Contacts of the helix formed by residues 28 - 59 (chain M) in PDB entry 2FJC
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 28 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M PRO* 1.3 88.8 - - - +
29M ALA* 1.3 61.0 + - - +
30M ARG* 3.2 23.2 + - - +
31M ALA* 3.7 24.7 + - + +
32M ILE* 3.2 16.4 + - - +
148M SER* 5.6 0.7 - - - -
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Residues in contact with ALA 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M PRO* 5.2 0.8 - - - +
28M ASP* 1.3 72.7 + - - +
30M ARG* 1.3 74.6 + - - +
32M ILE* 3.1 11.3 - - + +
33M ALA* 2.8 31.5 + - - +
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Residues in contact with ARG 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ASP* 3.2 12.4 + - - +
29M ALA* 1.3 88.4 + - - +
31M ALA* 1.3 60.2 + - - +
33M ALA* 3.2 27.2 + - - +
34M ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ASP* 3.7 23.7 + - + +
29M ALA 3.4 0.4 - - - -
30M ARG* 1.3 77.8 - - - +
32M ILE* 1.3 59.6 + - - +
34M ALA* 3.1 6.9 + - - +
35M ILE* 2.9 34.6 + - + +
148M SER* 3.6 31.4 - - - +
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Residues in contact with ILE 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ASP 3.2 17.5 - - - +
29M ALA* 3.1 25.8 - - + +
31M ALA* 1.3 75.7 - - - +
33M ALA* 1.3 57.2 + - - +
35M ILE* 3.4 10.1 + - - +
36M CYS* 2.9 38.4 + - - -
93M LEU* 3.4 41.7 - - + +
150M ASP* 6.0 0.7 - - - +
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Residues in contact with ALA 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M ALA 2.8 19.2 + - - +
30M ARG* 3.5 32.5 - - - +
31M ALA 3.2 0.2 - - - -
32M ILE* 1.3 75.1 - - - +
34M ALA* 1.3 65.7 + - - +
36M CYS* 3.4 6.5 + - - +
37M GLU* 3.0 24.8 + - - +
40M ARG* 5.5 0.3 + - - -
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Residues in contact with ALA 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M ARG 2.9 17.2 + - - +
31M ALA* 3.5 7.0 - - - +
33M ALA* 1.3 76.5 - - - +
35M ILE* 1.3 62.8 + - - +
37M GLU* 3.3 7.8 + - - +
38M GLN* 3.1 25.1 + - - +
144M LEU* 4.0 19.5 - - + -
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Residues in contact with ILE 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M ALA* 2.9 23.1 + - + +
32M ILE* 3.7 7.4 - - - +
34M ALA* 1.3 77.2 - - - +
36M CYS* 1.3 57.3 + - - +
38M GLN* 3.0 9.1 + - - +
39M LEU* 2.8 48.0 + - + +
93M LEU* 4.1 10.3 - - + -
141M THR* 4.6 3.8 - - + +
144M LEU* 4.1 20.4 - - + -
145M ALA* 3.7 18.8 - - + +
148M SER* 3.6 24.7 - - - +
150M ASP* 3.8 15.0 - - + +
153M THR* 4.0 16.4 - - + -
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Residues in contact with CYS 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M ILE* 2.9 28.9 + - - +
33M ALA* 3.7 6.7 - - - +
34M ALA 3.3 0.2 - - - -
35M ILE* 1.3 76.4 - - - +
37M GLU* 1.3 57.2 + - - +
39M LEU* 4.2 0.9 - - - -
40M ARG* 2.8 47.6 + - - +
90M LEU* 3.5 29.3 - - + +
93M LEU* 3.7 31.9 - - - -
95M ALA* 3.9 11.2 - - - -
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Residues in contact with GLU 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ALA 3.0 14.4 + - - +
34M ALA* 3.5 12.3 - - - +
35M ILE 3.2 0.2 - - - -
36M CYS* 1.3 76.3 - - - +
38M GLN* 1.3 65.8 + - + +
40M ARG* 3.4 31.0 + - - +
41M GLN* 3.2 19.9 + - - +
107M LEU* 4.9 10.7 - - - +
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Residues in contact with GLN 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M ALA 3.1 15.1 + - - +
