Contacts of the helix formed by residues 113 - 143 (chain L) in PDB entry 2X17
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 ASP 113 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L LEU* 3.8 12.2 - - - +
3L SER 5.2 0.7 + - - -
6L MET* 3.8 15.3 - - + +
64L ARG* 4.4 6.5 + - - -
108L ALA* 2.8 24.5 + - - +
111L GLU* 3.1 16.5 - - + +
112L LYS* 1.3 71.8 - - - +
114L TYR* 1.3 61.3 + - - +
115L SER* 3.6 10.9 + - - -
116L THR* 2.7 34.1 + - - +
117L ARG* 3.2 18.2 + - - +
102Q TYR* 5.2 1.7 + - - -
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Residues in contact with TYR 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L LYS* 3.1 46.5 + - + +
113L ASP* 1.3 74.7 + - - +
115L SER* 1.3 56.9 + - - +
117L ARG* 3.7 8.9 - - + +
118L ALA* 2.8 32.7 + - - +
102Q TYR* 3.5 54.0 - + + -
105Q ALA* 4.0 9.0 - - + -
106Q ALA* 3.6 18.8 - - + +
109Q GLU* 3.0 36.9 + - - -
117Q ARG* 3.4 22.7 + - - -
124Q ILE* 3.5 14.2 - - + +
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Residues in contact with SER 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L TYR* 3.0 17.6 + - - -
64L ARG* 3.3 28.4 + - - -
113L ASP* 3.2 3.7 + - - -
114L TYR* 1.3 79.3 - - - +
116L THR* 1.3 57.6 + - - +
118L ALA* 3.9 1.9 - - - +
119L PHE* 3.0 24.8 + - - +
102Q TYR* 2.7 28.3 + - - -
124Q ILE* 3.8 11.4 + - - +
125Q ASN* 5.0 0.7 - - - +
128Q VAL* 3.7 16.5 - - - +
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Residues in contact with THR 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L LEU* 3.6 9.0 - - - +
6L MET* 3.9 22.0 - - + -
10L LEU* 4.0 19.7 - - + -
60L TYR* 2.9 20.7 + - + -
108L ALA* 4.1 4.9 - - + -
113L ASP* 2.7 32.7 + - - -
115L SER* 1.3 73.0 - - - +
117L ARG* 1.3 62.1 + - - +
119L PHE* 3.3 1.7 + - + +
120L LEU* 2.9 45.2 + - + +
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Residues in contact with ARG 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L ALA* 3.6 31.2 - - - +
108L ALA* 3.7 10.2 - - + +
109L GLU* 3.0 30.7 + - + +
113L ASP 3.2 16.8 + - - +
114L TYR* 3.7 9.9 - - + +
116L THR* 1.3 77.2 - - - +
118L ALA* 1.3 59.1 + - - +
120L LEU* 3.4 11.4 + - - +
121L GLU* 3.2 31.1 + - - +
124L ILE* 3.5 17.2 - - - +
114N TYR* 3.5 27.0 + - - +
117N ARG* 5.2 11.1 - - - +
118N ALA* 5.9 0.6 - - - +
117Q ARG* 5.4 9.4 - - - +
121Q GLU* 5.0 2.8 + - - +
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Residues in contact with ALA 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L TYR 2.8 18.8 + - - +
115L SER 3.9 2.7 - - - +
117L ARG* 1.3 73.6 - - - +
119L PHE* 1.3 65.0 + - - +
121L GLU* 3.4 15.6 - - - +
122L TRP* 4.5 1.0 + - - +
117Q ARG* 5.9 0.6 - - - +
121Q GLU* 3.6 25.8 - - - +
124Q ILE* 3.8 17.5 - - + -
125Q ASN* 3.5 30.8 + - - +
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Residues in contact with PHE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L LEU* 4.4 3.8 - - + -
56L ARG* 3.5 29.6 - - + -
57L PHE* 3.6 32.5 - + - -
60L TYR* 3.5 48.9 - + + -
115L SER 3.0 19.0 + - - +
116L THR 3.5 6.1 - - - +
118L ALA* 1.3 77.6 - - - +
120L LEU* 1.3 67.6 + - + +
121L GLU 3.2 1.3 + - - -
122L TRP* 3.5 18.9 + - + +
123L PHE* 3.5 29.4 - + - -
125Q ASN* 4.0 5.3 + - - +
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Residues in contact with LEU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L LEU* 5.2 0.4 - - + -
57L PHE* 4.2 21.5 - - + -
101L ILE* 4.4 15.5 - - + -
