Contacts of the helix formed by residues 82 - 111 (chain S) in PDB entry 2JD6
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 SER 82 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 2.9 15.6 + - - -
80S TRP* 4.1 0.2 - - - +
81S GLU* 1.3 83.0 - - - +
83S PRO* 1.4 76.1 - - - +
84S LEU* 3.8 9.0 + - - +
85S LYS* 2.8 34.9 + - - +
86S ALA* 2.8 12.3 + - - +
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Residues in contact with PRO 83 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 3.3 6.7 - - - +
31S PHE* 3.5 31.4 - - + -
34S LEU* 4.0 8.5 - - + -
36S LEU* 3.9 19.3 - - + -
39S PHE* 4.9 1.1 - - + -
82S SER* 1.4 85.6 - - - +
84S LEU* 1.3 61.3 + - - +
86S ALA* 3.2 3.8 + - - +
87S PHE* 3.0 27.0 + - - -
141S LEU* 3.7 12.3 - - + -
151S LEU* 4.0 26.9 - - + -
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Residues in contact with LEU 84 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82S SER* 3.0 9.9 + - - +
83S PRO* 1.3 78.3 - - - +
85S LYS* 1.3 71.8 + - - +
87S PHE 3.3 1.0 + - - -
88S GLU* 2.9 42.6 + - - +
138S LEU* 3.9 38.1 - - + +
141S LEU* 3.8 25.9 - - + +
142S LYS* 4.1 18.8 - - + -
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Residues in contact with LYS 85 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S TRP* 4.0 7.2 - - + -
81S GLU* 3.8 35.2 - - + +
82S SER* 2.8 29.6 + - - +
84S LEU* 1.3 81.8 - - + +
86S ALA* 1.3 52.5 + - - +
88S GLU* 2.7 39.7 + - - +
89S ALA* 2.8 32.9 + - - +
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Residues in contact with ALA 86 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S MET* 3.6 13.0 - - - +
30S TYR* 4.0 13.7 - - + -
31S PHE* 3.7 24.2 - - + -
80S TRP* 3.8 21.6 - - + +
82S SER 2.8 10.4 + - - +
83S PRO 3.3 9.9 - - - +
85S LYS* 1.3 75.8 - - - +
87S PHE* 1.3 57.7 + - - +
89S ALA* 2.9 7.0 + - - +
90S ALA* 2.8 24.0 + - - -
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Residues in contact with PHE 87 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S PHE* 3.6 16.8 - + - -
39S PHE* 3.6 31.0 - + + -
42S TRP* 4.1 14.8 - + - -
43S MET* 3.6 25.1 - - + -
83S PRO 3.0 20.2 + - - +
84S LEU 3.3 2.4 + - - +
86S ALA* 1.3 74.7 - - - +
88S GLU* 1.3 60.9 + - - +
90S ALA* 3.8 4.3 - - + +
91S TYR* 2.9 30.3 + - - +
134S VAL* 3.9 22.4 - - + +
137S ILE* 3.5 42.4 - - + -
138S LEU* 3.6 16.3 - - + +
141S LEU* 3.6 18.4 - - + -
158S LEU* 4.7 1.6 - - + -
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Residues in contact with GLU 88 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S LEU* 2.9 38.3 + - + +
85S LYS* 2.7 46.2 + - + +
86S ALA 3.2 0.2 - - - -
87S PHE* 1.3 77.6 - - - +
89S ALA* 1.3 56.9 + - - +
91S TYR* 3.8 2.4 - - - +
92S GLU* 2.9 30.3 + - - +
138S LEU* 3.9 20.9 - - + -
142S LYS* 4.4 11.2 - - - +
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Residues in contact with ALA 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU* 5.2 1.5 - - + +
27S MET* 3.8 9.0 - - + -
80S TRP* 3.3 30.7 - - + +
85S LYS 2.8 10.8 + - - +
86S ALA 2.9 8.7 + - - +
88S GLU* 1.3 77.0 - - - +
90S ALA* 1.3 55.7 + - - +
92S GLU* 3.4 12.9 + - - +
93S HIS* 2.9 28.2 + - - +
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Residues in contact with ALA 90 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S TYR* 3.9 22.7 + - + +
27S MET* 3.6 14.3 - - + +
43S MET* 4.5 8.1 - - + -
86S ALA 2.8 17.5 + - - +
87S PHE* 3.8 10.5 - - + +
89S ALA* 1.3 68.6 - - - +
91S TYR* 1.3 56.5 + - - +
93S HIS* 3.0 8.8 + - - +
94S GLU* 2.7 38.3 + - - +
134S VAL* 4.1 13.9 - - + -
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Residues in contact with TYR 91 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S PHE 2.9 18.8 + - - +
88S GLU* 3.8 3.6 - - - +
90S ALA* 1.3 72.5 - - - +
92S GLU* 1.3 67.9 + - - +
94S GLU* 3.1 4.5 + - + +
95S LYS* 3.0 53.8 + - + +
131S GLU* 3.8 23.1 - - + -
134S VAL* 3.6 11.3 - - + +
135S LYS* 3.3 58.0 - - + +
138S LEU* 3.9 17.7 - - + -
1X MET* 3.2 28.3 - - + +
65X ASN* 4.6 2.4 + - - -