35M ILE 3.0 9.3 + - - +
37M GLU* 1.3 77.3 - - - +
39M LEU* 1.3 67.2 + - - +
41M GLN* 3.0 13.1 + - - +
42M HIS* 2.9 30.9 + - - -
137M ARG* 3.5 35.0 + - - +
140M GLN* 3.7 16.4 + - - +
141M THR* 3.1 33.6 + - + +
144M LEU* 4.2 18.4 - - + -
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Residues in contact with LEU 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ILE* 2.8 24.9 + - + +
36M CYS 3.6 4.7 - - - +
38M GLN* 1.3 76.7 - - - +
40M ARG* 1.3 63.1 + - - +
42M HIS* 3.0 15.3 + - + +
43M VAL* 2.9 27.1 + - - +
86M ILE* 3.8 16.7 - - + +
89M ARG* 4.1 17.7 - - + -
90M LEU* 3.6 24.0 - - + +
93M LEU* 3.8 29.2 - - + -
141M THR* 3.7 24.7 - - + -
153M THR* 4.3 1.8 - - + -
157M ILE* 4.2 13.7 - - + -
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Residues in contact with ARG 40 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ALA 5.5 0.2 + - - -
36M CYS* 2.8 36.9 + - - +
37M GLU* 3.6 33.2 + - - +
39M LEU* 1.3 76.0 - - - +
41M GLN* 1.3 62.0 + - - +
43M VAL 3.5 0.7 + - - -
44M ALA* 3.2 20.6 + - - +
90M LEU* 3.8 11.0 - - + +
95M ALA* 3.7 17.9 - - - +
96M GLN* 2.9 27.7 + - - +
98M PRO* 3.6 33.8 - - + +
107M LEU* 4.1 15.4 - - + +
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Residues in contact with GLN 41 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M GLU 3.2 8.5 + - - +
38M GLN* 3.0 17.2 + - - +
40M ARG* 1.3 77.7 - - - +
42M HIS* 1.3 62.4 + - - +
44M ALA* 3.2 6.5 + - - +
45M ASP* 2.8 42.3 + - - +
107M LEU* 3.5 29.6 + - + +
109M GLY* 4.5 4.0 - - - +
133M TYR* 3.9 11.7 + - - -
137M ARG* 3.3 37.0 + - - +
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Residues in contact with HIS 42 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M GLN* 2.9 30.4 + - - -
39M LEU* 3.4 21.1 - - + +
41M GLN* 1.3 79.8 + - - +
43M VAL* 1.3 58.0 + - - +
45M ASP* 3.2 8.7 + - - +
46M LEU* 2.8 37.2 + - - +
86M ILE* 4.0 12.1 - - + -
134M LEU* 5.3 2.0 - - - +
137M ARG* 3.5 31.0 - - + +
138M PHE* 3.3 44.7 - + + -
141M THR* 2.6 31.1 + - + -
157M ILE* 4.9 1.1 - - + -
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Residues in contact with VAL 43 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M LEU 2.9 20.3 + - - +
40M ARG 3.7 7.0 - - - +
42M HIS* 1.3 75.1 - - - +
44M ALA* 1.3 59.1 + - - +
46M LEU* 4.5 2.9 - - - -
47M GLY* 2.8 25.6 + - - -
83M PHE* 3.4 34.4 - - + +
86M ILE* 3.7 17.7 - - + -
87M ALA* 3.8 22.2 - - + +
90M LEU* 4.5 7.9 - - + -
98M PRO* 3.8 12.3 - - + +
104M TYR* 3.7 18.2 - - + +
58N TRP* 4.5 6.7 - - + -
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Residues in contact with ALA 44 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M ARG 3.2 6.9 + - - +
41M GLN 3.2 8.6 + - - +
43M VAL* 1.3 81.0 - - - +
45M ASP* 1.3 62.6 + - - +
47M GLY* 3.3 1.6 + - - -
48M VAL* 3.0 28.4 + - - +
104M TYR* 3.5 30.7 - - + +
107M LEU* 3.6 31.2 - - + -
108M SER* 3.9 7.9 - - - +
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Residues in contact with ASP 45 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M GLN* 2.8 32.3 + - - +
42M HIS* 3.8 4.6 + - - +
44M ALA* 1.3 71.2 - - - +
46M LEU* 1.3 61.1 + - - +
48M VAL* 3.2 1.6 + - - +
49M LEU* 2.8 29.8 + - - +
108M SER* 2.8 14.4 + - - -
109M GLY 2.7 29.0 + - - -
110M ILE* 3.6 18.0 + - + +
133M TYR* 3.1 31.2 + - - -
134M LEU* 3.8 14.6 - - + +
137M ARG* 4.9 2.1 - - - +