104L LEU* 3.6 60.6 - - + +
105L ALA* 3.7 8.5 - - + +
116L THR* 2.9 34.5 + - + +
117L ARG* 3.8 11.4 - - - +
118L ALA 3.3 0.8 - - - -
119L PHE* 1.3 80.9 - - + +
121L GLU* 1.3 63.8 + - - +
122L TRP 3.2 0.2 - - - -
123L PHE* 3.1 19.1 + - + +
124L ILE* 3.1 20.6 + - + +
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Residues in contact with GLU 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L ARG* 3.2 33.8 + - - +
118L ALA 3.4 14.8 - - - +
119L PHE 3.2 0.6 - - - -
120L LEU* 1.3 77.7 - - - +
122L TRP* 1.3 60.3 + - - +
124L ILE* 3.5 12.6 + - - +
125L ASN* 2.9 41.2 + - - +
117N ARG* 4.8 1.2 + - - +
118N ALA* 3.7 29.1 - - - +
121N GLU* 4.4 21.0 - - + +
121Q GLU* 4.6 15.8 - - + +
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Residues in contact with TRP 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1703 MET* 4.1 23.3 - - + -
1713 GLN 3.7 19.9 + - - -
53L HIS* 3.6 31.6 - + - -
56L ARG* 3.4 47.9 - - - +
118L ALA 4.5 0.6 + - - -
119L PHE* 3.5 13.5 + - + +
120L LEU 3.2 0.4 - - - -
121L GLU* 1.3 80.7 - - - +
123L PHE* 1.3 80.4 + + + +
125L ASN* 3.5 6.1 + - - +
126L GLU* 3.0 40.0 + - + +
1173L AG 3.9 9.6 - - - -
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Residues in contact with PHE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L GLU* 4.3 8.3 - - - -
53L HIS* 3.6 32.8 - - + -
56L ARG* 3.7 14.1 - - + -
57L PHE* 3.4 36.1 - + - -
101L ILE* 4.1 20.4 - - + -
119L PHE* 3.5 43.1 - + - -
120L LEU* 3.1 10.1 + - + +
122L TRP* 1.3 94.8 - + + +
124L ILE* 1.3 61.1 + - - +
126L GLU* 3.4 17.8 - - - +
127L GLN* 2.9 36.6 + - - +
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Residues in contact with ILE 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L ILE* 3.8 18.8 - - + -
102L TYR* 4.5 6.7 - - + -
105L ALA* 4.5 11.0 - - + -
117L ARG* 3.5 35.7 - - - +
120L LEU* 3.1 14.6 + - + +
121L GLU* 3.7 13.2 - - - +
122L TRP 3.4 0.2 - - - -
123L PHE* 1.3 78.0 - - - +
125L ASN* 1.3 60.6 + - - +
127L GLN* 3.5 5.0 + - - +
128L VAL* 3.3 21.8 + - - +
114N TYR* 3.6 41.1 - - + +
115N SER* 3.8 11.9 + - - +
118N ALA* 3.8 10.5 - - + -
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Residues in contact with ASN 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L GLU* 2.9 37.5 + - - +
122L TRP* 3.9 5.6 - - - +
124L ILE* 1.3 76.0 - - - +
126L GLU* 1.3 62.3 + - - +
128L VAL* 3.6 16.9 + - - +
129L GLU* 3.7 13.7 + - - +
115N SER 5.2 0.7 - - - +
118N ALA* 3.5 31.6 + - - +
119N PHE* 4.3 2.6 + - - -
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Residues in contact with GLU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1703 MET* 4.0 17.2 - - + +
53L HIS* 3.2 33.8 - - - +
122L TRP* 3.0 32.4 + - + +
123L PHE* 3.4 25.2 - - - +
124L ILE 3.3 0.4 - - - -
125L ASN* 1.3 75.4 - - - +
127L GLN* 1.3 81.4 + - - +
129L GLU* 3.2 8.6 + - - +
130L GLU* 3.0 48.9 + - + +
1173L AG 3.8 6.5 - - - -
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Residues in contact with GLN 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L GLU* 4.4 7.1 + - - -
50L GLU* 5.3 2.6 + - - -
94L GLU* 3.0 28.8 + - - +
97L ILE* 3.5 25.4 - - - +
98L SER* 3.1 34.9 + - - +
101L ILE* 4.5 10.0 - - + +
102L TYR* 6.0 1.8 - - + +
123L PHE 2.9 24.4 + - - +
124L ILE* 3.9 6.5 - - - +
125L ASN 3.4 0.2 - - - -
126L GLU* 1.3 100.5 + - - +
128L VAL* 1.3 60.6 + - - +
130L GLU* 3.7 3.3 + - - +
