Contacts of the helix formed by residues 113 - 144 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 3.7 17.7 - - - +
3H SER 5.6 0.5 + - - -
6H MET* 3.9 10.0 - - + +
60H TYR* 4.7 0.2 + - - -
64H ARG* 4.3 8.2 + - - -
108H ALA* 2.8 25.2 + - - +
111H GLU* 3.2 13.1 - - + +
112H LYS* 1.3 74.4 - - - +
114H TYR* 1.3 63.2 + - - +
115H SER* 3.6 14.2 + - - -
116H THR* 2.6 28.9 + - - +
117H ARG* 3.3 16.7 + - - +
102R TYR* 5.2 2.3 + - - -
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Residues in contact with TYR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LYS* 3.4 31.3 + - + +
113H ASP* 1.3 73.6 + - - +
115H SER* 1.3 57.1 + - - +
117H ARG* 3.3 9.4 + - + +
118H ALA* 2.8 32.9 + - - +
102R TYR* 3.5 59.1 - + + -
105R ALA* 4.2 10.1 - - + -
106R ALA* 3.4 22.2 - - + +
109R GLU* 3.0 37.2 + - - -
117R ARG* 4.0 19.3 + - - -
124R ILE* 3.8 14.8 - - + +
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Residues in contact with SER 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H TYR* 3.1 17.6 + - - -
64H ARG* 3.4 26.2 + - - -
113H ASP* 3.3 4.6 + - - -
114H TYR* 1.3 79.4 - - - +
116H THR* 1.3 56.6 + - - +
118H ALA* 3.7 2.1 + - - +
119H PHE* 3.1 24.1 + - - +
102R TYR* 2.8 28.0 + - - -
124R ILE* 3.8 11.6 + - - +
125R ASN* 5.0 1.0 - - - +
128R VAL* 3.6 18.3 - - - +
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Residues in contact with THR 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 3.7 7.4 - - - +
6H MET* 3.8 23.1 - - + -
10H LEU* 3.9 22.7 - - + -
60H TYR* 2.9 21.2 + - + -
108H ALA* 4.2 5.4 - - + -
113H ASP* 2.6 32.9 + - - -
114H TYR 3.3 0.2 - - - -
115H SER* 1.3 75.1 - - - +
117H ARG* 1.3 59.8 + - - +
119H PHE* 3.3 2.9 + - + +
120H LEU* 2.9 42.0 + - + +
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Residues in contact with ARG 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ALA* 3.7 32.2 - - - +
108H ALA* 3.8 9.1 - - + +
109H GLU* 3.1 30.9 + - + +
113H ASP 3.3 12.2 + - - +
114H TYR* 3.3 13.6 + - + +
116H THR* 1.3 79.6 - - - +
118H ALA* 1.3 60.6 + - - +
120H LEU* 3.5 4.2 + - - +
121H GLU* 3.3 35.5 + - - +
124H ILE* 3.4 22.6 - - - +
114K TYR* 3.5 25.7 + - - +
117K ARG* 5.4 8.7 - - - +
118K ALA 6.1 0.2 - - - +
117R ARG* 5.3 9.6 - - - +
121R GLU* 4.9 1.0 + - - +
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Residues in contact with ALA 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR 2.8 17.4 + - - +
115H SER 3.9 2.5 - - - +
117H ARG* 1.3 73.6 - - - +
119H PHE* 1.3 64.3 + - - +
121H GLU* 3.4 16.0 - - - +
122H TRP* 4.4 1.4 + - - +
117R ARG* 5.9 0.6 - - - +
121R GLU* 3.7 26.6 - - - +
124R ILE* 3.8 18.4 - - + -
125R ASN* 3.4 30.0 + - - +
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Residues in contact with PHE 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 4.3 4.0 - - + -
56H ARG* 3.5 29.2 - - + -
57H PHE* 3.5 37.2 - + - -
60H TYR* 3.6 46.4 - + + -
115H SER 3.1 18.2 + - - +
116H THR 3.3 8.0 + - - +
118H ALA* 1.3 78.1 - - - +
120H LEU* 1.3 67.2 + - + +
121H GLU 3.3 0.7 + - - -
122H TRP* 3.5 19.5 + - + +
123H PHE* 3.5 30.8 - + - -
125R ASN* 4.1 4.9 + - - +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 5.2 0.2 - - + -
57H PHE* 4.1 30.7 - - + -
101H ILE* 4.3 15.9 - - + -
104H LEU* 3.6 49.4 - - + +
105H ALA* 3.8 11.9 - - + +
108H ALA* 4.6 0.7 - - + -
116H THR* 2.9 34.1 + - + +
