Contacts of the helix formed by residues 113 - 143 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G TYR* 4.8 2.5 + - - -
2I LEU* 3.8 17.2 - - - +
3I SER 5.5 0.3 + - - -
6I MET* 4.0 10.9 - - + +
60I TYR* 4.5 0.2 + - - -
64I ARG* 4.8 4.9 + - - -
108I ALA* 2.8 22.7 + - - +
111I GLU* 3.2 12.2 - - + +
112I LYS* 1.3 73.6 - - - +
114I TYR* 1.3 61.7 + - - +
115I SER* 3.5 11.3 + - - -
116I THR* 2.7 37.2 + - - +
117I ARG* 3.2 19.9 + - - +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G TYR* 3.6 49.2 - + + -
105G ALA* 4.1 12.8 - - + -
106G ALA* 3.5 25.9 - - + +
109G GLU* 3.3 35.2 + - - -
117G ARG* 3.9 18.5 + - - -
124G ILE* 3.4 14.9 - - + +
112I LYS* 3.3 46.3 + - + +
113I ASP* 1.3 71.4 + - - +
115I SER* 1.3 60.1 + - - +
117I ARG* 3.5 8.4 + - + +
118I ALA* 2.9 30.8 + - - +
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Residues in contact with SER 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G TYR* 2.6 26.9 + - - -
124G ILE* 3.8 11.4 + - - +
125G ASN* 5.0 0.7 - - - +
127G GLN* 6.1 0.2 - - - +
128G VAL* 3.6 19.5 - - - +
60I TYR* 3.0 16.0 + - - -
64I ARG* 3.3 25.3 + - - -
113I ASP* 3.3 6.1 + - - -
114I TYR* 1.3 78.4 - - - +
116I THR* 1.3 57.2 + - - +
118I ALA* 3.3 3.3 + - - +
119I PHE* 3.0 26.0 + - - +
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Residues in contact with THR 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LEU* 3.6 9.4 - - - +
6I MET* 3.7 24.9 - - + -
10I LEU* 4.1 17.5 - - + -
60I TYR* 2.8 23.7 + - + -
108I ALA* 4.2 5.2 - - + -
113I ASP* 2.7 32.7 + - - -
115I SER* 1.3 73.7 - - - +
117I ARG* 1.3 60.1 + - - +
119I PHE* 3.4 2.2 + - + +
120I LEU* 3.1 44.6 + - + +
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Residues in contact with ARG 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 5.1 11.2 - - - +
121G GLU* 5.2 1.0 + - - +
105I ALA* 3.7 30.2 - - - +
108I ALA* 3.8 7.5 - - + +
109I GLU* 3.2 31.4 + - + +
113I ASP 3.2 18.4 + - - +
114I TYR* 3.7 10.8 - - + +
115I SER 3.3 0.2 - - - -
116I THR* 1.3 77.9 - - - +
118I ALA* 1.3 59.6 + - - +
120I LEU* 3.5 3.6 + - - +
121I GLU* 2.8 38.8 + - - +
124I ILE* 3.5 16.9 - - - +
114J TYR* 3.4 28.1 + - - +
117J ARG* 5.2 10.1 - - - +
118J ALA* 6.0 0.4 - - - +
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Residues in contact with ALA 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLU* 3.7 30.7 + - - +
124G ILE* 3.8 15.0 - - + -
125G ASN* 3.4 27.0 + - - +
114I TYR 2.9 18.1 + - - +
115I SER 3.3 3.3 + - - +
117I ARG* 1.3 74.3 - - - +
119I PHE* 1.3 65.6 + - - +
121I GLU* 3.4 16.0 - - - +
122I TRP* 4.4 1.0 + - - +
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Residues in contact with PHE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ASN* 4.2 4.9 + - - +
10I LEU* 4.1 4.9 - - + -
56I ARG* 3.6 22.0 - - + -
57I PHE* 3.5 36.8 - + - -
60I TYR* 3.6 53.6 - + + -
115I SER 3.0 17.1 + - - +
116I THR* 3.6 7.0 - - + +
117I ARG 3.3 0.2 - - - -
118I ALA* 1.3 77.0 - - - +
120I LEU* 1.3 69.9 + - + +
121I GLU 3.1 1.3 + - - -
122I TRP* 3.5 18.2 + - + +
123I PHE* 3.6 30.9 - + - -
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Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LEU* 5.2 0.2 - - + -
57I PHE* 4.2 15.7 - - + -
101I ILE* 4.2 21.8 - - + -
104I LEU* 3.6 60.1 - - + +
105I ALA* 3.7 10.1 - - + +
108I ALA* 4.5 1.3 - - + -
116I THR* 3.1 34.1 + - + +
117I ARG* 4.0 5.2 - - - +
118I ALA 3.4 0.2 - - - -
