Contacts of the helix formed by residues 113 - 143 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O TYR* 5.1 2.1 + - - -
1P MET 6.1 0.9 - - - -
2P LEU* 3.8 10.8 - - - +
3P SER 5.4 0.9 + - - -
6P MET* 3.7 19.7 - - + +
64P ARG* 4.6 4.9 + - - -
108P ALA* 2.7 25.9 + - - +
111P GLU* 3.2 10.8 - - + +
112P LYS* 1.3 69.4 - - - +
114P TYR* 1.3 62.7 + - - +
115P SER* 3.3 11.6 + - - -
116P THR* 2.7 35.4 + - - +
117P ARG* 3.2 21.8 + - - +
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Residues in contact with TYR 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O TYR* 3.6 49.5 - + + -
105O ALA* 4.0 12.3 - - + -
106O ALA* 3.4 24.8 - - + +
109O GLU* 2.9 39.2 + - - -
117O ARG* 3.6 19.8 + - - -
124O ILE* 3.4 13.9 - - + +
112P LYS* 3.3 39.4 + - + +
113P ASP* 1.3 73.8 + - - +
115P SER* 1.3 56.2 + - - +
117P ARG* 3.8 7.4 - - + +
118P ALA* 3.0 31.0 + - - +
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Residues in contact with SER 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O TYR* 2.5 29.8 + - - -
124O ILE* 3.7 11.6 + - - +
125O ASN* 5.0 0.9 - - - +
128O VAL* 4.0 15.5 - - - +
60P TYR* 3.0 16.7 + - - -
64P ARG* 3.3 26.6 + - - -
113P ASP* 3.2 4.6 + - - -
114P TYR* 1.3 75.5 - - - +
116P THR* 1.3 59.6 + - - +
118P ALA* 3.5 3.3 + - - +
119P PHE* 3.1 24.6 + - - +
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Residues in contact with THR 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LEU* 3.6 9.5 - - - +
6P MET* 3.8 22.9 - - + -
10P LEU* 3.9 22.4 - - + -
60P TYR* 2.8 24.2 + - + -
108P ALA* 4.3 4.5 - - + -
113P ASP* 2.7 32.1 + - - -
115P SER* 1.3 73.0 - - - +
117P ARG* 1.3 60.6 + - - +
119P PHE* 3.2 2.2 + - + +
120P LEU* 2.9 42.2 + - + +
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Residues in contact with ARG 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M TYR* 3.5 25.2 + - - +
117M ARG* 5.2 10.9 - - - +
118M ALA* 6.1 0.2 - - - +
117O ARG* 5.1 11.0 - - - +
121O GLU* 5.7 0.4 + - - -
105P ALA* 3.7 29.2 - - - +
108P ALA* 3.8 10.0 - - + +
109P GLU* 3.1 30.7 + - + -
113P ASP 3.2 17.8 + - - +
114P TYR* 3.8 10.3 - - + +
116P THR* 1.3 77.7 - - - +
118P ALA* 1.3 61.3 + - - +
120P LEU* 3.4 4.0 + - - +
121P GLU* 3.0 38.9 + - - +
124P ILE* 3.5 18.3 - - - +
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Residues in contact with ALA 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ARG* 5.7 0.8 - - - +
121O GLU* 3.4 33.0 - - - +
124O ILE* 3.9 15.3 - - + -
125O ASN* 3.6 26.6 + - - +
114P TYR 3.0 20.3 + - - +
115P SER 3.9 1.6 - - - +
117P ARG* 1.3 73.5 - - - +
119P PHE* 1.3 64.4 + - - +
121P GLU* 3.4 15.6 - - - +
122P TRP* 4.4 1.4 + - - +
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Residues in contact with PHE 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125O ASN* 4.1 6.2 + - - +
10P LEU* 4.3 3.1 - - + -
56P ARG* 3.4 30.5 - - + -
57P PHE* 3.5 37.2 - + - -
60P TYR* 3.6 46.7 - + + -
115P SER 3.1 14.9 + - - +
116P THR 3.2 9.8 + - - +
118P ALA* 1.3 77.1 - - - +
120P LEU* 1.3 68.6 + - + +
121P GLU 3.1 1.1 + - - -
122P TRP* 3.5 18.3 + - + +
123P PHE* 3.5 32.1 - + - -
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Residues in contact with LEU 120 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P LEU* 5.3 0.2 - - + -
57P PHE* 4.1 21.5 - - + -
101P ILE* 4.4 16.2 - - + +
104P LEU* 3.6 60.1 - - + +
105P ALA* 3.7 9.0 - - + +
108P ALA* 4.5 0.2 - - + -
