Contacts of the helix formed by residues 57 - 87 (chain D) in PDB entry 4E4E
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 57 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 4.7 1.8 - - - -
52D LEU* 3.9 0.5 - - - +
55D GLU* 2.7 23.5 + - - -
56D PRO* 1.3 76.1 - - - +
58D PRO* 1.3 73.4 - - - +
59D ALA* 3.8 8.6 + - - +
60D ASN* 3.2 27.0 + - - +
61D ALA* 3.1 20.4 + - - +
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Residues in contact with PRO 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 6.3 0.7 - - + -
78A PHE* 4.2 16.1 - - + -
79A THR* 3.6 10.8 - - + +
82A CYS* 3.8 36.6 - - + -
83A LEU* 6.1 4.9 - - + -
56D PRO 4.2 3.6 - - - +
57D SER* 1.3 87.1 - - - +
59D ALA* 1.3 58.1 + - - +
61D ALA* 3.2 2.9 + - - +
62D ARG* 2.9 38.1 + - - +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A MLY 6.2 4.7 - - + -
57D SER* 3.3 9.0 + - - +
58D PRO* 1.3 77.7 - - - +
60D ASN* 1.3 59.1 + - - +
62D ARG* 3.3 15.6 + - - +
63D MLY 3.0 53.8 + - - +
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Residues in contact with ASN 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 5.2 2.6 - - + +
51D LEU* 3.5 32.2 + - + +
52D LEU* 3.8 18.2 - - + -
55D GLU* 2.8 45.9 + - - +
57D SER* 3.2 14.6 + - - +
59D ALA* 1.3 73.8 - - - +
61D ALA* 1.3 65.4 + - - +
63D MLY 3.1 34.7 + - - +
64D MET* 3.0 24.9 + - - +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 3.9 30.4 - - + -
75A GLY 5.1 0.2 - - - +
78A PHE* 4.1 9.0 - - + -
79A THR* 3.5 22.7 - - + -
52D LEU* 3.7 8.8 - - + +
57D SER 3.1 12.3 + - - +
58D PRO 3.6 2.7 - - - +
60D ASN* 1.3 77.2 - - - +
62D ARG* 1.3 56.6 + - - +
64D MET* 3.1 7.3 + - - +
65D ILE* 2.9 31.9 + - - +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.8 24.2 - - - +
83A LEU* 4.7 12.9 - - - +
156A THR* 4.7 8.3 + - + -
157A VAL 2.4 34.7 + - - -
158A THR* 3.5 20.9 - - + +
159A GLY 5.3 3.4 + - - +
161A LEU 3.8 4.2 + - - -
163A PRO* 3.7 28.2 - - - +
58D PRO* 2.9 22.0 + - - +
59D ALA* 3.4 14.3 + - - +
61D ALA* 1.3 75.7 - - - +
63D MLY 1.3 59.3 + - - +
65D ILE* 3.3 13.9 + - + +
66D ALA* 3.0 27.0 + - - +
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Residues in contact with MLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A MLY 5.9 9.6 - - - -
48D LEU* 3.4 32.2 - - + +
51D LEU* 4.6 10.3 - - + -
55D GLU* 5.9 0.4 - - - -
59D ALA* 3.0 38.0 + - - +
60D ASN* 3.2 33.9 + - - +
62D ARG* 1.3 76.7 + - + +
64D MET* 1.3 62.2 + - - +
66D ALA* 3.2 21.2 + - - +
67D ILE* 3.5 5.5 + - - +
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 3.6 14.6 - - + -
42A VAL* 3.5 30.7 - - + -
71A ILE* 4.3 4.5 - - + -
45D PHE* 3.7 25.1 - - + -
48D LEU* 3.6 34.5 - - + +
49D SER* 4.9 2.5 - - - -
52D LEU* 3.6 33.4 - - - -
60D ASN 3.0 15.2 + - - +
61D ALA 3.1 5.4 + - - +
63D MLY 1.3 72.2 + - - -
65D ILE* 1.3 67.1 + - - +
67D ILE* 2.9 9.5 + - - -
68D GLN* 2.8 30.0 + - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 5.5 0.9 - - + -
71A ILE* 4.7 6.3 - - + +
72A MLY 4.8 28.3 - - + +