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Residues in contact with GLU 92 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88S GLU 2.9 19.0 + - - +
89S ALA* 3.7 11.5 - - - +
91S TYR* 1.3 77.3 - - - +
93S HIS* 1.3 59.0 + - - +
95S LYS* 3.3 13.0 + - + +
96S PHE* 3.0 26.6 + - + +
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Residues in contact with HIS 93 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S ARG* 5.3 1.1 - - + -
19S TYR* 4.1 28.3 - + - -
20S SER* 2.7 34.6 + - - -
23S LEU* 3.5 25.7 - - + +
24S TYR* 3.7 15.0 - + - -
89S ALA 2.9 14.3 + - - +
90S ALA* 3.0 8.9 + - - +
92S GLU* 1.3 75.8 + - - +
94S GLU* 1.3 59.8 + - - +
96S PHE* 3.1 33.0 + + - +
97S ILE* 2.9 35.3 + - + +
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Residues in contact with GLU 94 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S SER* 5.1 0.2 + - - -
24S TYR* 2.6 29.7 + - - +
46S GLN* 5.5 0.7 - - - -
50S GLU* 3.7 11.3 - - - +
90S ALA 2.7 17.5 + - - +
91S TYR* 3.1 7.4 + - - +
93S HIS* 1.3 75.7 - - - +
95S LYS* 1.3 57.1 + - - +
97S ILE* 3.2 6.2 + - - +
98S SER* 2.9 32.1 + - - -
127S GLN* 3.1 21.1 + - - +
130S GLU* 2.9 37.9 - - + +
131S GLU* 3.9 18.6 - - + -
134S VAL* 4.1 22.2 - - + -
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Residues in contact with LYS 95 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S TYR* 3.0 51.9 + - + +
92S GLU* 3.4 13.7 - - + +
94S GLU* 1.3 73.1 - - - +
96S PHE* 1.3 60.6 + - - +
98S SER* 3.4 2.9 + - - -
99S LYS* 3.0 26.9 + - - +
131S GLU* 4.1 21.5 - - + +
1X MET* 5.0 11.2 - - - -
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Residues in contact with PHE 96 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S ARG* 4.0 25.1 - - + -
19S TYR* 6.2 1.1 - + - -
92S GLU* 3.0 13.4 + - + +
93S HIS* 3.1 37.0 + + - +
95S LYS* 1.3 74.2 - - - +
97S ILE* 1.3 65.3 + - + +
99S LYS* 3.5 13.7 + - + +
100S SER* 3.0 27.7 + - - -
1669S SO4 3.4 40.4 - - - -
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Residues in contact with ILE 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S GLN* 4.1 17.5 - - - +
16S ARG* 4.2 20.9 - - + +
17S GLU* 4.4 16.4 - - - +
20S SER* 3.4 26.5 - - - +
50S GLU* 5.6 0.4 - - - +
93S HIS* 2.9 28.0 + - + +
94S GLU* 3.2 13.0 + - - +
96S PHE* 1.3 79.1 - - + +
98S SER* 1.3 65.8 + - - +
100S SER* 2.9 7.3 + - - -
101S ILE* 2.8 23.0 + - + +
127S GLN* 3.6 28.7 - - + +
201S FE 4.4 2.0 - - - -
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Residues in contact with SER 98 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94S GLU 2.9 10.3 + - - -
95S LYS 3.7 6.7 - - - -
96S PHE 3.4 0.2 - - - -
97S ILE* 1.3 76.7 - - - +
99S LYS* 1.3 56.3 + - - +
101S ILE* 3.1 5.2 + - - +
102S TYR* 2.8 57.5 + - - -
127S GLN* 3.1 25.9 + - - +
131S GLU* 2.6 28.6 + - - -
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Residues in contact with LYS 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95S LYS 3.0 14.2 + - - +
96S PHE* 3.5 19.5 - - + +
98S SER* 1.3 74.3 - - - +
100S SER* 1.3 57.3 + - - +
102S TYR* 3.2 13.6 + - + +
103S GLU* 2.9 63.7 + - + +
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Residues in contact with SER 100 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S GLN* 3.2 24.5 - - - +
16S ARG* 3.1 32.3 + - - +
96S PHE* 3.0 18.7 + - - -
97S ILE* 2.9 15.8 + - - -
99S LYS* 1.3 75.6 - - - +
101S ILE* 1.3 55.1 + - - -
103S GLU* 3.4 8.8 + - - +
104S LEU* 3.0 30.5 + - - +
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Residues in contact with ILE 101 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S GLN* 3.7 26.9 - - + +
17S GLU* 4.4 3.4 - - - +
57S PHE* 4.0 15.9 - - + -
97S ILE* 2.8 22.0 + - + +
98S SER* 3.8 7.2 - - - +
100S SER* 1.3 70.4 - - - +
102S TYR* 1.3 65.9 + - + +
104S LEU* 3.3 5.8 + - + +
105S ALA* 2.9 20.4 + - - +
120S LEU* 4.2 15.5 - - + +
123S PHE* 3.8 33.7 - - + -
124S ILE* 3.8 28.5 - - + +
127S GLN* 4.4 14.1 - - + -
