Contacts of the helix formed by residues 36 - 64 (chain Z) 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 LEU 36 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R PHE* 5.1 10.3 - - + -
31Z PHE* 2.8 38.2 + - + +
32Z GLU* 5.1 0.2 - - - -
34Z LEU* 4.2 19.7 - - + +
35Z GLY* 1.3 77.3 - - - +
37Z GLU* 1.3 62.9 + - - +
38Z GLY 3.4 0.2 + - - -
39Z PHE* 3.4 13.3 + - + +
40Z ALA* 3.1 18.9 + - - +
83Z PRO* 4.1 19.5 - - + -
151Z LEU* 4.3 28.0 - - + +
152Z PHE* 5.7 1.3 - - - +
155Z ASP* 3.3 31.0 - - + +
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Residues in contact with GLU 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R LYS* 2.9 46.3 + - + +
140R LYS* 6.3 0.2 - - - +
32Z GLU* 3.6 19.5 - - - +
35Z GLY* 3.3 13.3 + - - +
36Z LEU* 1.3 71.2 - - - +
38Z GLY* 1.3 59.5 + - - +
40Z ALA* 3.7 6.5 - - - +
41Z ASN* 3.0 39.9 + - - +
155Z ASP* 3.5 5.0 + - - +
159Z SER* 5.4 0.4 - - - -
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Residues in contact with GLY 38 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z GLU* 1.3 76.1 - - - +
39Z PHE* 1.3 59.7 + - - +
41Z ASN* 3.5 2.6 + - - +
42Z TRP* 3.0 28.4 + - - +
155Z ASP* 2.9 32.3 + - - -
158Z LEU* 3.6 12.0 - - - +
159Z SER* 3.8 18.6 - - - -
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Residues in contact with PHE 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Z PHE* 3.5 34.3 - + + -
36Z LEU* 3.4 12.8 + - + +
38Z GLY* 1.3 73.9 - - - +
40Z ALA* 1.3 59.8 + - - +
42Z TRP* 3.3 8.3 + - - +
43Z MET* 3.0 32.7 + - - +
87Z PHE* 3.7 28.2 - + - -
137Z ILE* 4.4 3.4 - - + -
141Z LEU* 4.1 16.8 - - + -
151Z LEU* 4.0 26.7 - - + -
154Z LEU* 4.0 16.6 - - + -
155Z ASP* 3.2 46.2 + - + -
158Z LEU* 3.6 24.9 - - + -
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Residues in contact with ALA 40 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 4.5 0.7 - - - +
28Z ALA* 3.4 27.8 - - - +
31Z PHE* 3.8 4.0 - - - +
32Z GLU* 3.4 33.9 - - - +
36Z LEU 3.1 17.6 + - - +
37Z GLU 3.7 5.2 - - - +
39Z PHE* 1.3 76.5 - - - +
41Z ASN* 1.3 57.0 + - - +
43Z MET 3.2 1.7 + - - -
44Z LYS* 3.0 32.9 + - - +
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Residues in contact with ASN 41 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Z GLU* 5.2 0.3 - - - +
37Z GLU* 3.0 25.4 + - - +
38Z GLY* 4.0 4.6 - - - +
40Z ALA* 1.3 73.9 - - - +
42Z TRP* 1.3 66.3 + - - +
44Z LYS* 3.6 25.5 + - - +
45Z ALA* 3.0 21.5 + - - +
159Z SER* 5.3 8.1 + - - +
161Z ARG 3.7 14.3 - - - +
162Z ALA* 4.5 6.2 - - - +
163Z PRO* 3.4 24.0 - - + +
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Residues in contact with TRP 42 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Z TYR* 5.8 0.9 - + - -
38Z GLY 3.0 15.0 + - - +
39Z PHE* 3.3 10.5 + - - +
41Z ASN* 1.3 74.6 - - - +
43Z MET* 1.3 85.7 + - + +
45Z ALA* 3.4 3.8 + - - +
46Z GLN* 3.0 46.8 + - + +
87Z PHE* 4.3 9.6 - + + -
133Z SER* 3.8 17.0 + - - -
134Z VAL* 4.3 21.3 - - + -
137Z ILE* 3.6 24.5 - - + +
158Z LEU* 3.6 37.2 - - + +
161Z ARG* 3.3 52.9 + - + +
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Residues in contact with MET 43 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Z TYR* 3.3 48.6 - - + +
27Z MET* 3.8 33.2 - - + -
28Z ALA* 3.8 7.2 - - + +
31Z PHE* 4.1 13.9 - - + -
39Z PHE 3.0 17.0 + - - +