75A GLY* 3.5 28.0 - - - +
76A GLY* 3.5 6.5 - - - +
79A THR* 3.5 26.7 - - + +
154A GLN 6.1 0.4 - - - +
156A THR* 4.1 22.2 - - + +
158A THR* 4.6 5.6 - - + -
61D ALA 2.9 19.9 + - - +
62D ARG* 3.3 14.1 - - - +
64D MET* 1.3 77.2 - - + +
66D ALA* 1.3 63.6 + - - +
67D ILE 3.2 0.2 + - - -
68D GLN* 3.3 23.5 + - - +
69D GLN* 4.2 2.1 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 4.6 19.7 - - - +
62D ARG 3.0 12.8 + - - +
63D MLY 3.3 15.7 - - - +
64D MET 3.1 0.2 - - - -
65D ILE* 1.3 77.8 - - - +
67D ILE* 1.3 62.3 + - + +
68D GLN 3.7 0.2 + - - -
69D GLN* 4.0 13.3 + - - +
70D ASN* 4.7 5.2 + - - -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ALA* 3.7 26.7 - - + +
44D GLN* 3.8 33.9 - - + +
45D PHE* 4.4 6.1 - - + +
48D LEU* 3.5 30.3 - - + -
63D MLY 3.6 3.4 - - - +
64D MET* 2.9 10.8 + - - +
66D ALA* 1.3 73.1 - - + +
68D GLN* 1.3 69.8 + - - +
69D GLN 3.1 2.7 - - - -
70D ASN* 3.0 24.3 + - + +
71D ILE* 3.0 18.9 + - + +
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Residues in contact with GLN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 2.6 53.2 + - + +
71A ILE* 3.3 34.8 - - + +
72A MLY 4.4 14.4 - - + +
45D PHE* 3.2 32.8 - - - -
64D MET 2.8 27.3 + - - +
65D ILE* 3.5 14.6 - - - +
67D ILE* 1.3 79.9 - - - +
69D GLN* 1.3 56.8 + - - +
71D ILE* 3.2 1.3 + - - +
72D MLY 2.9 29.2 + - - +
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MLY 4.7 25.2 - - - -
127C GLY 4.7 3.8 + - - -
129C GLN* 3.1 27.9 + - - +
152C TYR* 4.4 11.7 + - - -
65D ILE 4.2 2.1 + - - +
66D ALA 4.0 11.3 + - - +
67D ILE 3.1 0.8 + - - -
68D GLN* 1.3 79.2 - - - +
70D ASN* 1.3 61.8 + - - +
72D MLY 3.3 8.7 + - - +
73D PHE* 2.9 27.3 + - + +
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLN* 3.0 26.2 + - - +
41D ALA* 4.1 12.5 - - + +
44D GLN* 4.8 10.0 + - - +
66D ALA 4.7 5.6 + - - -
67D ILE* 3.0 18.2 + - + +
69D GLN* 1.3 77.1 + - - +
71D ILE* 1.3 67.8 + - - +
73D PHE* 4.4 2.2 - - - +
74D HIS* 2.9 43.1 + - + +
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Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.7 27.4 - - + -
64A MET* 5.0 3.6 - - + +
65A ILE* 4.6 2.2 - - - +
68A GLN* 3.0 39.7 - - + +
38D PHE* 3.9 17.9 - - + -
41D ALA* 3.6 27.1 - - + +
42D VAL* 4.6 2.0 - - + +
45D PHE* 3.9 32.1 - - + -
67D ILE* 3.0 13.7 + - + +
68D GLN* 3.2 5.8 + - - +
70D ASN* 1.3 76.2 - - - +
72D MLY 1.3 55.8 + - - +
75D GLY* 2.9 28.2 + - - -
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Residues in contact with MLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.1 24.3 - - + +
68A GLN* 4.2 17.2 + - + -
69A GLN* 5.6 9.4 - - - +
72A MLY 6.0 6.5 - - - -
68D GLN 2.9 15.7 + - - +
69D GLN* 3.6 7.9 - - - +
70D ASN 3.2 0.2 - - - -
71D ILE* 1.3 78.8 + - - +
73D PHE* 1.3 57.2 + - - +
76D GLY* 2.9 26.3 + - - -
154D GLN 4.2 4.1 - - - +
155D ASP* 3.2 45.3 - - - +
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Residues in contact with PHE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLN* 3.5 75.2 - - + +
130C GLY 4.6 0.2 - - - -