117H ARG* 3.5 10.1 + - - +
118H ALA 3.4 0.2 - - - -
119H PHE* 1.3 79.8 - - + +
121H GLU* 1.3 63.7 + - - +
122H TRP 3.2 1.3 - - - -
123H PHE* 3.0 18.9 + - + +
124H ILE* 3.0 18.8 + - + +
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Residues in contact with GLU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ARG* 3.3 36.3 + - - +
118H ALA 3.4 15.7 - - - +
119H PHE 3.2 0.8 - - - -
120H LEU* 1.3 78.1 - - - +
122H TRP* 1.3 60.8 + - - +
124H ILE* 3.4 10.4 + - - +
125H ASN* 3.3 37.8 + - - +
117K ARG* 5.2 1.6 + - - +
118K ALA* 3.9 22.3 - - - +
121K GLU* 4.2 24.1 - - + +
121R GLU* 4.1 17.9 - - + +
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Residues in contact with TRP 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H HIS* 3.8 15.5 - + - -
56H ARG* 3.3 41.8 - - - +
118H ALA 4.4 1.2 + - - +
119H PHE* 3.5 14.2 + - + +
121H GLU* 1.3 80.4 - - - +
123H PHE* 1.3 94.3 + + + +
125H ASN* 3.5 6.7 + - - +
126H GLU* 3.0 49.0 + - + +
1173H AG 4.1 5.2 - - - -
170Z MET* 4.2 19.1 - - + -
171Z GLN 3.9 7.8 + - - -
172Z GLY* 3.5 35.3 - - - -
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Residues in contact with PHE 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 3.8 9.6 - - - -
53H HIS* 3.6 34.5 - - + -
56H ARG* 3.7 14.1 - - + -
57H PHE* 3.5 26.9 - + - -
101H ILE* 4.1 21.0 - - + +
119H PHE* 3.5 44.2 - + - -
120H LEU* 3.0 11.2 + - - +
122H TRP* 1.3 99.8 - + + +
124H ILE* 1.3 62.2 + - - +
126H GLU* 3.4 18.2 - - - +
127H GLN* 3.1 34.4 + - - +
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ILE* 3.9 18.8 - - + -
102H TYR* 4.4 7.4 - - + -
105H ALA* 4.5 9.2 - - + -
117H ARG* 3.4 40.8 - - - +
120H LEU* 3.0 13.1 + - + +
121H GLU* 3.7 12.1 - - - +
122H TRP 3.4 0.2 - - - -
123H PHE* 1.3 77.5 - - - +
125H ASN* 1.3 60.4 + - - +
127H GLN* 3.7 4.7 + - - +
128H VAL* 3.2 23.7 + - - +
114K TYR* 3.5 42.2 - - + +
115K SER* 3.8 13.2 + - - +
118K ALA* 3.9 7.2 - - + -
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Residues in contact with ASN 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H GLU* 3.3 24.2 + - - +
122H TRP* 3.8 7.9 - - - +
124H ILE* 1.3 75.9 - - - +
126H GLU* 1.3 62.7 + - - +
128H VAL* 3.4 21.9 + - - +
129H GLU* 3.6 10.4 + - - +
115K SER 4.8 1.4 - - - +
118K ALA* 3.4 37.7 + - - +
119K PHE* 4.2 3.6 + - - +
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Residues in contact with GLU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H HIS* 3.1 33.9 - - - +
122H TRP* 3.0 35.7 + - + +
123H PHE* 3.3 27.4 - - - +
125H ASN* 1.3 76.9 - - - +
127H GLN* 1.3 86.8 + - - +
129H GLU* 3.3 6.6 + - - +
130H GLU* 3.1 42.7 + - + +
1173H AG 3.8 6.1 - - - -
170Z MET* 4.1 18.1 - - + +
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Residues in contact with GLN 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 4.8 6.5 + - - -
50H GLU* 5.2 2.2 + - - -
53H HIS* 5.0 0.6 - - - -
94H GLU* 2.9 32.3 + - - +
97H ILE* 3.5 26.1 - - + +
98H SER* 3.1 33.4 + - - +
101H ILE* 4.6 8.0 - - + +
123H PHE 3.1 20.5 + - - +
124H ILE* 4.0 6.1 - - - +
125H ASN 3.3 0.4 - - - -
126H GLU* 1.3 100.7 + - - +
128H VAL* 1.3 59.9 + - + +
130H GLU* 3.7 3.8 - - - +
131H GLU* 2.9 37.0 + - - +
64K ARG* 5.5 0.2 - - - -
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H ILE 3.2 19.5 - - - +
125H ASN* 3.5 13.0 - - - +
126H GLU 3.3 0.4 - - - -
127H GLN* 1.3 78.2 - - - +
