLU 3.7 2.7 - - - +
106A LEU* 1.3 78.5 - - - +
108A LEU* 1.3 60.9 + - + +
110A LEU* 3.4 3.0 + - - +
111A LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.1 33.7 - - + -
65A PHE* 4.5 3.6 - - + -
104A GLU* 2.9 24.9 + - + +
105A ARG* 3.8 16.8 - - - +
107A ALA* 1.3 81.1 - - + +
109A ASN* 1.3 61.9 + - - +
111A LEU* 4.2 6.3 - - + -
112A GLN* 2.7 40.6 + - + +
279A LEU* 3.9 34.5 - - + +
280A SER* 4.1 6.7 - - - -
281A LEU* 4.3 22.0 - - + +
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Residues in contact with ASN 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 2.9 26.1 + - + +
106A LEU* 3.3 8.7 + - + +
108A LEU* 1.3 76.4 - - - +
110A LEU* 1.3 57.8 + - - +
112A GLN* 4.0 9.2 + - - +
113A ARG* 3.0 30.8 + - - +
139B ARG 4.7 1.8 + - - -
140B LYS* 4.2 7.5 - - - +
141B THR 2.5 40.0 + - - +
142B THR* 4.8 0.7 - - - -
143B PRO* 3.3 25.2 - - + +
272B HIS* 5.6 7.1 + - - -
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Residues in contact with LEU 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.8 18.2 - - + -
21A TRP* 4.2 15.5 - - + -
57A GLY 5.9 0.4 - - - +
60A VAL* 3.8 30.1 - - + -
61A ALA 5.9 1.1 - - - +
64A VAL* 4.0 8.7 - - + -
106A LEU* 3.0 35.9 + - + +
107A ALA 3.8 2.7 - - - +
109A ASN* 1.3 75.7 - - - +
111A LEU* 1.3 65.9 + - - +
113A ARG* 3.2 3.9 + - + +
114A LEU* 2.9 40.3 + - + +
145A LEU* 4.7 10.5 - - + -
148A LEU* 4.4 13.0 - - + -
143B PRO* 4.0 18.4 - - + -
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Residues in contact with LEU 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.9 35.7 - - + -
55A LEU* 4.3 3.1 - - + -
56A ALA 3.3 23.5 - - - +
57A GLY 3.6 23.5 + - - +
58A LEU* 3.7 23.6 - - + +
61A ALA* 4.5 8.2 - - + +
90A VAL* 4.7 2.5 - - + -
107A ALA 2.9 17.7 + - - +
108A LEU* 3.8 8.3 - - + +
110A LEU* 1.3 76.4 - - - +
112A GLN* 1.3 57.5 + - - +
115A SER* 2.6 39.4 + - - +
279A LEU* 3.6 22.0 - - + -
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Residues in contact with GLN 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 3.7 19.2 + - - +
108A LEU* 2.7 32.1 + - - +
109A ASN* 4.0 4.6 - - - +
111A LEU* 1.3 72.8 - - - +
113A ARG* 1.3 58.1 + - - +
115A SER* 4.5 0.4 - - - -
116A GLY 2.9 23.2 + - - -
276A ALA* 3.6 10.5 - - + -
277A LEU 3.0 32.5 + - - +
278A ASP* 4.2 5.5 + - - +
279A LEU* 2.8 50.0 + - + +
272B HIS* 3.8 25.7 + - + -
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Residues in contact with ARG 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.0 24.2 + - - +
110A LEU* 3.2 7.2 + - + +
112A GLN* 1.3 76.9 - - - +
114A LEU* 1.3 74.7 + - + +
116A GLY* 3.3 2.4 + - - -
117A ILE* 3.1 35.8 + - - +
142A THR* 3.2 10.1 + - - -
145A LEU* 4.7 13.6 - - + +
149A GLU* 2.6 30.6 + - - +
271A THR 2.7 28.5 + - - -
272A HIS 5.3 1.2 - - - -
273A SER 5.5 0.4 - - - +
274A ALA 3.5 28.3 + - - +
276A ALA* 4.5 9.1 - - - +
143B PRO* 6.3 0.4 - - + -
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Residues in contact with LEU 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.6 15.3 - - + +
57A GLY* 4.1 19.7 - - - +
60A VAL* 4.5 5.2 - - + -
110A LEU* 2.9 26.9 + - + +
113A ARG* 1.3 84.7 - - + +