40Z ALA 3.2 7.8 + - - +
42Z TRP* 1.3 89.0 - - + +
44Z LYS* 1.3 58.0 + - - +
46Z GLN* 3.4 2.6 + - - +
47Z ALA* 2.9 28.1 + - - +
87Z PHE* 3.7 38.6 - - + -
90Z ALA* 4.6 5.6 - - + -
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Residues in contact with LYS 44 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 5.0 13.1 - - + +
58H TYR* 3.4 37.8 - - - -
59H ASN* 4.1 10.5 + - - -
25Z PHE* 4.9 10.1 - - + -
28Z ALA* 3.9 10.1 - - + -
32Z GLU* 3.2 20.6 + - - -
40Z ALA 3.0 16.8 + - - +
41Z ASN* 3.6 28.3 + - - +
42Z TRP 3.3 0.2 - - - -
43Z MET* 1.3 74.6 - - - +
45Z ALA* 1.3 63.2 + - - +
47Z ALA* 3.3 8.9 + - - +
48Z GLU* 3.2 26.9 + - - +
163Z PRO* 3.9 19.5 - - + -
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Residues in contact with ALA 45 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H LEU* 5.9 0.2 - - - +
41Z ASN 3.0 17.5 + - - +
42Z TRP 3.7 2.2 - - - +
44Z LYS* 1.3 75.1 - - - +
46Z GLN* 1.3 62.0 + - - +
48Z GLU* 3.5 8.1 + - - +
49Z GLU* 3.4 23.0 + - - +
161Z ARG* 3.6 28.7 + - + +
162Z ALA 3.8 22.9 - - - +
163Z PRO* 4.1 8.9 - - + +
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Residues in contact with GLN 46 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Z TYR* 3.9 23.6 - - + -
42Z TRP* 3.0 41.6 + - + +
43Z MET* 3.7 6.3 - - - +
44Z LYS 3.3 0.2 - - - -
45Z ALA* 1.3 75.9 - - - +
47Z ALA* 1.3 63.7 + - - +
49Z GLU* 3.2 19.4 + - - +
50Z GLU* 2.9 27.9 + - - +
94Z GLU* 5.7 0.2 - - - -
130Z GLU* 2.6 33.1 + - - +
133Z SER* 5.2 3.5 + - - -
134Z VAL* 5.6 3.6 - - + +
161Z ARG* 2.9 29.4 + - - +
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Residues in contact with ALA 47 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z ALA* 3.3 50.8 - - + +
24Z TYR* 4.2 3.3 - - - +
25Z PHE* 4.2 14.4 - - + +
43Z MET 2.9 18.1 + - - +
44Z LYS* 3.3 10.5 + - - +
46Z GLN* 1.3 76.3 - - - +
48Z GLU* 1.3 61.7 + - + +
50Z GLU* 3.4 1.3 + - - -
51Z ILE* 3.3 13.2 + - + +
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Residues in contact with GLU 48 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 5.7 2.4 - - - +
165H LEU* 3.9 20.1 - - + +
169H LEU* 3.8 15.2 - - + +
44Z LYS 3.2 8.9 + - - +
45Z ALA* 3.7 9.4 - - - +
46Z GLN 3.3 0.2 - - - -
47Z ALA* 1.3 74.8 - - + +
49Z GLU* 1.3 64.8 + - - +
51Z ILE* 3.2 17.4 + - + +
52Z GLY 3.1 16.6 + - - -
163Z PRO* 3.2 22.7 - - - +
164Z LYS* 2.9 28.3 + - - +
165Z LEU* 3.2 36.1 + - + +
166Z PRO* 3.5 2.4 - - - +
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Residues in contact with GLU 49 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H LEU 5.0 0.5 - - - +
169H LEU* 3.6 18.8 - - + +
170H MET* 3.1 35.1 + - - +
45Z ALA 3.4 4.9 + - - +
46Z GLN* 3.2 21.9 + - - +
48Z GLU* 1.3 78.1 - - - +
50Z GLU* 1.3 53.4 + - - +
52Z GLY* 3.1 4.3 + - - -
53Z HIS* 2.7 43.8 + - - +
130Z GLU* 4.9 1.3 - - - +
161Z ARG* 3.6 25.8 + - - +
164Z LYS* 5.4 3.8 + - - -
1173Z AG 2.9 22.6 - - - -
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Residues in contact with GLU 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Z GLU* 2.9 46.7 - - - +
20Z SER* 3.8 10.6 + - - -
21Z ALA* 3.7 9.4 - - - +
24Z TYR* 3.7 26.5 - - + -
46Z GLN* 2.9 36.7 + - - +
47Z ALA 3.7 3.1 - - - +
48Z GLU 3.3 0.4 - - - -
49Z GLU* 1.3 72.1 - - - +
51Z ILE* 1.3 60.5 + - - +