182C MLY 5.5 10.5 - - - -
34D PHE* 3.4 29.4 - + - -
69D GLN* 2.9 16.8 + - + +
70D ASN 4.2 1.6 - - - +
72D MLY 1.3 76.2 + - - +
74D HIS* 1.3 74.4 + + - +
77D GLY* 2.9 23.6 + - - -
153D ASN* 5.0 0.9 - - + -
154D GLN* 3.4 36.5 - - + +
170D TRP* 4.0 12.1 - + - -
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Residues in contact with HIS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLN* 4.5 5.9 + - - -
33D THR* 4.1 15.3 - - + -
34D PHE* 3.5 27.1 - + - +
37D GLY* 3.5 30.9 - - - -
38D PHE* 3.4 24.0 - - - +
70D ASN* 2.9 38.3 + - + +
73D PHE* 1.3 95.5 - + - +
75D GLY* 1.3 60.9 + - - +
77D GLY* 3.8 0.3 - - - -
78D PHE* 2.9 31.2 + - - +
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.4 12.1 - - - -
38D PHE* 3.4 27.4 - - - -
71D ILE 2.9 19.2 + - - -
74D HIS* 1.3 77.5 - - - +
76D GLY* 1.3 55.2 + - - +
78D PHE* 3.3 2.5 + - - +
79D THR* 2.9 36.1 + - - +
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.4 14.3 - - - +
72D MLY 2.9 16.2 + - - -
75D GLY* 1.3 76.0 - - - +
77D GLY* 1.3 56.1 + - - +
79D THR* 3.2 3.1 + - - -
80D ASN* 2.9 36.6 + - - +
154D GLN* 3.2 26.0 - - - -
156D THR* 5.0 1.8 - - - -
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Residues in contact with GLY 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D HIS* 4.2 0.2 - - - -
34D PHE* 3.6 21.9 - - - -
73D PHE 2.9 12.9 + - - -
75D GLY 3.3 0.2 - - - -
76D GLY* 1.3 74.9 - - - +
78D PHE* 1.3 63.5 + - - +
81D HIS* 2.6 33.4 + - - +
154D GLN* 3.4 24.9 - - - +
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 4.4 7.4 - - - -
57A SER 4.4 2.9 - - - -
58A PRO* 4.1 25.8 - - + -
61A ALA* 4.1 8.5 - - + -
2D VAL* 3.6 38.8 - - + -
3D THR 3.5 24.2 - - - -
5D PRO* 4.8 0.2 - - + -
31D HIS* 3.2 24.7 + - - -
34D PHE* 3.6 11.5 - - + +
35D VAL* 3.7 17.5 - - + -
38D PHE* 4.5 4.7 - + + -
74D HIS 2.9 17.5 + - - +
75D GLY* 3.6 3.6 - - - +
76D GLY 3.3 0.2 - - - -
77D GLY* 1.3 75.5 - - - +
79D THR* 1.3 72.0 + - + +
82D CYS* 3.0 41.9 + - - -
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Residues in contact with THR 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.6 24.1 - - + +
61A ALA* 3.4 30.5 - - + -
62A ARG* 3.9 12.3 - - - +
65A ILE* 3.9 7.8 - - + +
75D GLY 2.9 15.2 + - - +
76D GLY* 3.2 12.5 + - - -
78D PHE* 1.3 80.1 - - + +
80D ASN* 1.3 75.1 + - - +
82D CYS* 3.2 2.9 + - - +
83D LEU* 3.0 32.9 + - - +
156D THR* 4.1 7.1 + - - +
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Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLY 2.9 20.9 + - - +
79D THR* 1.3 73.9 + - - +
81D HIS* 1.3 60.2 + - - +
83D LEU* 3.4 9.0 + - - +
84D PHE* 2.9 27.5 + - - +
133D TRP* 3.4 34.0 - - + +
135D PHE* 3.2 17.5 - - - -
154D GLN* 3.1 23.6 + - - +
155D ASP 3.2 23.4 + - - -
156D THR* 2.7 25.8 + - - -
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Residues in contact with HIS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D HIS* 3.2 21.5 + + - -
30D HIS* 4.9 1.8 - - - +
31D HIS* 3.4 33.4 - + + +
34D PHE* 3.4 29.1 - + - -