116P THR* 2.9 34.8 + - + +
117P ARG* 3.8 7.9 - - - +
118P ALA 3.4 0.2 - - - -
119P PHE* 1.3 81.2 - - + +
121P GLU* 1.3 59.2 + - - +
122P TRP 3.2 0.4 - - - -
123P PHE* 2.9 23.0 + - + +
124P ILE* 3.0 22.7 + - + +
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Residues in contact with GLU 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ARG* 5.0 0.9 + - - +
118M ALA* 3.8 28.4 - - - +
121M GLU* 4.3 22.8 - - + +
121O GLU* 4.1 14.6 - - + +
117P ARG* 3.0 38.2 + - - +
118P ALA 3.4 16.2 - - - +
119P PHE 3.1 0.4 - - - -
120P LEU* 1.3 76.5 - - - +
122P TRP* 1.3 60.7 + - - +
124P ILE* 3.4 11.0 + - - +
125P ASN* 3.1 39.0 + - - +
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Residues in contact with TRP 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707 MET* 4.1 24.7 - - + -
1717 GLN 4.3 3.0 + - - -
1727 GLY* 3.8 29.2 - - - -
53P HIS* 3.5 37.2 - + - -
56P ARG* 3.5 44.8 - - - +
118P ALA 4.4 1.4 + - - +
119P PHE* 3.5 12.4 + - + +
120P LEU 3.2 1.0 - - - -
121P GLU* 1.3 78.6 - - - +
123P PHE* 1.3 82.8 + + + +
125P ASN* 3.5 6.7 + - + +
126P GLU* 3.0 38.3 + - + +
1171P AG 3.8 6.3 - - - -
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Residues in contact with PHE 123 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P GLU* 4.1 8.3 - - - -
53P HIS* 3.6 36.6 - - + -
56P ARG* 3.6 16.4 - - + -
57P PHE* 3.4 31.9 - + - -
101P ILE* 4.1 21.3 - - + +
119P PHE* 3.5 42.6 - + - -
120P LEU* 2.9 12.0 + - - +
122P TRP* 1.3 96.0 - + + +
124P ILE* 1.3 63.5 + - - +
126P GLU* 3.3 20.1 - - - +
127P GLN* 3.1 31.0 + - - +
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Residues in contact with ILE 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M TYR* 3.5 43.5 - - + +
115M SER* 3.8 12.9 + - - +
118M ALA* 3.8 8.3 - - + -
101P ILE* 3.8 18.4 - - + -
102P TYR* 4.4 6.5 - - + -
105P ALA* 4.4 10.3 - - + -
117P ARG* 3.5 35.7 - - - +
120P LEU* 3.0 14.5 + - + +
121P GLU* 3.4 13.9 + - - +
123P PHE* 1.3 78.6 - - - +
125P ASN* 1.3 61.1 + - - +
127P GLN* 3.6 3.8 + - - +
128P VAL* 3.3 22.3 + - - +
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Residues in contact with ASN 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M SER 5.1 0.9 - - - +
118M ALA* 3.5 32.2 + - - +
119M PHE* 4.2 3.8 + - - -
121P GLU* 3.1 36.0 + - - +
122P TRP* 3.8 7.0 - - + +
124P ILE* 1.3 74.8 - - - +
126P GLU* 1.3 64.1 + - - +
128P VAL* 3.7 17.6 + - - +
129P GLU* 3.8 7.8 + - - +
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Residues in contact with GLU 126 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707 MET* 4.1 16.6 - - + +
53P HIS* 3.2 31.5 - - + +
122P TRP* 3.0 32.1 + - + +
123P PHE* 3.3 33.1 - - - +
124P ILE 3.3 0.4 - - - -
125P ASN* 1.3 76.6 - - - +
127P GLN* 1.3 86.0 + - - +
129P GLU* 3.2 8.8 + - - +
130P GLU* 3.0 41.8 + - + +
1171P AG 3.9 6.3 - - - -
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Residues in contact with GLN 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M ARG* 5.2 0.4 - - - -
17P GLU* 4.8 3.8 + - - -
50P GLU* 5.1 3.6 + - - -
53P HIS* 5.1 1.2 - - - -
94P GLU* 2.9 34.3 + - - +
97P ILE* 3.6 28.8 - - + +
98P SER* 3.0 31.8 + - - +
101P ILE* 4.7 6.7 - - + -
102P TYR* 6.6 0.2 - - + -
123P PHE 3.1 21.6 + - - +
124P ILE* 4.1 4.9 - - - +
125P ASN 3.4 0.2 - - - -
126P GLU* 1.3 100.4 + - - +
128P VAL* 1.3 58.7 + - - +
130P GLU* 3.6 6.4 + - - +
131P GLU* 2.9 35.3 + - - +
