Contacts of the helix formed by residues 43 - 74 (chain K) in PDB entry 6CP3
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 ILE 43 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H LEU* 3.7 24.0 - - + -
37K VAL* 3.9 10.1 - - + +
40K ASN* 3.3 25.9 + - + +
41K PRO 3.2 1.8 - - - -
42K SER* 1.3 77.6 + - - +
44K LYS* 1.3 60.1 + - - +
45K ASP 3.4 1.6 - - - -
46K THR* 2.9 28.1 + - + +
47K VAL* 2.8 47.2 + - + +
37L VAL* 4.4 13.0 - - + +
38L SER* 4.3 19.5 - - - -
41L PRO* 3.7 19.1 - - + +
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Residues in contact with LYS 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 6.3 1.3 - - + -
37K VAL* 3.7 24.4 - - + +
41K PRO 3.7 10.4 + - - +
42K SER 3.4 1.4 - - - -
43K ILE* 1.3 77.8 - - - +
45K ASP* 1.3 58.2 + - - +
47K VAL* 3.0 6.9 + - + -
48K PHE* 2.7 59.1 + - + +
46T THR* 4.3 32.7 + - + -
47T VAL* 5.8 0.7 - - + -
50T MET* 3.1 40.1 - - - +
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Residues in contact with ASP 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K SER 4.8 5.8 + - - +
43K ILE 3.4 0.2 - - - -
44K LYS* 1.3 78.0 - - - +
46K THR* 1.3 60.6 + - - +
48K PHE* 4.7 2.9 - - - -
49K PRO* 4.1 12.0 - - - +
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Residues in contact with THR 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K SER 4.4 3.6 + - - -
43K ILE* 2.9 37.1 + - + +
45K ASP* 1.3 81.4 + - - +
47K VAL* 1.3 57.8 + - - +
48K PHE 3.7 0.2 - - - -
49K PRO* 4.2 8.5 - - - +
50K MET* 4.8 2.6 + - - +
41L PRO 6.0 1.6 - - - +
44L LYS* 3.7 31.8 + - - -
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Residues in contact with VAL 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 3.9 22.2 - - + -
37K VAL* 4.7 3.1 - - + -
43K ILE* 2.8 43.0 + - + +
44K LYS* 3.8 10.1 - - - +
46K THR* 1.3 79.9 - - + +
48K PHE* 1.3 64.4 + - - +
49K PRO 3.3 2.7 - - - -
50K MET* 3.0 11.9 + - + +
51K ALA* 2.8 30.8 + - - +
34L ILE* 4.8 8.7 - - + +
37L VAL* 3.7 29.8 - - + -
44L LYS* 4.2 6.1 - - - +
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Residues in contact with PHE 48 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K PHE* 6.1 3.1 - + - -
33K LEU* 4.7 11.7 - - + -
44K LYS* 2.7 54.1 + - + +
45K ASP* 5.1 1.6 - - - -
47K VAL* 1.3 74.1 - - - +
49K PRO* 1.3 68.2 - - + +
51K ALA* 4.2 3.5 - - + +
52K ILE* 3.4 27.2 + - + +
50T MET* 4.4 20.0 - - + -
53T LEU* 6.0 9.6 - - + -
147X PRO* 4.6 11.0 - - + -
148X ALA* 3.6 26.7 - - + -
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Residues in contact with PRO 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K ASP 4.1 16.6 - - - +
46K THR 4.2 5.8 - - - +
47K VAL 3.8 2.5 - - - -
48K PHE* 1.3 93.6 - - + +
50K MET* 1.3 51.5 + - - +
52K ILE* 3.0 9.5 + - + +
53K LEU* 2.8 33.0 + - - +
148X ALA* 4.5 1.8 - - + -
149X GLY* 3.3 37.4 - - - +
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Residues in contact with MET 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K THR 4.8 1.3 + - - +
47K VAL* 3.0 12.4 + - + +
49K PRO* 1.3 77.9 - - - +
51K ALA* 1.3 58.3 + - - +
53K LEU* 3.0 13.8 - - + +
54K GLY* 2.9 25.1 + - - -
30L PHE* 5.0 3.3 - - + -
33L LEU* 3.7 38.8 - - + -
34L ILE* 4.7 12.1 - - + -
37L VAL* 3.8 24.0 - - + -
44L LYS* 3.4 37.5 - - - +
48L PHE* 4.2 23.8 - - + -