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Residues in contact with TYR 102 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98S SER* 2.8 51.1 + - - +
99S LYS* 3.8 12.3 - - + +
101S ILE* 1.3 73.6 - - + +
103S GLU* 1.3 53.8 + - + +
105S ALA* 3.0 8.5 + - - +
106S ALA* 2.7 37.1 + - - +
124S ILE* 4.6 13.9 - - + -
127S GLN* 5.7 3.0 - - + +
131S GLU* 4.5 1.7 + - - -
64X ARG* 3.4 13.0 + - - -
112X LYS 5.8 1.8 - - - -
114X TYR* 3.6 48.7 - + + -
115X SER* 3.0 25.1 + - - -
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Residues in contact with GLU 103 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99S LYS* 2.9 47.4 + - + +
100S SER* 3.7 7.8 - - - +
102S TYR* 1.3 77.6 - - + +
104S LEU* 1.3 57.6 + - - +
106S ALA* 3.1 8.5 + - + +
107S LEU* 2.8 29.4 + - - +
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Residues in contact with LEU 104 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S MET* 3.9 19.5 - - - -
9S ALA* 3.8 31.6 - - + +
10S LEU* 4.2 11.4 - - + -
13S GLN* 3.7 37.2 - - + +
16S ARG* 5.6 0.7 - - - +
57S PHE* 4.2 13.0 - - + -
100S SER 3.0 14.0 + - - +
101S ILE* 3.3 9.2 + - + +
103S GLU* 1.3 73.9 - - - +
105S ALA* 1.3 65.4 + - - +
107S LEU* 3.3 7.2 + - + +
108S ALA* 2.9 24.4 + - - +
120S LEU* 3.6 19.1 - - + +
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Residues in contact with ALA 105 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101S ILE 2.9 17.1 + - - +
102S TYR* 3.3 10.5 - - - +
104S LEU* 1.3 73.9 - - - +
106S ALA* 1.3 64.5 + - - +
108S ALA* 3.1 3.3 + - - +
109S GLU* 3.1 22.4 + - - +
117S ARG* 3.7 22.8 - - - +
120S LEU* 3.6 12.7 - - + +
124S ILE* 4.5 7.6 - - + -
114X TYR* 3.7 25.4 - - + -
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Residues in contact with ALA 106 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S TYR 2.7 12.8 + - - +
103S GLU* 3.4 11.2 - - + +
105S ALA* 1.3 73.3 - - - +
107S LEU* 1.3 60.2 + - - +
109S GLU* 3.1 8.0 + - - +
110S GLU* 2.8 46.7 + - - +
114X TYR* 3.5 18.6 + - + +
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Residues in contact with LEU 107 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S ARG* 4.2 25.6 - - + +
6S MET* 3.7 20.2 - - + +
9S ALA* 3.6 30.5 - - + -
103S GLU 2.8 19.9 + - - +
104S LEU* 3.5 8.3 - - + +
106S ALA* 1.3 72.6 - - - +
108S ALA* 1.3 62.3 + - - +
110S GLU* 3.3 22.9 + - + +
111S GLU* 3.2 29.8 + - + +
----------------------------------------------------------
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Residues in contact with ALA 108 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S MET* 3.5 19.9 - - + +
104S LEU 2.9 17.0 + - - +
105S ALA 3.6 3.8 - - - +
107S LEU* 1.3 76.5 - - - +
109S GLU* 1.3 60.2 + - - +
111S GLU* 3.0 3.5 + - - -
112S LYS 3.0 7.8 + - - -
113S ASP* 2.9 47.4 + - + +
116S THR* 4.3 4.9 - - + -
117S ARG* 3.9 19.5 - - + +
120S LEU* 4.7 0.4 - - + -
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Residues in contact with GLU 109 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105S ALA 3.1 12.5 + - - +
106S ALA* 3.1 6.0 + - - +
108S ALA* 1.3 76.4 - - - +
110S GLU* 1.3 63.2 + - + +
111S GLU 3.1 1.2 + - - -
112S LYS* 3.3 25.3 + - - +
113S ASP 6.0 0.4 - - - -
117S ARG* 3.1 38.1 + - + +
114X TYR* 3.0 31.7 + - - -
----------------------------------------------------------
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Residues in contact with GLU 110 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106S ALA* 2.8 32.2 + - - +
107S LEU* 3.4 22.7 - - + +
108S ALA 3.1 0.2 - - - -
109S GLU* 1.3 78.6 - - + +
111S GLU* 1.3 58.1 + - + +
112S LYS* 3.6 1.7 - - - +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S SER* 3.1 34.6 + - - -
5S ARG* 3.7 23.0 - - - +
6S MET* 4.0 21.9 - - + +
107S LEU* 3.2 19.5 - - + +
108S ALA 3.0 3.9 + - - +
110S GLU* 1.3 77.8 - - + +
112S LYS* 1.3 75.1 + - - +
113S ASP* 3.1 9.7 + - + +
----------------------------------------------------------
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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