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Residues in contact with LEU 46 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M HIS 2.8 26.4 + - - +
43M VAL* 3.7 4.7 - - - +
45M ASP* 1.3 71.8 - - - +
47M GLY* 1.3 58.9 + - - +
49M LEU* 3.2 1.9 + - + -
50M TYR* 2.8 30.5 + - - +
79M VAL* 3.4 32.9 - - + +
82M ALA* 4.0 7.0 - - + -
83M PHE* 3.8 32.1 - - + +
86M ILE* 3.9 25.6 - - + -
134M LEU* 3.6 30.5 - - + -
138M PHE* 3.9 13.9 - - + -
160M ILE* 6.2 0.2 - - + -
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Residues in contact with GLY 47 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M VAL 2.8 17.0 + - - -
44M ALA 3.7 2.0 - - - -
46M LEU* 1.3 77.5 - - - +
48M VAL* 1.3 60.6 + - - +
50M TYR* 3.3 18.2 + - - +
51M ILE* 3.5 5.0 + - - +
83M PHE* 3.7 18.5 - - - -
104M TYR* 4.6 3.8 - - - -
51N ILE* 5.5 1.7 - - - +
101N MET* 3.2 21.5 - - - +
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Residues in contact with VAL 48 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M ALA 3.0 20.8 + - - +
45M ASP 3.7 4.5 - - - +
47M GLY* 1.3 75.3 - - - +
49M LEU* 1.3 63.3 + - - +
51M ILE* 3.3 4.9 + - - +
52M LYS* 3.0 20.4 + - + +
104M TYR* 4.2 6.7 - - + +
105M LEU* 4.7 7.6 - - + -
108M SER* 3.4 23.1 - - - +
110M ILE* 3.6 31.9 - - + +
112M GLU* 3.9 25.1 - - + +
101N MET* 3.8 22.4 - - - -
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Residues in contact with LEU 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M ASP 2.8 16.8 + - - +
46M LEU* 3.6 6.1 - - - +
48M VAL* 1.3 77.0 - - - +
50M TYR* 1.3 56.0 + - - +
52M LYS* 3.0 10.9 + - + -
53M LEU* 2.7 56.4 + - + +
56M TYR* 6.1 0.9 - - + -
79M VAL* 3.9 14.6 - - + -
110M ILE* 4.2 14.1 - - + +
127M VAL* 5.6 2.5 - - + -
130M ASP* 4.2 22.0 - - + +
131M PHE* 3.8 25.1 - - + -
134M LEU* 3.6 29.2 - - + -
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Residues in contact with TYR 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M LEU 2.8 13.6 + - - +
47M GLY* 3.3 14.1 - - - +
48M VAL 3.2 0.2 - - - -
49M LEU* 1.3 77.1 - - - +
51M ILE* 1.3 73.8 + - + +
53M LEU* 3.6 3.7 + - - +
54M HIS* 2.8 51.2 + + - -
76M TYR* 3.3 42.2 - + + -
79M VAL* 4.0 8.2 - - + +
80M THR* 3.6 23.9 - - + +
83M PHE* 6.3 1.3 - - + -
50N TYR* 3.4 38.3 + + - -
51N ILE* 6.5 0.9 - - + -
80N THR* 2.7 30.0 + - - +
83N PHE* 5.3 4.7 - + - -
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Residues in contact with ILE 51 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M GLY 3.5 4.2 + - - +
48M VAL 3.3 6.5 + - - +
49M LEU 3.2 0.4 - - - -
50M TYR* 1.3 89.4 - - + +
52M LYS* 1.3 67.3 + - - +
53M LEU 3.2 0.2 - - - -
54M HIS* 3.0 17.9 + - + +
55M ASN* 3.0 11.3 + - - +
101M MET* 3.9 11.4 - - + -
112M GLU* 4.8 1.6 - - - +
47N GLY* 5.6 1.8 - - - +
50N TYR* 6.6 0.2 - - + -
51N ILE* 5.0 2.9 - - + -
83N PHE* 5.0 7.2 - - + -
99N ALA* 3.7 5.1 - - - +
100N SER* 3.6 33.2 - - - +
101N MET* 3.6 32.1 - - + +
104N TYR* 3.5 31.2 - - + +
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Residues in contact with LYS 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M VAL* 3.0 17.8 + - + +
49M LEU* 3.5 10.1 - - + +
51M ILE* 1.3 77.9 - - - +
53M LEU* 1.3 62.2 + - - +
55M ASN* 3.0 23.2 + - - +
56M TYR* 3.2 41.0 + - + -
110M ILE* 3.7 9.6 - - + +
111M ALA* 2.7 33.5 + - - +
112M GLU* 4.4 2.0 - - + -
113M GLU* 4.0 23.6 - - + +
126M ARG* 5.3 3.1 + - - +
130M ASP* 2.7 37.6 + - - +
99N ALA 4.9 2.5 - - - -