53Z HIS* 3.2 13.7 + - - +
54Z ALA* 3.0 23.9 + - - +
94Z GLU* 4.7 1.9 - - - +
97Z ILE* 5.6 1.4 - - - +
127Z GLN* 5.0 4.0 + - - -
130Z GLU* 3.0 17.6 - - - +
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Residues in contact with ILE 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ILE* 4.8 26.5 - - + -
165H LEU* 4.1 20.0 - - + -
18Z LEU* 4.9 15.9 - - + -
21Z ALA* 3.7 15.3 - - + -
47Z ALA* 3.3 17.7 + - + +
48Z GLU* 3.2 19.0 + - + +
50Z GLU* 1.3 76.2 - - - +
52Z GLY* 1.3 57.9 + - - +
54Z ALA* 3.2 9.7 + - - +
55Z LEU* 3.0 36.3 + - + +
165Z LEU* 6.3 1.3 - - + -
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Residues in contact with GLY 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H PRO* 6.0 0.2 - - - -
169H LEU* 3.6 24.0 - - - +
48Z GLU 3.1 7.1 + - - -
49Z GLU 3.1 9.3 + - - -
51Z ILE* 1.3 74.3 - - - +
53Z HIS* 1.3 60.6 + - - +
55Z LEU* 3.3 13.5 + - - +
56Z ARG* 3.0 33.9 + - - +
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Residues in contact with HIS 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H LEU* 6.3 0.9 - - + -
170H MET 5.9 0.9 - - - -
17Z GLU* 3.6 25.8 + - - +
49Z GLU* 2.7 37.8 + - - +
50Z GLU* 3.2 17.6 + - - +
52Z GLY* 1.3 77.0 - - - +
54Z ALA* 1.3 63.2 + - - +
56Z ARG* 3.3 7.4 + - - +
57Z PHE* 3.3 28.8 + - - -
122Z TRP* 4.2 8.6 - + - -
123Z PHE* 3.6 14.8 - + + -
126Z GLU* 3.0 41.4 + - + -
127Z GLN* 4.8 0.2 + - - -
130Z GLU* 4.9 6.3 - - + -
1173Z AG 2.2 31.7 - - - -
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Residues in contact with ALA 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE* 5.4 3.4 - - + -
14Z LEU* 3.5 29.6 - - + +
17Z GLU* 4.0 8.9 - - + +
18Z LEU* 3.8 31.0 - - + -
50Z GLU 3.0 13.4 + - - +
51Z ILE 3.4 10.3 - - - +
53Z HIS* 1.3 77.2 - - - +
55Z LEU* 1.3 56.9 + - + +
57Z PHE* 3.3 2.7 + - - -
58Z TYR* 3.0 23.8 + - - +
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Residues in contact with LEU 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE* 3.7 30.5 - - + -
44H LYS* 4.9 16.4 - - + +
48H GLU* 5.6 1.8 - - - +
163H PRO* 6.2 0.4 - - + -
165H LEU* 5.3 4.5 - - + -
166H PRO* 4.0 31.9 - - + -
169H LEU* 5.4 0.2 - - + -
51Z ILE* 3.0 29.4 + - + +
52Z GLY* 3.3 15.9 + - - +
54Z ALA* 1.3 74.8 - - + +
56Z ARG* 1.3 59.3 + - + +
58Z TYR* 3.3 11.0 + - + +
59Z ASN* 2.8 43.1 + - - +
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Residues in contact with ARG 56 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H MET 3.7 6.3 + - - -
171H GLN* 3.5 16.2 - - - +
172H GLY 3.1 40.2 + - - +
52Z GLY 3.0 19.7 + - - +
53Z HIS* 3.5 11.7 - - - +
54Z ALA 3.2 0.4 - - - -
55Z LEU* 1.3 77.0 - - - +
57Z PHE* 1.3 61.2 - - - +
59Z ASN* 3.8 9.1 + - - +
60Z TYR* 3.3 15.2 + - - +
119Z PHE* 3.5 19.6 - - + -
122Z TRP* 3.4 52.7 - - - +
123Z PHE* 3.7 12.2 - - + -
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Residues in contact with PHE 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z LEU* 3.7 36.1 - - + +
13Z GLN* 3.5 34.8 - - + -
14Z LEU* 4.0 18.8 - - + -
17Z GLU* 4.4 9.6 - - + -
53Z HIS 3.3 21.3 + - - -
54Z ALA 3.6 7.4 - - - +
55Z LEU 3.3 0.4 - - - -
56Z ARG* 1.3 78.3 - - - +
58Z TYR* 1.3 64.0 + - - +
60Z TYR* 3.3 2.1 + - - +
61Z ILE* 3.1 29.0 + - + +
101Z ILE* 4.0 11.7 - - + -
104Z LEU* 4.4 0.9 - - + -