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Residues in contact with ALA 51 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K VAL* 3.9 6.7 - - + +
30K PHE* 6.4 0.2 - - + -
33K LEU* 3.8 37.7 - - + -
47K VAL 2.8 16.2 + - - +
48K PHE* 4.2 4.3 - - + +
50K MET* 1.3 77.0 - - - +
52K ILE* 1.3 51.3 + - - +
54K GLY* 3.0 2.5 + - - +
55K PHE* 2.7 36.9 + - - +
30L PHE* 6.4 0.7 - - - -
34L ILE* 4.0 20.8 - - + +
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Residues in contact with ILE 52 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K PHE* 6.3 2.0 - - + -
48K PHE* 3.4 16.6 + - + +
49K PRO 3.0 17.1 + - - +
51K ALA* 1.3 75.0 - - - +
53K LEU* 1.3 66.1 + - - +
55K PHE* 3.9 14.8 - - + -
56K ALA* 3.6 17.8 + - - +
53T LEU* 5.9 7.9 - - + -
147X PRO* 4.3 13.7 - - + -
148X ALA* 3.7 30.3 - - + -
149X GLY 4.0 1.3 - - - +
150X THR* 3.9 21.8 - - + +
154X LEU* 5.2 0.2 - - - +
158X LEU* 3.8 34.3 - - + +
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Residues in contact with LEU 53 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K PRO 2.8 12.0 + - - +
50K MET* 3.0 18.2 - - + +
52K ILE* 1.3 76.6 - - - +
54K GLY* 1.3 57.0 + - - +
56K ALA* 2.9 21.5 + - - +
57K LEU* 3.2 29.0 + - + +
30L PHE* 4.1 18.2 - - + -
48L PHE* 4.9 19.1 - - + -
52L ILE* 5.0 11.0 - - + -
150X THR* 5.4 1.1 - - + -
151X PRO* 3.8 33.2 - - + -
154X LEU* 3.8 27.6 - - + -
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Residues in contact with GLY 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K VAL* 3.9 11.1 - - - +
50K MET 2.9 14.9 + - - -
51K ALA* 3.0 2.4 + - - -
53K LEU* 1.3 69.2 - - - +
55K PHE* 1.3 64.5 + - - +
57K LEU* 4.6 0.7 - - - -
58K SER* 3.1 25.0 + - - -
30L PHE* 3.6 41.6 - - - -
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Residues in contact with PHE 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ILE* 3.6 42.6 - - + +
29K VAL* 3.7 10.4 - - + +
30K PHE* 3.5 37.9 - + + -
51K ALA 2.7 20.8 + - - +
52K ILE* 3.9 19.5 - - + +
54K GLY* 1.3 73.2 - - - +
56K ALA* 1.3 85.0 + - + +
58K SER* 3.0 5.0 + - - -
59K GLU* 3.0 31.4 + - + +
57T LEU* 3.6 36.1 - - + -
158X LEU* 4.7 7.6 - - + -
161X ILE* 4.5 14.4 - - + -
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Residues in contact with ALA 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K ILE 3.6 14.4 - - - +
53K LEU 2.9 5.8 + - - +
55K PHE* 1.3 91.7 - - + +
57K LEU* 1.3 58.2 + - + +
59K GLU* 2.9 7.1 + - - +
60K ALA* 2.9 27.9 + - - +
63K LEU* 5.4 0.2 - - - +
154X LEU* 4.7 15.5 - - + -
157X LEU* 4.4 20.4 - - + +
158X LEU* 5.1 12.1 - - + -
161X ILE* 5.8 2.0 - - + -
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Residues in contact with LEU 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K LEU* 3.2 54.7 - - + +
54K GLY* 4.6 3.6 - - - -
56K ALA* 1.3 77.0 - - + +
58K SER* 1.3 56.9 + - - +
59K GLU 3.6 0.2 - - - -
60K ALA* 4.4 14.1 - - + +
61K THR* 4.4 8.5 - - - +
26L ILE* 3.6 14.0 - - - +
30L PHE* 4.8 1.6 - - + -
52L ILE* 6.2 4.5 - - + -
55L PHE* 3.6 35.5 - - + -
154X LEU* 4.5 16.4 - - + -
157X LEU* 5.9 1.1 - - + -
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Residues in contact with SER 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ALA* 4.7 3.8 - - - +
26K ILE* 4.2 8.3 - - - +
54K GLY 3.1 21.3 + - - -
55K PHE 3.0 5.2 + - - -
57K LEU* 1.3 75.2 - - - +
59K GLU* 1.3 59.7 + - - +
60K ALA 3.6 0.4 - - - -