77D GLY 2.6 29.6 + - - +
80D ASN* 1.3 73.2 - - - +
82D CYS* 1.3 67.4 + - - +
84D PHE* 3.2 6.4 + + - +
85D TRP* 2.9 39.3 + + - +
133D TRP* 3.9 10.0 - + - -
154D GLN* 3.6 13.9 - - - -
168D ASP* 3.9 1.5 + - - -
172D HIS* 4.1 0.6 + - - -
301D MN 2.3 34.5 + - - -
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Residues in contact with CYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.5 33.7 - - + -
5D PRO* 3.9 18.3 - - + +
31D HIS* 3.8 11.9 - - - -
78D PHE* 3.0 42.8 + - - -
79D THR 3.2 5.6 + - - +
81D HIS* 1.3 76.3 - - - +
83D LEU* 1.3 64.7 + - - +
85D TRP* 3.3 5.1 + - - +
86D GLU* 3.0 30.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 5.7 7.0 - - + -
62A ARG* 5.9 4.0 - - - -
79D THR* 3.0 21.5 + - - +
80D ASN* 3.5 13.9 - - - +
82D CYS* 1.3 76.1 - - + +
84D PHE* 1.3 64.1 + - - +
86D GLU* 3.3 1.1 + - - -
87D ASN* 3.0 14.2 + - - +
135D PHE* 4.2 16.6 - - + -
156D THR* 4.7 4.5 - - - +
163D PRO* 3.7 37.0 - - + -
166D ALA* 4.1 9.6 - - + -
201D ARG* 2.8 45.2 + - - +
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Residues in contact with PHE 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 4.9 4.0 - - + -
26D HIS* 3.9 26.5 - + - -
80D ASN 2.9 17.0 + - - +
81D HIS* 3.5 6.5 - + - +
83D LEU* 1.3 76.3 - - - +
85D TRP* 1.3 86.6 + + - +
87D ASN* 3.1 17.0 + - - +
88D LEU* 3.4 37.1 - - + +
133D TRP* 3.9 11.7 - + + -
166D ALA* 3.1 23.3 - - - +
167D ILE* 3.9 1.1 - - + -
168D ASP* 3.6 25.4 - - + -
185D TYR* 3.7 12.1 - - - -
189D ILE* 3.6 30.7 - - + -
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Residues in contact with TRP 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 4.0 11.9 - - + -
6D ASP 5.8 0.4 - - - +
7D LEU* 3.5 28.7 - - + -
8D MLY 5.6 3.2 + - - +
9D TRP* 3.6 32.2 + + + -
23D ASN* 4.0 19.7 - - - -
26D HIS* 3.4 40.4 - + + -
27D TYR* 3.7 33.6 - + + -
31D HIS* 2.8 32.2 + + - -
81D HIS* 2.9 33.8 + + + +
82D CYS* 4.0 2.0 - - - +
84D PHE* 1.3 96.5 - + - +
86D GLU* 1.3 63.9 + - + +
88D LEU* 3.4 19.9 + - + +
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Residues in contact with GLU 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 5.8 3.3 - - + +
6D ASP 4.6 4.0 - - - +
8D MLY 2.8 53.8 + - - +
82D CYS* 3.0 18.1 + - + +
84D PHE 3.1 0.4 - - - -
85D TRP* 1.3 79.4 - - + +
87D ASN* 1.3 55.7 + - - +
88D LEU 3.3 4.2 + - - +
194D ASN* 3.7 9.9 + - - -
197D GLU* 3.4 34.8 - - - +
201D ARG* 3.3 20.9 - - - +
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Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU 3.0 17.2 + - - +
84D PHE* 3.1 12.9 + - - +
86D GLU* 1.3 75.5 - - - +
88D LEU* 1.3 61.9 + - - +
164D LEU 4.5 4.9 - - - +
165D VAL* 4.1 12.8 - - + +
166D ALA 2.8 41.3 + - - +
167D ILE* 4.7 1.4 - - - +
193D VAL* 3.5 8.2 - - + +
194D ASN* 2.9 34.0 + - - +
197D GLU* 4.4 3.1 - - + -
201D ARG* 2.8 30.9 + - - +
----------------------------------------------------------
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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