119I PHE* 1.3 81.0 - - + +
121I GLU* 1.3 63.4 + - - +
122I TRP 3.2 0.7 - - - -
123I PHE* 3.0 18.6 + - + +
124I ILE* 3.0 24.6 + - + +
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Residues in contact with GLU 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLU* 4.1 17.2 - - + +
117I ARG* 2.8 43.3 + - - +
118I ALA 3.4 16.2 - - - +
119I PHE 3.1 0.6 - - - -
120I LEU* 1.3 78.6 - - - +
122I TRP* 1.3 61.3 + - - +
124I ILE* 3.4 9.5 + - - +
125I ASN* 3.2 38.6 + - - +
117J ARG* 4.9 2.1 + - - +
118J ALA* 3.7 27.9 - - - +
121J GLU* 4.4 18.7 - - + +
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Residues in contact with TRP 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700 MET* 4.1 21.3 - - + -
1710 GLN* 3.2 36.4 + - + +
53I HIS* 3.5 31.2 - + - -
56I ARG* 3.4 47.2 - - - +
118I ALA 4.4 1.4 + - - +
119I PHE* 3.5 13.1 + - + +
120I LEU 3.2 0.2 - - - -
121I GLU* 1.3 79.7 - - - +
123I PHE* 1.3 76.4 - + + +
125I ASN* 3.6 6.3 + - - +
126I GLU* 3.0 42.8 + - + +
1173I AG 3.8 11.2 - - - -
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Residues in contact with PHE 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU* 4.4 7.4 - - - -
53I HIS* 3.7 23.8 - - + -
56I ARG* 3.6 29.2 - - + -
57I PHE* 3.5 33.4 - + - -
101I ILE* 4.1 20.6 - - + -
119I PHE* 3.6 42.6 - + - -
120I LEU* 3.0 11.0 + - - +
122I TRP* 1.3 91.3 - + + +
124I ILE* 1.3 61.3 + - - +
126I GLU* 3.4 18.4 - - - +
127I GLN* 2.9 37.1 + - - +
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Residues in contact with ILE 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I ILE* 3.8 18.2 - - + -
102I TYR* 4.5 7.1 - - + -
105I ALA* 4.5 12.1 - - + -
117I ARG* 3.5 36.1 - - - +
120I LEU* 3.0 16.3 + - + +
121I GLU* 3.7 12.8 - - - +
122I TRP 3.4 0.2 - - - -
123I PHE* 1.3 78.3 - - - +
125I ASN* 1.3 59.8 + - - +
127I GLN* 4.2 3.8 - - - +
128I VAL* 3.2 24.8 + - - +
114J TYR* 3.5 39.9 - - + +
115J SER* 3.9 10.3 + - - +
118J ALA* 3.8 10.5 - - + -
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Residues in contact with ASN 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I GLU* 3.2 27.6 + - - +
122I TRP* 3.9 6.1 - - - +
124I ILE* 1.3 74.3 - - - +
126I GLU* 1.3 64.0 + - - +
128I VAL* 3.5 19.5 + - - +
129I GLU* 3.6 8.1 + - - +
115J SER 4.9 1.6 - - - +
118J ALA* 3.4 38.1 + - - +
119J PHE* 4.1 4.3 + - - +
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Residues in contact with GLU 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700 MET* 3.8 19.3 - - + -
53I HIS* 3.3 24.4 + - - +
122I TRP* 3.0 33.3 + - + +
123I PHE* 3.4 26.1 - - - +
124I ILE 3.4 0.2 - - - -
125I ASN* 1.3 77.1 - - - +
127I GLN* 1.3 85.7 + - - +
129I GLU* 3.1 7.9 + - - +
130I GLU* 3.1 50.2 + - + +
1173I AG 3.8 6.5 - - - -
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Residues in contact with GLN 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU* 4.3 9.7 + - - -
50I GLU* 5.2 1.8 + - - -
53I HIS* 4.9 1.0 - - - -
94I GLU* 2.8 28.1 + - - +
97I ILE* 3.6 23.8 - - - +
98I SER* 3.4 31.2 + - - +
101I ILE* 4.5 11.0 - - + +
123I PHE* 2.9 23.0 + - - +
124I ILE* 4.2 5.2 - - - +
125I ASN 3.4 0.4 - - - -
126I GLU* 1.3 99.6 + - - +
128I VAL* 1.3 60.0 + - + +
130I GLU* 3.8 6.1 + - - +
131I GLU* 3.0 35.3 + - - +
64J ARG* 5.2 0.4 - - - -
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Residues in contact with VAL 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ILE 3.2 18.6 + - - +