131L GLU* 2.9 36.6 + - - +
64N ARG* 5.3 0.4 - - - -
115N SER* 6.1 0.4 - - - +
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Residues in contact with VAL 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124L ILE 3.3 17.7 - - - +
125L ASN* 3.7 11.9 - - - +
126L GLU 3.2 0.6 - - - -
127L GLN* 1.3 77.3 - - + +
129L GLU* 1.3 61.5 - - + +
131L GLU* 4.3 1.4 - - - +
132L ALA* 3.3 23.6 + - - +
60N TYR* 4.2 15.0 - - + -
63N ASP* 4.2 21.4 - - + +
64N ARG* 4.0 28.0 - - - +
115N SER* 3.8 31.6 - - - +
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Residues in contact with GLU 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1703 MET* 3.7 24.5 - - + +
125L ASN 3.7 7.5 + - - +
126L GLU* 3.2 12.4 + - - +
128L VAL* 1.3 79.4 - - + +
130L GLU* 1.3 57.4 + - + +
132L ALA* 3.5 5.0 + - - +
133L SER* 2.9 31.3 + - - -
63N ASP* 6.1 2.2 - - - +
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Residues in contact with GLU 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1703 MET* 5.6 5.2 - - - +
46L GLN* 2.6 34.5 + - - +
49L GLU* 4.9 1.4 - - - +
50L GLU* 3.0 14.1 - - - +
53L HIS* 4.4 4.5 - - + -
94L GLU* 3.0 37.5 - - - +
126L GLU* 3.0 41.7 + - + +
127L GLN* 3.7 7.2 + - - +
129L GLU* 1.3 74.5 - - + +
131L GLU* 1.3 65.5 + - - +
133L SER* 3.3 6.4 + - - -
134L VAL* 3.1 30.8 + - - +
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Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L TYR* 3.7 21.3 + - + -
94L GLU* 4.0 24.5 - - + +
95L LYS* 3.6 25.6 - - - +
98L SER* 2.7 31.0 + - - +
102L TYR* 4.8 0.5 + - - -
127L GLN* 2.9 17.6 + - - +
128L VAL 4.3 2.7 - - - +
130L GLU* 1.3 75.6 - - - +
132L ALA* 1.3 56.5 - - - +
134L VAL* 3.4 0.7 + - - -
135L LYS* 3.0 33.2 + - - +
63N ASP 5.2 3.1 - - - +
64N ARG* 3.8 26.6 + - - +
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Residues in contact with ALA 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128L VAL 3.3 18.4 + - - +
129L GLU* 3.8 4.3 - - - +
131L GLU* 1.3 77.4 - - - +
133L SER* 1.3 60.8 + - - +
135L LYS* 4.3 5.1 - - - +
136L LYS* 3.2 25.8 + - - +
62N TYR 5.4 0.4 - - - +
63N ASP* 3.6 40.7 + - + +
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Residues in contact with SER 133 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L TRP* 3.8 18.2 - - - -
46L GLN* 5.1 4.1 + - - -
129L GLU 2.9 20.0 + - - -
130L GLU* 3.6 9.0 - - - -
131L GLU 3.2 0.2 - - - -
132L ALA* 1.3 78.3 - - - +
134L VAL* 1.3 60.5 + - - +
136L LYS* 3.8 11.9 - - - +
137L ILE* 3.5 22.6 - - - +
161L ARG* 5.3 0.9 + - - -
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Residues in contact with VAL 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L TYR* 4.9 7.2 - - + +
42L TRP* 4.3 18.2 - - + -
46L GLN* 5.6 3.6 - - + +
87L PHE* 3.8 24.2 - - + +
90L ALA* 4.1 6.1 - - + -
91L TYR* 3.7 35.7 - - + +
94L GLU* 4.1 19.5 - - + -
130L GLU* 3.1 19.8 + - - +
131L GLU 4.0 2.7 - - - +
133L SER* 1.3 76.4 - - - +
135L LYS* 1.3 59.9 + - - +
136L LYS 3.2 0.2 - - - -
137L ILE* 3.2 7.0 + - - +
138L LEU* 3.0 24.5 + - - +
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Residues in contact with LYS 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L TYR* 3.6 44.1 - - + +
131L GLU 3.0 18.5 + - - +
132L ALA* 4.3 5.2 - - - +
134L VAL* 1.3 77.4 - - - +
136L LYS* 1.3 57.9 + - - +
138L LEU* 3.2 13.6 + - + +
139L ASP* 2.7 69.0 + - - +
142L LYS* 5.3 5.9 - - - +
65N ASN* 3.7 37.1 + - + +