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Residues in contact with VAL 128 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M TYR* 4.0 17.7 - - + -
63M ASP* 4.1 14.9 - - + +
64M ARG* 3.8 28.9 + - - +
115M SER* 3.6 36.3 - - - +
124P ILE 3.3 17.5 - - - +
125P ASN* 3.7 12.3 - - - +
126P GLU 3.3 0.2 - - - -
127P GLN* 1.3 76.5 - - - +
129P GLU* 1.3 61.7 + - - +
131P GLU* 4.2 1.6 - - - +
132P ALA* 3.3 23.4 + - - +
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Residues in contact with GLU 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707 MET* 3.7 23.5 - - + +
63M ASP* 5.8 5.4 - - - +
125P ASN 3.8 7.5 + - - +
126P GLU* 3.2 9.9 + - - +
128P VAL* 1.3 78.2 - - - +
130P GLU* 1.3 59.4 + - + +
132P ALA* 3.5 5.1 + - + +
133P SER* 3.0 29.8 + - - -
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Residues in contact with GLU 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707 MET* 5.8 4.4 - - + +
24P TYR* 4.7 0.2 + - - -
46P GLN* 2.9 28.5 + - - +
50P GLU* 2.8 21.4 - - - +
53P HIS* 3.3 10.5 - - + -
94P GLU* 3.0 33.7 - - - +
126P GLU* 3.0 41.5 + - + +
127P GLN* 3.7 7.9 + - - +
128P VAL 3.4 0.2 - - - -
129P GLU* 1.3 75.1 - - - +
131P GLU* 1.3 63.6 + - - +
133P SER* 3.3 6.8 + - - -
134P VAL* 3.2 31.9 + - - +
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Residues in contact with GLU 131 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET 5.1 5.2 + - - -
63M ASP 5.5 2.0 - - - +
64M ARG* 3.8 25.0 + - - +
91P TYR* 3.7 22.7 + - + -
94P GLU* 3.5 27.5 - - + +
95P LYS* 3.8 24.0 - - - +
98P SER* 2.7 32.1 + - - +
102P TYR* 5.2 0.5 + - - -
127P GLN 2.9 17.6 + - - +
128P VAL 4.2 2.9 - - - +
130P GLU* 1.3 75.0 - - - +
132P ALA* 1.3 57.2 + - - +
134P VAL* 3.4 0.7 + - - -
135P LYS* 2.9 32.8 + - - +
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Residues in contact with ALA 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M TYR 5.3 0.4 - - - +
63M ASP* 3.4 48.6 + - - +
128P VAL 3.3 14.4 + - - +
129P GLU* 3.9 5.2 - - - +
130P GLU 3.3 0.2 - - - -
131P GLU* 1.3 78.2 - - - +
133P SER* 1.3 57.5 + - - +
135P LYS* 4.2 5.5 - - - +
136P LYS* 3.1 29.6 + - - +
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Residues in contact with SER 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P TRP* 3.6 20.8 + - - -
46P GLN* 5.2 3.3 + - - -
129P GLU 3.0 18.7 + - - -
130P GLU* 3.5 8.5 - - - -
131P GLU 3.2 0.2 - - - -
132P ALA* 1.3 78.2 - - - +
134P VAL* 1.3 61.7 + - - +
136P LYS* 3.8 7.1 - - - +
137P ILE* 3.6 25.7 + - - +
161P ARG* 5.1 1.4 + - - -
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Residues in contact with VAL 134 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P TYR* 4.8 6.7 - - + +
42P TRP* 4.3 18.8 - - + -
43P MET* 6.5 0.4 - - + -
46P GLN* 5.6 0.9 - - - +
87P PHE* 3.7 30.1 - - + +
90P ALA* 4.1 6.5 - - + +
91P TYR* 3.8 35.7 - - + +
94P GLU* 4.1 18.4 - - + -
130P GLU* 3.2 20.3 + - - +
131P GLU 4.0 2.9 - - - +
133P SER* 1.3 76.5 - - - +
135P LYS* 1.3 60.4 + - - +
137P ILE 3.3 1.9 + - - -
138P LEU* 3.0 24.9 + - - +
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Residues in contact with LYS 135 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET* 5.2 1.3 - - - -
65M ASN* 3.5 39.7 + - + +
91P TYR* 3.6 43.0 - - + +
131P GLU 2.9 19.3 + - - +
132P ALA* 4.2 5.6 - - - +
134P VAL* 1.3 74.3 - - - +
136P LYS* 1.3 60.2 + - - +
138P LEU* 3.4 14.0 - - + +