125I ASN* 3.6 12.3 - - - +
126I GLU 3.2 0.6 - - - -
127I GLN* 1.3 77.5 - - - +
129I GLU* 1.3 61.8 + - - +
131I GLU* 4.2 1.1 - - - +
132I ALA* 3.4 24.1 + - - +
60J TYR* 4.2 15.9 - - + -
63J ASP* 4.2 18.8 - - + +
64J ARG* 3.9 29.8 - - - +
115J SER* 3.8 32.8 - - - +
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Residues in contact with GLU 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700 MET* 3.1 28.0 - - + +
125I ASN 3.6 8.2 + - - +
126I GLU 3.1 10.3 + - - +
128I VAL* 1.3 81.5 - - - +
130I GLU* 1.3 57.1 + - - +
132I ALA* 3.8 3.8 + - - +
133I SER* 3.1 27.0 + - - -
63J ASP* 6.1 2.2 - - - -
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Residues in contact with GLU 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700 MET* 5.2 6.6 - - + +
46I GLN* 2.6 33.8 + - - +
49I GLU* 4.3 1.4 - - - +
50I GLU* 3.0 10.4 - - - +
53I HIS* 3.4 17.3 - - - -
94I GLU* 3.0 33.5 - - - +
126I GLU* 3.1 34.2 + - + +
127I GLN* 3.6 5.2 + - - +
129I GLU* 1.3 77.7 - - + +
131I GLU* 1.3 63.9 + - - +
133I SER* 3.3 5.6 + - - -
134I VAL* 3.1 30.3 + - + +
1173I AG 4.2 3.6 - - - -
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Residues in contact with GLU 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I TYR* 3.7 22.3 + - + -
94I GLU* 4.0 23.9 + - + +
95I LYS* 3.6 25.0 - - - +
98I SER* 2.7 32.3 + - - +
102I TYR* 4.7 2.6 + - - -
127I GLN 3.0 19.6 + - - +
128I VAL* 4.2 4.3 - - - +
130I GLU* 1.3 75.8 - - - +
132I ALA* 1.3 57.3 + - - +
134I VAL 3.4 1.0 + - - -
135I LYS* 2.9 31.1 + - - +
1J MET 5.6 3.8 + - - -
63J ASP 5.5 1.6 - - - +
64J ARG* 4.0 23.1 + - - +
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Residues in contact with ALA 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I VAL 3.4 16.6 + - - +
129I GLU* 4.1 4.7 - - - +
130I GLU 3.3 0.4 - - - -
131I GLU* 1.3 76.2 - - - +
133I SER* 1.3 59.1 + - - +
135I LYS* 4.0 5.5 - - - +
136I LYS* 3.0 30.5 + - - +
62J TYR 5.3 0.9 - - - +
63J ASP* 3.5 41.4 + - + +
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Residues in contact with SER 133 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I TRP* 3.6 20.9 - - - -
46I GLN* 5.1 4.8 + - - -
129I GLU 3.1 19.3 + - - -
130I GLU* 3.5 9.4 - - - -
131I GLU 3.2 0.2 - - - -
132I ALA* 1.3 79.8 - - - +
134I VAL* 1.3 61.6 + - - +
136I LYS* 3.7 9.8 + - - +
137I ILE* 3.6 23.5 + - - +
161I ARG* 5.2 0.7 + - - -
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Residues in contact with VAL 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I TYR* 4.7 7.2 - - + +
42I TRP* 4.4 17.0 - - + -
46I GLN* 5.7 3.8 - - + +
87I PHE* 3.7 27.9 - - + +
90I ALA* 4.1 6.5 - - + -
91I TYR* 3.7 35.7 - - + +
94I GLU* 4.0 20.4 - - + +
130I GLU* 3.1 17.7 + - + +
131I GLU 3.9 3.1 - - - +
133I SER* 1.3 74.4 - - - +
135I LYS* 1.3 60.9 + - - +
137I ILE 3.4 2.1 + - - -
138I LEU* 3.0 25.7 + - + +
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Residues in contact with LYS 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I TYR* 3.5 41.2 - - + +
131I GLU 2.9 18.4 + - - +
132I ALA* 4.0 7.4 - - - +
133I SER 3.4 0.2 - - - -
134I VAL* 1.3 75.2 - - - +
136I LYS* 1.3 58.8 + - - +
138I LEU* 3.3 13.5 + - + +
139I ASP* 2.7 72.9 + - - +
142I LYS* 5.4 4.8 - - - +
65J ASN* 3.6 39.2 + - + +
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Residues in contact with LYS 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 GLY* 6.0 2.0 - - - +