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Residues in contact with LYS 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 GLU* 2.9 40.3 + - - +
132L ALA 3.2 18.6 + - - +
133L SER* 3.8 11.4 - - - +
135L LYS* 1.3 78.7 - - - +
137L ILE* 1.3 66.8 - - + +
139L ASP* 3.7 6.9 + - - +
140L LYS* 3.4 54.0 + - - +
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Residues in contact with ILE 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L PHE* 4.4 3.4 - - + -
42L TRP* 3.5 38.6 - - + +
87L PHE* 3.7 36.1 - - + -
133L SER* 3.5 13.7 - - - +
134L VAL 3.2 2.1 + - - +
136L LYS* 1.3 84.7 - - + +
138L LEU* 1.3 64.2 + - - +
140L LYS* 3.2 10.3 + - + +
141L LEU* 3.0 28.6 + - + +
154L LEU* 4.5 10.8 - - + -
158L LEU* 3.9 31.0 - - + -
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L LEU* 3.8 3.0 - - + +
87L PHE* 3.4 37.2 - - + +
88L GLU* 3.7 26.5 - - + -
91L TYR* 3.6 30.1 - - + -
134L VAL 3.0 12.9 + - - +
135L LYS* 3.2 15.0 + - + +
137L ILE* 1.3 76.6 - - - +
139L ASP* 1.3 63.9 + - - +
141L LEU* 3.2 6.6 + - - +
142L LYS* 3.0 53.0 + - + +
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Residues in contact with ASP 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345 LEU 6.0 1.3 - - - +
355 GLY* 5.8 8.8 - - - -
135L LYS* 2.7 56.8 + - - +
136L LYS* 3.9 6.6 - - - +
138L LEU* 1.3 82.0 - - - +
140L LYS* 1.3 58.7 + - + +
142L LYS* 3.5 15.0 + - - +
143L PHE* 3.0 26.3 + - - +
65N ASN* 4.4 4.7 - - - +
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Residues in contact with LYS 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 GLY 4.8 15.3 - - - +
375 GLU* 6.4 0.4 - - - -
1525 PHE* 4.6 18.5 - - + -
1555 ASP* 5.8 4.0 + - - -
136L LYS* 3.4 50.8 + - + +
137L ILE* 3.2 14.0 + - + +
139L ASP* 1.3 78.7 - - + +
141L LEU* 1.3 57.8 + - - +
143L PHE* 3.4 12.3 - - + +
144L ALA* 3.3 24.3 + - - +
150L ILE* 4.9 2.1 - - - +
154L LEU* 3.9 36.1 - - + +
157L GLU* 4.2 15.6 + - - -
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Residues in contact with LEU 141 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L PHE* 4.0 17.5 - - + -
83L PRO* 3.4 33.2 - - + +
84L LEU* 3.7 23.7 - - + +
87L PHE* 3.7 28.3 - - + -
137L ILE* 3.0 20.2 + - + +
138L LEU* 3.2 6.9 + - - +
140L LYS* 1.3 75.9 - - - +
142L LYS* 1.3 61.5 + - - +
143L PHE 3.2 0.2 - - - -
144L ALA* 3.2 25.9 - - + +
145L LYS* 3.8 2.9 + - - -
151L LEU* 3.8 28.3 - - + -
154L LEU* 4.1 9.9 - - + -
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Residues in contact with LYS 142 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L LEU* 3.5 23.1 - - + +
88L GLU* 4.2 11.9 - - - -
135L LYS* 5.3 5.3 - - - +
138L LEU* 3.0 30.5 + - + +
139L ASP* 3.6 19.8 + - - +
141L LEU* 1.3 75.0 - - - +
143L PHE* 1.3 62.0 + - - +
144L ALA 3.2 0.4 - - - -
145L LYS* 3.3 32.2 - - - +
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Residues in contact with PHE 143 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345 LEU* 5.3 10.3 - - + -
365 LEU* 5.0 11.2 - - + -
1485 PRO* 3.6 45.2 - - + +
1515 LEU* 3.6 31.0 - - + -
1525 PHE* 4.6 19.5 - + + -
139L ASP 3.0 18.0 + - - +
140L LYS* 3.4 13.5 - - + +
141L LEU 3.2 0.4 - - - -
142L LYS* 1.3 75.2 - - - +
144L ALA* 1.3 58.2 + - - +
145L LYS 3.8 1.5 + - - -
150L ILE* 4.5 9.6 - - + +
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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