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Residues in contact with LEU 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LEU* 2.7 40.3 + - + +
50M TYR 3.8 4.9 - - - +
52M LYS* 1.3 73.3 - - - +
54M HIS* 1.3 56.6 + - - +
56M TYR* 3.4 5.1 + - + +
57M HIS* 2.8 28.9 + - - +
72M LEU* 4.0 15.2 - - + +
75M TYR* 3.9 15.9 - - + -
76M TYR* 3.7 32.3 - - + +
79M VAL* 3.6 30.5 - - + -
127M VAL* 3.8 31.9 - - + -
131M PHE* 4.9 2.9 - - + -
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Residues in contact with HIS 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M TYR* 2.8 56.1 + + - -
51M ILE* 3.0 12.0 + - + +
53M LEU* 1.3 74.3 - - - +
55M ASN* 1.3 61.7 + - - +
57M HIS* 3.1 7.6 + - - +
58M TRP* 2.8 62.7 + + + -
76M TYR* 3.4 38.1 + + - -
80N THR* 4.7 1.6 + - - -
83N PHE* 3.5 28.8 - + + -
84N ASP* 3.8 14.7 + - - +
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Residues in contact with ASN 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M ILE 3.0 8.5 + - - +
52M LYS* 3.0 14.1 - - - +
54M HIS* 1.3 77.3 - - - +
56M TYR* 1.3 59.2 + - - +
58M TRP* 4.2 0.6 - - - -
59M HIS* 2.8 55.3 + - - +
113M GLU* 3.1 43.2 + - + +
115M GLU 3.4 13.9 + - - +
116M LYS* 5.0 3.8 - - - +
118M ILE* 5.5 0.9 - - - +
99N ALA* 3.1 38.4 + - + +
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Residues in contact with TYR 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LEU* 6.1 0.4 - - + -
52M LYS* 3.2 47.5 + - + -
53M LEU* 3.9 8.7 - - + +
55M ASN* 1.3 75.0 - - - +
57M HIS* 1.3 67.6 + - - +
59M HIS 4.4 0.2 - - - +
60M ILE* 3.0 32.9 + - - +
72M LEU* 3.8 15.9 - - + -
113M GLU* 2.6 42.9 + - + -
118M ILE* 3.7 23.6 - - + -
123M ALA* 3.7 22.9 - - + -
126M ARG* 3.3 19.5 - - + +
127M VAL* 3.5 32.1 - - + -
130M ASP* 5.4 0.4 - - - -
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Residues in contact with HIS 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M LEU 2.8 17.0 + - - +
54M HIS* 3.1 12.3 - - - +
56M TYR* 1.3 78.8 - - - +
58M TRP* 1.3 82.8 + + - +
60M ILE* 4.2 6.1 - - - +
65M PHE* 4.3 1.4 - - - -
69M HIS* 2.7 79.9 + + - -
72M LEU* 3.8 14.3 - - + +
73M GLU* 3.8 25.4 + - + -
76M TYR* 3.6 13.1 + + + -
84N ASP* 3.7 4.7 - - - -
614N FE 2.3 29.9 - - - -
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Residues in contact with TRP 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M HIS* 2.8 50.2 + + + +
55M ASN* 3.8 2.2 - - - +
57M HIS* 1.3 88.9 - + - +
59M HIS* 1.3 71.5 + + - +
60M ILE 3.7 3.8 + - - +
65M PHE* 4.8 5.6 - - - -
69M HIS* 5.0 1.3 - + - -
43N VAL* 4.5 0.9 - - + -
83N PHE* 3.5 33.9 - + - -
84N ASP* 3.3 19.7 + - - -
87N ALA* 3.3 29.0 - - + +
88N GLU* 3.9 12.0 + - + +
91N LEU* 3.4 38.5 - - + +
97N ALA* 3.9 15.0 - - + -
98N PRO 3.6 20.9 - - - -
99N ALA* 3.8 15.7 - - + -
104N TYR* 3.7 4.7 - - - -
----------------------------------------------------------
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Residues in contact with HIS 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M ASN* 2.8 40.1 + - - +
56M TYR 3.9 0.2 - - - -
58M TRP* 1.3 86.3 - + + +
60M ILE* 1.3 66.4 + - - +
61M TYR* 4.1 2.4 - - - +
116M LYS* 3.4 15.8 - - + +
117M GLU* 3.2 25.1 - - - +
118M ILE* 3.0 23.5 + - + +
91N LEU* 3.7 16.6 - - + +
96N GLN* 4.0 15.5 - - + -
97N ALA* 3.2 44.2 + - - -
99N ALA* 4.1 9.4 - - + -
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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