371 GLU* 2.8 42.7 + - + +
132I ALA 3.0 19.3 + - - +
133I SER* 3.8 9.2 - - - +
134I VAL 3.3 0.2 - - - -
135I LYS* 1.3 77.9 - - - +
137I ILE* 1.3 64.2 + - + +
139I ASP* 3.7 6.9 + - - +
140I LYS* 3.4 52.8 + - + +
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Residues in contact with ILE 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I PHE* 4.2 7.4 - - + -
42I TRP* 3.5 38.4 - - + +
87I PHE* 3.7 36.8 - - + -
133I SER 3.6 13.0 + - - +
134I VAL 3.4 1.4 + - - +
135I LYS 3.3 0.4 - - - -
136I LYS* 1.3 78.2 - - + +
138I LEU* 1.3 61.2 + - - +
140I LYS* 3.1 10.2 + - + +
141I LEU* 2.9 32.0 + - + +
154I LEU* 4.6 10.3 - - + -
158I LEU* 4.0 31.6 - - + -
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Residues in contact with LEU 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I LEU* 3.9 3.8 - - + +
87I PHE* 3.5 30.6 - - + +
88I GLU* 3.7 26.9 - - + +
91I TYR* 3.6 30.3 - - + -
134I VAL 3.0 16.9 + - - +
135I LYS* 3.5 13.0 - - + +
137I ILE* 1.3 75.9 - - - +
139I ASP* 1.3 64.4 + - - +
141I LEU* 3.1 13.3 + - - +
142I LYS* 2.9 55.5 + - + +
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Residues in contact with ASP 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 LEU 6.1 0.4 - - - +
351 GLY* 6.1 4.7 - - - -
135I LYS* 2.7 57.9 + - - +
136I LYS* 3.9 6.1 + - - +
138I LEU* 1.3 80.2 - - - +
140I LYS* 1.3 58.4 + - + +
142I LYS* 3.4 15.6 + - - +
143I PHE* 2.9 26.7 + - - +
65J ASN* 4.5 3.6 - - - +
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Residues in contact with LYS 140 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 GLY* 4.4 17.3 - - - +
371 GLU* 6.2 0.6 - - - +
1521 PHE* 4.7 16.8 - - + -
1551 ASP* 5.6 5.1 + - - -
136I LYS* 3.4 44.3 + - + +
137I ILE* 3.1 13.5 + - + +
139I ASP* 1.3 77.7 - - + +
141I LEU* 1.3 62.3 + - - +
143I PHE* 3.4 14.7 - - + +
144I ALA* 3.4 20.8 + - - +
150I ILE* 4.8 1.2 - - - +
154I LEU* 3.9 33.0 - - + +
157I GLU* 4.0 16.6 + - - -
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Residues in contact with LEU 141 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I PHE* 4.1 14.6 - - + -
83I PRO* 3.5 32.5 - - + +
84I LEU* 3.7 23.9 - - + +
87I PHE* 3.7 29.8 - - + -
137I ILE* 2.9 23.6 + - + +
138I LEU* 3.1 6.7 + - - +
140I LYS* 1.3 75.9 - - - +
142I LYS* 1.3 63.6 + - - +
143I PHE 3.2 0.2 - - - -
144I ALA* 3.2 24.6 + - + +
145I LYS* 3.8 3.1 + - - -
151I LEU* 3.8 28.3 - - + -
154I LEU* 4.2 8.3 - - + -
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Residues in contact with LYS 142 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I LEU* 3.5 20.8 - - + +
88I GLU* 4.2 13.5 - - - -
135I LYS* 5.4 3.6 - - - +
138I LEU* 2.9 32.8 + - + +
139I ASP* 3.5 20.8 + - - +
141I LEU* 1.3 75.5 - - - +
143I PHE* 1.3 61.4 + - - +
144I ALA 3.3 0.9 + - - -
145I LYS* 3.4 34.5 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 LEU 5.6 7.0 - - - -
361 LEU* 5.4 7.6 - - + -
1481 PRO* 3.6 47.0 - - + +
1511 LEU* 3.7 27.4 - - + -
1521 PHE* 5.0 13.5 - + + -
139I ASP 2.9 17.3 + - - +
140I LYS* 3.4 15.3 - - + +
141I LEU 3.2 0.2 - - - -
142I LYS* 1.3 75.7 - - - +
144I ALA* 1.3 56.7 + - - +
145I LYS 3.7 1.8 + - - -
150I ILE* 4.4 16.1 - - + +
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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
------------------------------------------------------------
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