129H GLU* 1.3 62.2 + - + +
131H GLU* 4.1 1.6 - - - +
132H ALA* 3.2 23.7 + - - +
60K TYR* 4.3 15.0 - - + -
63K ASP* 4.3 20.0 - - + +
64K ARG* 4.1 29.2 - - - +
115K SER* 3.8 29.2 - - - +
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H ASN 3.6 8.4 + - - +
126H GLU 3.3 8.6 + - - +
127H GLN 3.3 0.4 - - - -
128H VAL* 1.3 79.4 - - + +
130H GLU* 1.3 53.9 + - + +
132H ALA* 3.4 4.9 + - - +
133H SER* 2.8 37.3 + - - -
63K ASP* 6.3 0.7 - - - -
170Z MET* 3.4 27.7 - - + +
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Residues in contact with GLU 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TYR* 4.7 0.2 + - - -
46H GLN* 2.7 35.3 + - - +
49H GLU* 4.7 1.6 - - - +
50H GLU* 3.1 13.3 - - - +
53H HIS* 3.4 12.1 - - - -
94H GLU* 3.1 36.7 - - - +
126H GLU* 3.1 36.6 + - + +
127H GLN* 3.4 7.6 + - - +
129H GLU* 1.3 77.2 - - + +
131H GLU* 1.3 60.3 + - - +
133H SER* 3.4 5.7 + - - -
134H VAL* 3.2 32.8 + - - +
170Z MET* 6.0 2.8 - - - +
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Residues in contact with GLU 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H TYR* 3.7 23.5 + - + -
94H GLU* 4.1 20.2 - - + +
95H LYS* 3.9 21.5 - - - +
98H SER* 2.7 34.2 + - - +
102H TYR* 4.6 2.6 + - - -
127H GLN* 2.9 19.6 + - - +
128H VAL* 4.1 3.1 - - - +
130H GLU* 1.3 75.4 - - - +
132H ALA* 1.3 57.7 + - - +
134H VAL* 3.3 1.6 + - - -
135H LYS* 2.9 33.2 + - - +
63K ASP 5.2 2.7 - - - +
64K ARG* 4.0 22.9 + - - +
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Residues in contact with ALA 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H VAL 3.2 18.3 + - - +
129H GLU* 3.8 4.3 - - - +
131H GLU* 1.3 79.1 - - - +
133H SER* 1.3 57.7 + - - +
134H VAL 3.4 0.2 - - - -
135H LYS* 4.3 5.1 - - - +
136H LYS* 3.2 29.1 + - - +
62K TYR 5.5 0.2 - - - +
63K ASP* 3.5 42.1 + - + +
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Residues in contact with SER 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H TRP* 3.7 20.0 + - - -
46H GLN* 5.2 3.1 + - - -
129H GLU 2.8 18.2 + - - -
130H GLU* 3.6 8.7 - - - -
131H GLU 3.2 0.2 - - - -
132H ALA* 1.3 78.9 - - - +
134H VAL* 1.3 61.6 + - - +
136H LYS* 4.0 6.5 - - - +
137H ILE* 3.4 26.6 + - - +
161H ARG* 5.1 2.1 + - - -
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Residues in contact with VAL 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TYR* 4.7 7.4 - - + +
42H TRP* 4.4 18.4 - - + -
46H GLN* 6.0 1.6 - - + +
87H PHE* 3.8 25.5 - - + +
90H ALA* 4.1 5.6 - - + -
91H TYR* 3.8 37.2 - - + +
94H GLU* 4.1 17.0 - - + -
130H GLU* 3.2 20.0 + - - +
131H GLU 3.9 2.7 - - - +
133H SER* 1.3 77.5 - - - +
135H LYS* 1.3 60.2 + - - +
136H LYS 3.3 0.2 - - - -
137H ILE* 3.2 4.7 + - - +
138H LEU* 2.9 25.3 + - - +
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Residues in contact with LYS 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H TYR* 3.6 43.0 - - + +
131H GLU 2.9 19.1 + - - +
132H ALA* 4.3 5.2 - - - +
134H VAL* 1.3 77.0 - - - +
136H LYS* 1.3 63.3 + - - +
138H LEU* 3.5 12.0 - - + +
139H ASP* 2.8 68.5 + - - +
142H LYS* 5.5 3.9 - - - +
65K ASN* 3.4 39.3 + - + +
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Residues in contact with LYS 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 GLU* 3.0 41.8 + - - +
132H ALA 3.2 19.1 + - - +
133H SER* 4.0 9.0 - - - +
135H LYS* 1.3 80.2 - - - +
137H ILE* 1.3 64.8 + - + +