139P ASP* 2.7 63.9 + - - +
142P LYS* 5.4 4.4 - - - +
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Residues in contact with LYS 136 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354 GLY* 6.1 0.9 - - - +
374 GLU* 2.9 43.7 + - + +
132P ALA 3.1 20.6 + - - +
133P SER* 3.8 8.7 - - - +
134P VAL 3.3 0.4 - - - -
135P LYS* 1.3 77.3 - - - +
137P ILE* 1.3 63.3 + - + +
139P ASP* 3.8 7.2 + - - +
140P LYS* 3.4 48.6 + - + +
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Residues in contact with ILE 137 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P PHE* 4.3 3.8 - - + -
42P TRP* 3.6 33.9 - - + +
87P PHE* 3.7 35.7 - - + -
133P SER* 3.6 17.0 - - - +
134P VAL 3.3 1.4 + - - +
136P LYS* 1.3 79.8 - - + +
138P LEU* 1.3 65.4 + - - +
140P LYS* 3.2 10.1 + - + +
141P LEU* 3.0 29.7 + - + +
154P LEU* 4.8 10.5 - - + -
158P LEU* 3.8 33.0 - - + -
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Residues in contact with LEU 138 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P LEU* 3.8 3.6 - - + +
87P PHE* 3.5 31.3 - - + +
88P GLU* 3.8 24.0 - - + -
91P TYR* 3.6 29.2 - - + -
134P VAL 3.0 13.2 + - - +
135P LYS* 3.3 16.6 + - + +
137P ILE* 1.3 76.4 - - - +
139P ASP* 1.3 66.1 + - - +
141P LEU* 3.0 15.3 + - - +
142P LYS* 3.0 53.5 + - + +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344 LEU 6.1 1.6 - - - +
354 GLY* 6.1 5.2 - - - -
65M ASN* 4.4 4.2 - - - +
135P LYS* 2.7 54.8 + - - +
136P LYS* 4.0 6.6 - - - +
138P LEU* 1.3 82.1 - - - +
140P LYS* 1.3 57.6 + - + +
142P LYS* 3.4 15.3 + - - +
143P PHE* 3.0 26.2 + - - +
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Residues in contact with LYS 140 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354 GLY* 4.4 18.6 - - - +
374 GLU* 5.7 1.2 + - - +
1524 PHE* 4.8 15.4 - - + -
1554 ASP* 5.4 6.5 + - - -
136P LYS* 3.4 40.3 + - + +
137P ILE* 3.2 13.5 + - + +
139P ASP* 1.3 77.6 - - + +
141P LEU* 1.3 61.8 + - - +
143P PHE* 3.4 13.2 + - + +
144P ALA* 3.3 22.0 + - - +
150P ILE* 5.0 1.0 - - - +
154P LEU* 3.8 35.3 - - + +
157P GLU* 3.6 21.4 + - - -
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Residues in contact with LEU 141 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P PHE* 4.2 12.1 - - + -
83P PRO* 3.4 35.7 - - + +
84P LEU* 3.8 24.4 - - + +
87P PHE* 3.6 29.8 - - + -
137P ILE* 3.0 24.5 + - + +
138P LEU* 3.0 6.5 + - - +
140P LYS* 1.3 76.1 - - - +
142P LYS* 1.3 60.8 + - - +
143P PHE 3.2 0.4 - - - -
144P ALA* 3.5 20.6 + - + +
145P LYS* 3.8 4.0 + - - -
151P LEU* 3.8 29.4 - - + -
154P LEU* 4.4 7.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 142 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P LEU* 3.7 20.0 - - + -
88P GLU* 4.2 12.8 - - - -
135P LYS* 5.4 4.0 - - - +
138P LEU* 3.0 32.2 + - + +
139P ASP* 3.5 18.3 + - - +
140P LYS 3.4 0.2 - - - -
141P LEU* 1.3 75.0 - - - +
143P PHE* 1.3 63.6 + - - +
144P ALA 3.2 0.4 - - - -
145P LYS* 3.3 35.0 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344 LEU* 5.1 15.0 - - + -
364 LEU* 5.0 12.1 - - + -
1484 PRO* 4.2 35.4 - - + +
1514 LEU* 3.7 29.6 - - + -
1524 PHE* 5.1 13.5 - + + -
139P ASP 3.0 16.8 + - - +
140P LYS* 3.4 15.3 - - + +
141P LEU 3.2 0.4 - - - -
142P LYS* 1.3 76.4 - - - +
144P ALA* 1.3 58.1 + - - +
145P LYS 3.7 1.4 + - - -
150P ILE* 4.5 16.2 - - + +
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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