Contacts of the helix formed by residues 113 - 139 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L ARG 3.4 9.2 - - - +
56L GLY* 5.1 4.5 - - - -
57L ALA 5.6 1.0 + - - -
112L HIS* 1.3 81.3 - - - +
114L VAL* 1.3 67.6 + - - +
115L GLN* 2.9 46.5 - - - +
116L ASP* 3.2 33.6 + - - +
117L HIS* 3.2 12.1 + - - -
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Residues in contact with VAL 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L MET* 4.4 13.4 - - + +
55L ARG 3.0 36.8 + - - +
56L GLY* 3.8 5.8 - - - +
57L ALA 3.4 27.6 - - - +
58L ASN* 5.1 0.9 - - + -
59L PHE* 4.1 10.8 - - - -
62L VAL* 4.3 23.3 - - + -
112L HIS 4.2 1.1 - - - -
113L ASN* 1.3 73.2 + - - +
115L GLN* 1.3 63.8 + - + +
117L HIS* 3.2 4.2 + - - +
118L LEU* 2.8 46.9 + - + +
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Residues in contact with GLN 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ALA* 5.8 0.6 - - - +
57L ALA* 5.3 3.6 + - + +
58L ASN* 5.9 3.2 - - - +
113L ASN* 2.9 18.8 - - - +
114L VAL* 1.3 81.8 - - + +
116L ASP* 1.3 62.6 + - - +
118L LEU* 3.3 12.3 + - - +
119L LYS* 3.0 43.4 + - - +
165L ASN 3.2 21.6 + - - -
166L ILE* 3.3 13.8 - - - +
167L GLU* 2.8 53.7 + - + +
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Residues in contact with ASP 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ILE* 4.1 29.5 - - + +
112L HIS 4.8 0.7 + - - -
113L ASN* 3.2 34.3 + - + +
115L GLN* 1.3 78.8 - - - +
117L HIS* 1.3 62.5 + - - +
119L LYS* 3.3 13.3 + - - +
120L GLU* 3.0 26.6 + - + +
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Residues in contact with HIS 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L GLN* 4.6 2.2 - - - -
50L ALA* 3.4 24.1 - - + -
53L ASN* 3.4 18.2 + - + -
54L MET* 3.7 27.6 - - + -
107L TYR* 2.6 32.5 + + - +
108L PRO 4.9 1.3 - - - -
111L ILE* 3.2 40.3 + - + +
112L HIS* 3.4 24.5 - - - -
113L ASN 3.2 8.1 + - - -
114L VAL 3.6 6.3 - - - +
116L ASP* 1.3 76.3 - - - +
118L LEU* 1.3 56.8 + - - +
120L GLU 3.2 0.5 + - - -
121L LEU* 2.7 41.3 + - - +
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Residues in contact with LEU 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L MET* 5.0 1.1 - - + -
58L ASN* 5.8 0.2 - - - +
62L VAL* 3.8 28.0 - - + -
65L MET* 5.1 3.6 - - + -
66L LEU* 5.4 0.2 - - + -
114L VAL* 2.8 34.9 + - + +
115L GLN* 3.5 15.3 - - - +
117L HIS* 1.3 76.7 - - - +
119L LYS* 1.3 56.4 + - - +
121L LEU* 3.6 9.8 - - + +
122L ALA* 2.8 25.5 + - - +
162L ILE* 3.3 40.1 - - + +
165L ASN* 3.7 35.0 - - + +
166L ILE* 3.9 10.8 - - + -
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Residues in contact with LYS 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG* 4.4 8.4 + - - +
115L GLN* 3.0 35.2 + - - +
116L ASP* 3.7 12.3 + - - +
118L LEU* 1.3 72.6 - - - +
120L GLU* 1.3 69.2 + - + +
122L ALA* 3.3 3.8 + - - +
123L ASP* 3.1 29.4 + - - +
166L ILE* 4.0 36.8 - - + -
167L GLU 5.7 0.7 - - - -
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Residues in contact with GLU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L TYR* 3.5 25.6 - - + +
108L PRO* 3.9 11.3 - - + +
111L ILE* 3.7 21.3 - - + +
116L ASP* 3.0 19.5 + - + +
119L LYS* 1.3 77.0 - - - +
121L LEU* 1.3 61.7 + - - +
123L ASP* 3.4 13.3 + - - +
124L ARG* 2.9 52.7 + - - +
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Residues in contact with LEU 121 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ILE* 3.9 27.4 - - + +
47L THR* 4.2 9.2 - - - -
50L ALA* 3.6 32.3 - - + -
54L MET* 4.6 0.9 - - + -
66L LEU* 3.7 32.8 - - + -
107L TYR* 4.0 2.9 - - + +
117L HIS 2.7 30.3 + - - +
118L LEU* 3.6 12.6 - - + +
120L GLU* 1.3 71.5 - - - +
122L ALA* 1.3 56.2 + - - +
124L ARG* 3.2 3.9 + - - +
125L TYR* 2.8 50.6 + - + -