119Z PHE* 3.6 24.5 - + - -
120Z LEU* 4.1 12.6 - - + -
123Z PHE* 3.4 28.5 - + - -
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Residues in contact with TYR 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE* 3.8 29.2 - + + -
28H ALA 3.1 23.4 + - - -
29H ALA* 3.9 17.9 - - + -
32H GLU* 3.1 25.0 + - - +
44H LYS* 3.4 31.2 - - - -
14Z LEU* 3.6 11.8 - - + +
54Z ALA 3.0 13.7 + - - +
55Z LEU* 3.4 15.3 - - + +
57Z PHE* 1.3 79.0 - - - +
59Z ASN* 1.3 75.4 + - - +
61Z ILE* 3.5 1.7 + - - +
62Z TYR* 3.3 50.7 + + - -
68Z VAL* 4.0 19.3 - - + -
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Residues in contact with ASN 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LYS* 4.3 7.6 + - - -
55Z LEU* 2.8 29.7 + - - +
56Z ARG* 4.1 9.5 - - - +
58Z TYR* 1.3 90.8 - - - +
60Z TYR* 1.3 65.2 + - - +
62Z TYR* 3.7 4.8 + - - +
63Z ASP* 3.2 33.5 + - - +
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Residues in contact with TYR 60 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1280 VAL* 4.2 16.8 - - + -
2Z LEU* 4.2 1.3 - - + -
10Z LEU* 3.9 24.7 - - + -
56Z ARG 3.3 6.5 + - - +
57Z PHE 3.3 3.1 + - - +
59Z ASN* 1.3 75.4 - - - +
61Z ILE* 1.3 68.0 - - + +
63Z ASP* 3.2 7.8 + - + +
64Z ARG* 3.0 52.4 + - + +
115Z SER* 3.1 12.9 - - - -
116Z THR* 2.9 45.0 + - + -
119Z PHE* 3.5 61.0 - + + -
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Residues in contact with ILE 61 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Z LEU* 4.5 4.0 - - - +
7Z LEU* 3.8 14.4 - - + -
10Z LEU* 4.0 43.5 - - + +
11Z ASN* 4.3 10.3 - - - +
14Z LEU* 4.0 13.2 - - + -
57Z PHE 3.1 19.9 + - - +
58Z TYR 3.8 4.9 - - - +
59Z ASN 3.4 0.2 - - - -
60Z TYR* 1.3 78.6 - - + +
62Z TYR* 1.3 59.5 + - + +
64Z ARG* 3.2 8.7 + - - +
66Z GLY* 2.8 25.3 + - - -
67Z ARG 3.5 25.6 - - - +
68Z VAL* 3.7 26.2 - - + +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1320 ALA* 5.3 0.5 - - - +
29H ALA* 2.6 34.2 + - - +
32H GLU* 3.7 29.4 - - + +
33H ASP* 3.8 24.7 - - + -
58Z TYR* 3.3 47.4 + + + +
59Z ASN* 4.3 3.8 - - - +
60Z TYR 3.3 0.2 - - - -
61Z ILE* 1.3 74.7 - - - +
63Z ASP* 1.3 65.7 + - - +
64Z ARG 3.2 0.2 - - - -
65Z ASN* 3.4 11.4 + - - -
66Z GLY 3.4 22.4 - - - +
67Z ARG* 3.5 7.4 + - - -
68Z VAL* 3.4 32.4 + - + -
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Residues in contact with ASP 63 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1280 VAL* 4.3 20.1 - - + +
1290 GLU* 5.7 5.6 - - - +
1310 GLU* 5.1 2.1 - - - +
1320 ALA* 3.5 39.4 + - + +
59Z ASN* 3.2 24.5 + - - +
60Z TYR* 3.2 13.8 + - - +
62Z TYR* 1.3 78.6 - - - +
64Z ARG* 1.3 62.7 + - - +
65Z ASN* 3.3 2.8 + - - +
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Residues in contact with ARG 64 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020 TYR* 3.5 11.1 + - - -
1270 GLN 5.2 0.4 - - - -
1280 VAL* 3.8 37.5 + - - +
1310 GLU* 3.9 26.2 + - - +
1Z MET* 3.8 37.2 - - - +
2Z LEU* 3.8 25.6 + - + +
60Z TYR* 3.0 42.9 + - + +
61Z ILE 3.2 3.1 + - - +
62Z TYR 3.2 0.2 - - - -
63Z ASP* 1.3 78.3 + - - +
65Z ASN* 1.3 68.7 + - - +
66Z GLY* 3.3 3.0 + - - -
113Z ASP* 4.6 5.3 + - - -
115Z SER* 3.2 33.0 + - - -
----------------------------------------------------------
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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