139H ASP* 3.8 7.2 + - - +
140H LYS* 3.4 48.9 + - - +
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Residues in contact with ILE 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H PHE* 4.6 2.7 - - + -
42H TRP* 3.6 33.9 - - + +
87H PHE* 3.8 34.3 - - + -
133H SER* 3.4 19.7 - - - +
134H VAL 3.2 2.7 + - - +
136H LYS* 1.3 80.0 - - + +
138H LEU* 1.3 65.3 - - - +
140H LYS* 3.3 10.8 + - + +
141H LEU* 3.1 27.9 + - + +
154H LEU* 4.7 10.1 - - + -
158H LEU* 3.8 32.5 - - + -
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LEU* 4.0 4.0 - - + +
87H PHE* 3.4 41.6 - - + +
88H GLU* 3.8 25.1 - - + -
91H TYR* 3.6 29.6 - - + -
134H VAL 2.9 15.7 + - - +
135H LYS* 3.2 12.5 + - + +
137H ILE* 1.3 77.1 - - - +
139H ASP* 1.3 59.8 + - - +
141H LEU* 3.1 7.3 + - - +
142H LYS* 3.0 52.5 + - + +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 GLY* 6.2 3.4 - - - -
135H LYS* 2.8 57.9 + - - +
136H LYS* 4.1 6.7 - - - +
138H LEU* 1.3 77.0 - - - +
140H LYS* 1.3 57.9 + - + +
142H LYS* 3.4 22.6 + - - +
143H PHE* 3.0 25.3 + - - +
65K ASN* 4.6 2.3 - - - +
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Residues in contact with LYS 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 GLY* 4.5 17.3 - - - +
372 GLU* 6.2 0.7 - - - -
1522 PHE* 4.6 17.9 - - + -
1552 ASP* 5.5 5.8 + - - -
136H LYS* 3.4 40.1 + - + +
137H ILE* 3.3 12.9 + - + +
138H LEU 3.2 0.6 - - - -
139H ASP* 1.3 77.3 - - + +
141H LEU* 1.3 59.3 + - - +
143H PHE* 3.3 11.4 - - + +
144H ALA* 3.2 24.8 + - - +
150H ILE* 5.0 1.6 - - - +
154H LEU* 3.8 33.1 - - + +
157H GLU* 3.5 22.8 + - - -
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H PHE* 4.1 15.0 - - + -
83H PRO* 3.4 32.8 - - + +
84H LEU* 3.8 24.4 - - + +
87H PHE* 3.5 31.2 - - + -
137H ILE* 3.1 20.2 + - + +
138H LEU* 3.1 8.1 + - - +
140H LYS* 1.3 73.4 - - - +
142H LYS* 1.3 63.6 + - - +
143H PHE 3.1 1.3 - - - -
144H ALA* 3.4 23.4 + - + +
145H LYS* 4.1 1.9 + - - -
151H LEU* 3.8 28.5 - - + -
154H LEU* 4.3 9.6 - - + -
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Residues in contact with LYS 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LEU* 3.6 22.4 - - + +
88H GLU* 4.5 11.0 - - - -
135H LYS* 5.5 3.8 - - - +
138H LEU* 3.0 31.4 + - + +
139H ASP* 3.4 23.9 + - - +
141H LEU* 1.3 77.1 - - - +
143H PHE* 1.3 57.2 + - - +
145H LYS* 2.9 40.5 - - - +
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Residues in contact with PHE 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342 LEU 5.6 7.2 - - - -
362 LEU* 5.5 7.0 - - + -
1482 PRO* 3.7 45.6 - - + +
1512 LEU* 3.9 24.7 - - + -
1522 PHE* 5.0 12.1 - + + -
139H ASP 3.0 13.8 + - - +
140H LYS* 3.3 17.0 - - + +
141H LEU 3.1 0.2 - - - -
142H LYS* 1.3 78.9 - - - +
144H ALA* 1.3 55.4 + - - +
145H LYS* 3.3 6.3 + - - +
150H ILE* 4.5 16.4 - - + +
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Residues in contact with ALA 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LYS 3.2 14.6 + - - +
141H LEU* 3.4 15.4 + - + +
142H LYS 3.4 0.6 - - - -
143H PHE* 1.3 73.5 - - - +
145H LYS* 1.3 64.9 + - - +
146H ASP 3.6 0.9 - - - -
147H SER* 3.9 19.3 + - - +
150H ILE* 3.6 37.5 - - + -
151H LEU* 4.5 6.9 - - + +
154H LEU* 5.1 2.9 - - + -
----------------------------------------------------------
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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