162L ILE* 4.1 11.4 - - + -
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Residues in contact with ALA 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG* 3.4 34.5 - - - +
118L LEU 2.8 18.1 + - - +
119L LYS* 3.5 4.9 - - - +
121L LEU* 1.3 77.1 - - - +
123L ASP* 1.3 57.0 + - - +
125L TYR* 4.5 0.9 - - - -
126L ALA* 2.8 31.9 + - - +
159L LEU* 3.4 9.9 - - - +
162L ILE* 3.9 13.6 - - + +
163L GLU* 4.3 6.1 - - + -
166L ILE* 4.3 4.9 - - + -
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Residues in contact with ASP 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG* 2.8 30.7 + - - +
119L LYS* 3.1 13.2 + - - +
120L GLU* 3.6 17.3 - - - +
121L LEU 3.1 0.2 - - - -
122L ALA* 1.3 76.3 - - - +
124L ARG* 1.3 69.0 + - - +
126L ALA* 3.3 3.9 + - - +
127L ILE* 3.1 30.7 + - + +
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Residues in contact with ARG 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L LEU* 3.8 18.8 - - + -
46L ILE* 4.1 15.0 - - + +
104L LEU* 3.8 19.4 - - + +
105L LYS* 2.9 54.6 + - - +
106L SER 3.7 4.0 + - - -
107L TYR* 2.9 34.9 - - - +
108L PRO* 3.6 14.6 - - - +
120L GLU* 2.9 41.5 + - - +
121L LEU* 3.2 4.8 + - - +
123L ASP* 1.3 77.6 - - - +
125L TYR* 1.3 66.0 + - - +
127L ILE* 3.3 9.6 + - - +
128L VAL* 3.1 26.3 + - - +
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Residues in contact with TYR 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L LEU* 3.5 35.9 - - + -
47L THR* 2.6 38.8 + - + +
66L LEU* 5.5 0.2 - - + -
69L PHE* 3.6 10.7 - + - +
73L LEU* 3.4 12.2 - - + +
121L LEU* 2.8 41.8 + - + +
122L ALA 3.8 3.4 - - - +
124L ARG* 1.3 72.5 - - - +
126L ALA* 1.3 53.9 + - - +
128L VAL* 3.2 1.9 + - - +
129L ALA* 2.6 39.6 + - - +
155L LEU* 4.3 9.1 - - + +
158L PHE* 3.8 37.0 - + + -
159L LEU* 4.1 13.7 - - + -
162L ILE* 3.5 27.1 - - + -
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Residues in contact with ALA 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG* 3.4 32.5 - - + +
122L ALA 2.8 19.7 + - - +
123L ASP* 3.4 6.3 - - - +
124L ARG 3.2 0.2 - - - -
125L TYR* 1.3 77.6 - - - +
127L ILE* 1.3 58.0 + - + +
129L ALA* 4.2 0.2 - - - -
130L ASN* 2.8 44.3 + - - +
159L LEU* 3.9 14.5 - - + +
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Residues in contact with ILE 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLN* 4.3 10.5 - - - +
103L PRO* 4.5 16.8 - - + +
104L LEU* 3.9 24.2 - - + -
105L LYS* 5.5 3.4 - - + +
123L ASP* 3.1 19.5 + - + +
124L ARG* 3.6 13.5 - - - +
125L TYR 3.2 0.2 - - - -
126L ALA* 1.3 77.8 - - + +
128L VAL* 1.3 62.4 + - - +
130L ASN* 4.1 3.3 - - - +
131L ASP* 3.0 28.1 + - + +
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Residues in contact with VAL 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLN* 3.4 36.3 - - + +
40L PHE* 3.6 27.1 - - + -
43L LEU* 4.0 17.0 - - + -
104L LEU* 3.9 17.9 - - + -
124L ARG 3.1 13.9 + - - +
125L TYR 3.8 3.8 - - - +
127L ILE* 1.3 75.5 - - - +
129L ALA* 1.3 58.0 + - - +
131L ASP* 3.8 0.5 - - - +
132L VAL* 2.9 30.0 + - - +
155L LEU* 3.5 21.1 - - + -
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Residues in contact with ALA 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125L TYR 2.6 24.3 + - - +
126L ALA* 3.7 5.6 - - - +
128L VAL* 1.3 73.1 - - - +
130L ASN* 1.3 56.8 + - - +
132L VAL* 3.2 9.5 - - - +
133L ARG* 3.0 36.6 + - - +
155L LEU* 3.9 24.0 - - + +
156L ASP* 3.7 17.3 - - - +
159L LEU* 4.4 10.5 - - + -
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Residues in contact with ASN 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG 3.1 19.8 + - - -
19J ASN* 3.6 3.9 - - - -
20J ASP* 2.8 37.3 + - - +
126L ALA* 2.8 31.1 + - - +
127L ILE* 4.1 2.8 - - - +
129L ALA* 1.3 73.4 - - - +
131L ASP* 1.3 64.9 + - - +