115A SER* 1.3 61.3 + - - +
117A ILE* 3.2 3.3 + - + -
118A ALA* 2.9 26.7 + - - +
145A LEU* 5.8 2.0 - - + -
148A LEU* 3.6 57.9 - - + +
149A GLU* 4.3 7.6 - - + +
151A TYR* 5.3 3.8 - - + -
152A ALA* 3.5 20.0 - - + +
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Residues in contact with SER 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL 3.1 19.0 + - - +
55A LEU* 3.7 12.1 - - - +
56A ALA* 3.2 22.6 + - - +
111A LEU 2.6 25.5 + - - -
114A LEU* 1.3 76.2 - - - +
116A GLY* 1.3 58.1 + - - +
118A ALA 3.3 0.5 + - - -
119A THR* 2.8 35.6 + - - -
277A LEU* 3.6 23.3 - - - -
279A LEU* 3.9 1.6 - - - +
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Residues in contact with GLY 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN 2.9 17.6 + - - -
113A ARG 3.7 1.8 - - - -
114A LEU 3.2 0.2 - - - -
115A SER* 1.3 78.4 - - - +
117A ILE* 1.3 60.6 + - - +
119A THR* 3.5 5.5 + - - -
120A LEU* 3.1 24.1 + - - +
274A ALA* 3.9 6.2 - - - +
275A LYS 3.3 25.2 - - - +
276A ALA* 4.3 0.4 - - - -
277A LEU* 3.8 8.7 - - - +
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Residues in contact with ILE 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.1 40.3 + - + +
114A LEU* 3.2 10.5 + - + +
116A GLY* 1.3 73.7 - - - +
118A ALA* 1.3 65.2 + - - +
119A THR 3.3 0.2 + - - -
120A LEU* 3.3 2.3 + - - +
121A THR* 2.9 29.8 + - - +
149A GLU* 3.4 39.5 - - + +
152A ALA* 3.7 14.1 - - + -
153A VAL* 3.9 24.9 - - + +
270A LEU 3.4 26.5 - - - +
271A THR* 4.5 2.5 - - + -
274A ALA* 4.0 5.8 - - + -
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Residues in contact with ALA 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.8 22.6 - - + +
56A ALA* 3.8 15.9 - - + -
114A LEU 2.9 15.4 + - - +
115A SER 3.7 4.0 - - - +
117A ILE* 1.3 77.0 - - - +
119A THR* 1.3 57.5 + - - +
121A THR* 3.4 0.6 + - - -
122A ARG* 2.9 27.4 + - - +
152A ALA 3.6 22.2 + - - +
155A VAL* 4.2 0.4 - - + -
156A GLY* 3.5 14.6 - - - +
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Residues in contact with THR 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 4.9 1.8 - - - +
53A GLY* 3.6 17.9 - - - -
54A VAL* 2.8 32.6 + - + +
83A ARG* 5.2 2.7 + - - +
115A SER 2.8 22.2 + - - -
116A GLY* 3.7 7.4 - - - -
117A ILE 3.2 0.2 - - - -
118A ALA* 1.3 74.2 - - - +
120A LEU* 1.3 65.9 + - - +
122A ARG* 3.3 4.0 + - - +
123A ALA* 3.1 20.4 + - - +
277A LEU* 4.0 11.2 - - + +
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Residues in contact with LEU 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLY 3.1 15.0 + - - +
117A ILE 3.9 2.2 - - - +
119A THR* 1.3 77.3 - - - +
121A THR* 1.3 66.5 + - - +
123A ALA* 3.0 14.3 + - + +
124A TYR* 3.0 49.7 + - + -
251A LEU* 5.2 4.9 - - + -
269A ALA* 3.7 35.0 - - + +
270A LEU* 4.1 4.9 - - + +
273A SER 4.9 2.0 - - - +
274A ALA* 3.8 20.4 - - + +
275A LYS 5.3 0.9 - - - +
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Residues in contact with THR 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 2.9 24.5 + - - +
118A ALA* 3.7 4.9 - - - -
120A LEU* 1.3 77.6 - - - +
122A ARG* 1.3 62.6 + - - +
124A TYR* 3.0 4.0 + - - +
125A VAL* 2.9 22.6 + - + +