61K THR* 3.6 13.1 + - - -
23L GLY* 4.2 14.9 - - - +
26L ILE* 3.3 31.8 - - - +
27L ALA* 3.8 17.3 + - - -
30L PHE* 3.6 15.4 - - - -
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Residues in contact with GLU 59 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K LEU* 5.6 1.0 - - - +
22K ALA* 3.3 14.5 - - - +
26K ILE* 3.3 31.1 - - + +
55K PHE* 3.0 23.5 + - + +
56K ALA* 2.9 11.9 + - - +
58K SER* 1.3 77.6 - - - +
60K ALA* 1.3 57.6 + - - +
61K THR 3.2 2.2 - - - -
62K GLY* 2.9 23.0 + - - -
63K LEU* 3.0 32.7 + - + +
57T LEU 5.4 1.6 - - - -
60T ALA* 4.5 4.0 - - - +
61T THR* 3.3 27.9 + - - +
161X ILE* 5.4 4.5 - - + -
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Residues in contact with ALA 60 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K ALA 2.9 13.8 + - - +
57K LEU* 4.4 10.5 - - + -
58K SER 3.6 0.8 - - - +
59K GLU* 1.3 72.6 - - - +
61K THR* 1.3 55.7 + - + +
63K LEU* 3.0 21.2 + - + +
64K PHE* 2.7 45.8 + - + -
157X LEU* 4.4 23.6 - - + -
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Residues in contact with THR 61 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K LEU 4.4 15.3 - - - +
58K SER* 3.6 14.7 + - - -
60K ALA* 1.3 76.3 - - + +
62K GLY* 1.3 62.9 + - - +
64K PHE* 2.9 46.1 + - + +
19L LEU* 3.3 18.7 + - - +
22L ALA* 3.9 29.9 - - + +
23L GLY* 4.2 6.9 - - - -
26L ILE* 4.7 6.5 - - + -
55L PHE* 6.5 0.2 - - + -
59L GLU* 5.4 8.1 - - + +
63L LEU* 5.4 5.4 - - + -
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Residues in contact with GLY 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLY 4.9 0.2 - - - -
19K LEU* 4.4 21.5 - - - +
22K ALA* 4.6 8.6 - - - +
58K SER 5.0 0.4 + - - -
59K GLU* 2.9 10.7 + - - -
61K THR* 1.3 82.0 + - - +
63K LEU* 1.3 58.5 + - - +
65K CYS* 2.9 22.6 + - - +
66K LEU* 3.8 9.2 + - - +
19L LEU* 3.7 14.1 - - - +
23L GLY* 5.7 0.8 - - - -
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Residues in contact with LEU 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K GLU* 3.0 29.5 + - + +
60K ALA* 3.0 29.0 + - + +
62K GLY* 1.3 73.4 - - - +
64K PHE* 1.3 66.5 + - - +
66K LEU* 3.8 20.2 - - + +
67K MET* 3.6 15.6 - - - +
60T ALA 5.5 5.6 - - - +
64T PHE* 5.9 4.0 - - + -
157X LEU* 5.3 4.0 - - + -
161X ILE* 3.6 41.5 - - + -
164X LEU* 4.6 11.0 - - + -
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Residues in contact with PHE 64 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K ALA* 2.7 22.4 + - + -
61K THR* 2.9 32.7 + - + +
63K LEU* 1.3 77.6 - - - +
65K CYS* 1.3 51.0 + - - +
67K MET* 3.0 27.7 + - + +
68K VAL* 2.8 35.4 + - + +
19L LEU* 4.2 8.1 - - + -
63L LEU* 3.9 22.9 - - + -
66L LEU* 4.3 29.2 - - + -
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Residues in contact with CYS 65 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K SER 3.3 22.5 - - - +
16K THR 3.3 24.5 - - - +
18K GLY* 3.5 19.3 - - - -
19K LEU 4.3 2.7 - - - +
61K THR 3.4 0.2 + - - -
62K GLY 2.9 15.0 + - - +
64K PHE* 1.3 76.4 - - - +
66K LEU* 1.3 56.9 + - - +
68K VAL* 3.0 10.8 + - - +
69K SER 2.8 22.7 + - - -
16L THR* 3.7 15.0 - - - -
19L LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 66 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K THR* 3.8 22.3 + - + -
19K LEU* 4.6 7.4 - - + -
62K GLY 3.8 10.7 + - - +
63K LEU* 3.8 30.3 - - + +
65K CYS* 1.3 79.9 - - - +