133L ARG* 2.5 35.2 + - - +
134L LYS* 3.3 30.9 + - - +
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Residues in contact with ASP 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L ARG* 2.8 41.2 + - - -
36L GLN* 3.6 2.5 - - - +
39L GLN* 3.0 28.2 + - - +
103L PRO* 5.8 0.2 - - - +
127L ILE* 3.0 20.9 + - + +
128L VAL 3.8 2.2 - - - +
130L ASN* 1.3 74.9 - - - +
132L VAL* 1.3 67.3 + - - +
134L LYS* 3.0 19.2 + - - +
135L ALA 3.0 8.3 + - - -
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Residues in contact with VAL 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L GLN* 3.6 32.8 - - - +
40L PHE* 4.3 20.4 - - + -
128L VAL 2.9 19.9 + - - +
129L ALA* 3.2 16.2 - - - +
131L ASP* 1.3 74.4 - - - +
133L ARG* 1.3 67.6 + - - +
135L ALA* 3.1 10.4 + - - +
136L ILE* 3.3 13.2 + - - +
148L LEU* 3.9 32.1 - - + +
151L ALA* 4.7 0.7 - - + -
152L SER* 4.0 21.1 - - - +
155L LEU* 4.8 3.4 - - + -
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Residues in contact with ARG 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ASN* 2.9 23.2 + - - +
20J ASP* 3.1 13.9 + - - -
21J VAL* 3.2 23.0 - - - +
83J ARG* 4.1 5.4 - - - +
141J ASP* 4.2 7.6 - - - +
142J ASP* 4.4 7.9 - - + +
143J ASP* 4.0 8.3 - - - +
129L ALA* 3.0 19.2 + - - +
130L ASN* 2.5 34.9 + - - +
131L ASP 3.1 0.4 - - - -
132L VAL* 1.3 76.8 - - - +
134L LYS* 1.3 64.3 + - + +
136L ILE* 3.3 24.9 - - + +
137L GLY 4.4 0.2 + - - -
152L SER* 3.7 15.0 - - - +
156L ASP* 2.6 43.2 + - - -
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Residues in contact with LYS 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ASP* 2.4 42.6 + - - -
130L ASN* 3.3 22.2 + - - +
131L ASP* 3.0 10.1 + - - +
133L ARG* 1.3 75.9 - - + +
135L ALA* 1.3 67.1 + - - +
136L ILE 2.9 3.5 + - - -
137L GLY* 3.1 11.7 + - - +
138L GLU* 3.3 14.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L LEU* 3.9 19.6 - - + +
35L ARG* 4.4 4.0 - - - +
36L GLN* 3.6 22.9 - - - +
131L ASP* 3.0 7.9 + - - +
132L VAL* 3.1 10.7 + - - +
134L LYS* 1.3 77.2 - - - +
136L ILE* 1.3 56.7 + - - +
138L GLU* 3.5 13.4 - - - +
139L ALA* 2.9 31.0 + - - +
148L LEU* 3.7 12.9 - - + +
----------------------------------------------------------
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Residues in contact with ILE 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J ASP* 3.7 28.7 - - + +
143J ASP* 3.5 17.7 - - - +
132L VAL 3.5 8.7 - - - +
133L ARG* 3.3 18.6 - - + +
134L LYS 2.9 0.4 - - - -
135L ALA* 1.3 78.5 - - - +
137L GLY* 1.3 63.3 + - - +
139L ALA* 3.2 21.5 + - - +
145L ALA* 3.9 14.4 - - + +
148L LEU* 3.9 21.1 - - + -
149L THR* 3.5 38.6 - - - +
152L SER* 3.7 11.9 - - - +
----------------------------------------------------------
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Residues in contact with GLY 137 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J ASP* 4.3 9.8 + - - -
133L ARG 4.4 0.4 + - - -
134L LYS* 3.1 7.4 + - - +
136L ILE* 1.3 81.4 - - - +
138L GLU* 1.3 59.8 + - - +
139L ALA 3.2 5.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L LEU* 3.6 29.5 - - + +
35L ARG* 3.8 14.2 + - - -
134L LYS* 3.3 13.6 + - - +
135L ALA* 3.1 13.2 + - - +
137L GLY* 1.3 76.6 - - - +
139L ALA* 1.3 61.3 + - - +
140L LYS* 3.5 11.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L LEU* 4.0 15.7 - - + -
135L ALA 2.9 11.0 + - - +
136L ILE 3.3 16.3 - - - +
137L GLY 3.2 5.2 - - - +
138L GLU* 1.3 77.0 - - - +
140L LYS* 1.3 63.8 + - - +
141L ASP 4.3 1.8 - - - +
144L THR* 4.4 5.8 - - + -
145L ALA* 3.9 31.4 - - + +
148L LEU* 4.1 5.2 - - + -
----------------------------------------------------------
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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