135A ILE* 4.7 1.3 - - + -
153A VAL* 3.4 41.6 - - + +
156A GLY* 4.0 4.7 - - - -
158A GLY* 3.5 24.2 - - - +
270A LEU* 3.5 30.5 - - + +
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Residues in contact with ARG 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.6 24.7 - - + +
81A GLY 2.6 27.6 + - - -
82A ALA* 4.3 0.4 - - - +
83A ARG* 3.4 44.6 - - - +
118A ALA 2.9 17.9 + - - +
119A THR 3.7 5.2 - - - +
120A LEU 3.3 0.2 - - - -
121A THR* 1.3 77.3 - - - +
123A ALA* 1.3 63.0 + - - +
125A VAL* 3.3 5.8 + - + +
126A GLU* 3.0 39.0 + - + +
155A VAL 3.1 26.1 + - - -
156A GLY 3.1 21.7 + - - +
157A GLY* 5.4 0.2 - - - -
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Residues in contact with ALA 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG* 4.8 1.7 - - - +
119A THR 3.1 12.2 + - - +
120A LEU* 3.0 18.9 + - + +
122A ARG* 1.3 77.8 - - - +
124A TYR* 1.3 60.6 + - - +
126A GLU* 3.5 11.3 + - - +
127A ALA* 3.1 22.7 + - - +
251A LEU* 3.7 24.1 - - + +
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Residues in contact with TYR 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.0 46.5 + - + -
121A THR 3.0 7.2 + - - +
123A ALA* 1.3 74.1 - - - +
125A VAL* 1.3 66.5 + - - +
127A ALA* 3.2 9.9 + - - +
128A LEU* 3.3 21.7 + - - +
135A ILE* 3.4 19.3 - - + -
249A MET* 3.5 8.5 + - + -
250A THR* 3.3 44.6 - - - -
251A LEU* 3.6 21.5 + - + +
254A ALA* 3.7 22.7 - - + -
267A VAL* 3.7 31.2 - - + +
269A ALA* 4.4 4.9 - - - +
270A LEU* 3.6 13.0 - - + -
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Residues in contact with VAL 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR 2.9 17.7 + - - +
122A ARG* 3.3 11.4 + - + +
124A TYR* 1.3 76.1 - - - +
126A GLU* 1.3 61.1 + - + +
128A LEU* 3.0 21.6 + - - +
129A ALA* 3.4 8.1 + - - +
135A ILE* 4.0 15.3 - - + +
156A GLY 4.0 6.1 - - - +
157A GLY* 3.5 37.0 - - - +
158A GLY* 3.9 7.0 - - - +
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Residues in contact with GLU 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG* 2.9 44.0 + - - -
122A ARG* 3.0 22.2 + - + +
123A ALA* 3.9 9.1 - - - +
125A VAL* 1.3 79.9 - - + +
127A ALA* 1.3 62.7 + - - +
129A ALA* 3.1 24.8 + - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ALA 3.1 14.7 + - - +
124A TYR* 3.4 14.4 - - - +
125A VAL 3.2 0.2 - - - -
126A GLU* 1.3 76.2 - - - +
128A LEU* 1.3 63.2 + - + +
129A ALA 3.4 2.5 + - - +
131A THR* 5.8 0.3 - - - +
251A LEU* 4.1 29.4 - - + +
254A ALA* 5.4 0.4 - - + -
255A LYS* 3.4 34.2 - - + +
258A ALA* 5.4 0.3 - - - +
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Residues in contact with LEU 128 (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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124A TYR 3.4 12.1 - - - +
125A VAL* 3.0 11.8 + - - +
127A ALA* 1.3 80.7 - - + +
129A ALA* 1.3 64.7 + - - +
130A GLY 3.5 0.2 + - - -
131A THR* 2.7 33.7 + - - +
133A ALA* 3.5 36.5 - - + +
134A GLN* 3.9 6.3 - - - +
135A ILE* 3.7 32.3 - - + -
254A ALA* 3.6 31.4 - - + +
258A ALA* 3.6 16.6 - - + -
265A VAL* 4.3 6.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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