67K MET* 1.3 55.9 + - + +
69K SER* 2.9 11.7 + - - -
70K PHE* 2.5 36.7 + - + +
64T PHE* 3.8 33.9 - - + -
67T MET* 4.7 7.9 - - + -
68T VAL* 4.6 12.1 - - + -
164X LEU* 6.3 2.5 - - + -
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Residues in contact with MET 67 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K LEU 3.6 11.9 - - - +
64K PHE* 3.0 40.3 + - + +
66K LEU* 1.3 81.2 - - + +
68K VAL* 1.3 63.9 + - + +
70K PHE* 2.9 30.0 + - + +
71K LEU* 3.3 22.1 + - + +
66L LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 68 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K SER* 4.7 1.8 - - - -
64K PHE* 2.8 22.5 + - + +
65K CYS* 3.3 11.4 - - - +
67K MET* 1.3 81.5 - - + +
69K SER* 1.3 59.0 + - - +
71K LEU* 4.3 12.2 - - + +
72K LEU* 3.2 23.3 + - + +
12L ALA* 5.3 1.6 - - + +
16L THR* 4.2 17.0 - - + +
19L LEU* 5.7 0.9 - - + -
66L LEU* 4.1 26.9 - - + -
69L SER* 4.1 21.5 - - - +
73L LEU* 6.0 2.0 - - + +
----------------------------------------------------------
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Residues in contact with SER 69 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ALA* 2.9 19.4 + - - +
15K SER* 3.3 24.3 + - - -
16K THR* 2.9 27.5 + - - -
65K CYS 2.8 6.3 + - - -
66K LEU* 2.9 15.5 + - - -
68K VAL* 1.3 78.6 - - - +
70K PHE* 1.3 47.9 + - - +
72K LEU* 3.0 3.8 + - - +
73K LEU* 2.4 35.9 + - - +
68T VAL* 4.6 5.1 - - - +
----------------------------------------------------------
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Residues in contact with PHE 70 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K LEU* 2.5 18.8 + - + +
67K MET* 2.9 18.5 + - + +
69K SER* 1.3 72.0 - - - +
71K LEU* 1.3 57.5 + - + +
73K LEU* 2.9 17.8 + - + +
74K PHE* 2.7 71.3 + + + +
67T MET* 6.5 1.1 - - + -
71T LEU* 6.0 3.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 71 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K LYS* 4.9 0.3 - - - -
67K MET* 3.7 22.9 - - + +
68K VAL* 4.3 10.3 - - + +
70K PHE* 1.3 81.5 - - + +
72K LEU* 1.3 63.2 + - - +
74K PHE* 3.1 29.5 - - - +
70L PHE* 5.7 4.5 - - + -
73L LEU* 3.9 26.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K LYS* 3.3 34.3 - - + +
11K GLY 3.4 15.7 - - - +
12K ALA* 4.1 6.7 - - - +
15K SER* 3.4 28.0 - - - +
68K VAL* 3.2 18.9 + - + +
69K SER 3.0 9.7 + - - +
71K LEU* 1.3 76.1 - - + +
73K LEU* 1.3 62.1 + - - +
9L TYR* 3.8 34.1 - - + +
12L ALA* 4.5 10.5 - - + +
13L GLY* 4.0 13.2 - - - +
73L LEU* 4.8 14.6 - - + -
----------------------------------------------------------
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Residues in contact with LEU 73 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K LYS* 3.3 16.1 + - - -
9K TYR* 4.2 17.2 - - + -
12K ALA* 4.0 17.0 - - + +
69K SER* 2.4 24.8 + - - +
70K PHE* 3.0 20.2 - - + +
72K LEU* 1.3 71.7 - - - +
74K PHE* 1.3 88.6 + - + +
68T VAL* 6.2 7.0 - - + -
71T LEU* 3.7 26.5 - - + -
72T LEU* 3.7 32.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE 74 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K LYS* 2.7 26.0 + - - +
70K PHE* 2.7 59.3 + + + +
71K LEU* 3.1 23.2 + - - +
72K LEU 3.4 0.2 - - - -
73K LEU* 1.3 103.9 - - + +
71T LEU* 4.6 9.6 - - + -
----------------------------------------------------------
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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