Contacts of the helix formed by residues 58 - 87 (chain I) in PDB entry 1F33
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 ASN 58 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ALA* 5.8 1.3 - - + -
58H ASN* 3.7 34.6 - - + +
59H PHE 4.1 0.2 - - - +
60H ILE* 4.5 2.5 - - - +
56I GLY 3.4 0.4 + - - -
57I ALA* 1.3 77.2 - - + +
59I PHE* 1.3 62.9 + - - +
60I ILE 3.7 1.1 - - - -
61I ALA* 3.5 20.4 - - - +
62I VAL* 3.1 31.6 + - + +
114I VAL* 4.4 2.3 - - + +
115I GLN* 5.9 2.9 - - - +
118I LEU* 5.8 0.4 - - - +
165I ASN* 3.1 32.3 + - - +
58L ASN* 3.4 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I HIS 4.6 1.1 - - - -
54I MET* 3.3 41.0 - - + +
56I GLY 3.2 10.0 + - - +
58I ASN* 1.3 75.3 - - - +
60I ILE* 1.3 76.8 + - + +
62I VAL* 3.2 3.1 + - - +
63I HIS* 2.7 67.5 + + + +
114I VAL* 4.2 7.6 - - + -
160L TRP* 4.3 9.6 - + - -
161L PHE* 3.7 36.6 - + - -
164L SER* 3.2 41.5 - - - +
165L ASN* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I PHE* 1.3 86.1 - - + +
61I ALA* 1.3 68.1 + - - +
63I HIS* 3.3 2.9 + - + +
64I GLU* 2.9 59.1 + - + +
58L ASN* 4.6 3.6 - - - +
61L ALA* 3.6 33.9 - - + +
62L VAL* 4.5 1.8 - - + +
65L MET* 4.0 18.4 - - + -
161L PHE* 3.5 42.0 - - + -
165L ASN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ILE* 3.5 21.1 - - + +
61H ALA* 4.1 8.5 - - + -
58I ASN* 3.5 20.1 + - - +
59I PHE 3.4 0.6 - - - -
60I ILE* 1.3 83.1 - - - +
62I VAL* 1.3 57.4 + - - +
64I GLU* 3.5 7.6 + - - +
65I MET* 2.9 29.3 + - - +
61L ALA* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ILE* 4.9 1.1 - - + -
54I MET* 3.5 29.8 - - + -
58I ASN* 3.1 39.2 + - - +
59I PHE 3.2 2.9 + - - +
61I ALA* 1.3 74.7 - - - +
63I HIS* 1.3 66.0 + - - +
65I MET* 3.5 8.6 - - + +
66I LEU* 3.0 30.2 + - + +
114I VAL* 4.2 11.0 - - + -
118I LEU* 3.8 22.4 - - + -
165I ASN* 4.3 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I HIS* 2.7 84.2 + + - -
52I TRP* 4.7 1.6 - + - -
54I MET* 4.1 7.8 - - - -
59I PHE* 2.7 39.7 + + + +
60I ILE* 3.4 5.2 - - + +
62I VAL* 1.3 75.2 - - - +
64I GLU* 1.3 73.0 + - + +
66I LEU* 3.6 1.0 + - - +
67I ASP 3.4 5.2 + - - -
82J GLU* 4.5 7.1 + - - -
160L TRP* 4.0 20.5 - + - -
161L PHE* 3.9 32.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I HIS* 5.0 0.2 - - - -
60I ILE* 2.9 43.1 + - + +
61I ALA* 4.0 5.4 - - - +
63I HIS* 1.3 79.3 - - + +
65I MET* 1.3 66.7 + - - +
67I ASP* 3.0 19.7 + - - +
68I GLY* 3.1 9.0 + - - -
609I TRS 3.3 36.0 + - - +
161L PHE* 5.1 3.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ILE* 4.0 23.3 - - + -
61I ALA 2.9 20.7 + - - +
62I VAL* 3.5 15.7 - - + +
64I GLU* 1.3 76.1 - - - +
66I LEU* 1.3 77.5 + - + +
68I GLY* 3.0 12.9 + - - -
69I PHE* 3.1 51.9 + - + -
118I LEU* 5.1 1.8 - - + -
161I PHE* 4.0 13.7 - - + -
162I ILE* 4.5 12.3 - - + -
165I ASN* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I THR* 3.3 24.8 - - + +
51I HIS* 3.9 22.2 - - + +
54I MET* 3.4 33.4 - - + -
62I VAL* 3.0 23.9 + - + +
63I HIS 3.8 4.3 - - - +
65I MET* 1.3 86.5 - - + +
67I ASP* 1.3 63.9 + - - +
69I PHE* 3.0 34.4 + - + +
70I ARG 3.1 9.4 + - - -
118I LEU* 5.5 0.7 - - + -
121I LEU* 3.7 27.8 - - + -
125I TYR* 5.0 1.1 - - - +
162I ILE* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I THR* 5.4 0.2 - - - -
48I LYS* 2.8 34.0 + - - +
51I HIS* 3.9 19.4 + - + -
63I HIS 3.4 2.8 + - - +
64I GLU* 3.0 12.4 + - - +
66I LEU* 1.3 78.1 - - - +
68I GLY* 1.3 65.6 + - - +
70I ARG* 3.2 28.8 + - - +
71I THR* 3.3 13.1 + - - -
78J ASP* 4.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I GLU 3.1 7.6 + - - -
65I MET* 3.0 9.5 + - - -
67I ASP* 1.3 78.5 + - - +
69I PHE* 1.3 63.9 + - - +
71I THR* 3.1 18.9 + - - -
72I ALA* 3.2 11.7 + - - +
158I PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I THR* 4.5 0.2 - - + -
65I MET* 3.5 45.1 - - + -
66I LEU* 3.0 20.7 + - + +
68I GLY* 1.3 76.7 - - - +
70I ARG* 1.3 54.3 + - - +
72I ALA* 3.0 4.2 + - - +
73I LEU* 2.7 39.1 + - - +
125I TYR* 3.6 25.8 - + - +
158I PHE* 3.4 55.0 - + + -
161I PHE* 3.7 25.1 - + + -
162I ILE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I SER* 4.1 25.4 - - - +
47I THR* 4.5 7.1 - - + +
48I LYS* 2.9 37.8 - - + +
66I LEU 3.1 7.1 + - - +
67I ASP* 3.3 23.4 + - - +
69I PHE* 1.3 80.2 - - - +
71I THR* 1.3 67.6 + - - +
73I LEU* 3.3 11.8 + - - +
74I ILE* 2.9 51.0 + - - +
74J ILE* 2.9 40.7 - - - +
77J LEU* 5.1 3.6 - - - +
78J ASP* 3.5 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I ASP* 3.3 13.2 + - - -
68I GLY* 3.1 12.8 + - - -
70I ARG* 1.3 86.2 + - - +
72I ALA* 1.3 64.9 + - - +
74I ILE* 3.3 6.6 + - - +
75I ASP* 3.1 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I GLY 3.2 6.1 + - - +
69I PHE 3.0 8.4 + - - +
71I THR* 1.3 76.8 - - - +
73I LEU* 1.3 67.3 + - - +
75I ASP* 3.1 9.8 + - - +
76I HIS* 3.1 30.8 + - + -
154I ASP* 4.3 11.9 - - - +
158I PHE* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I PHE* 3.9 19.8 - - + +
43I LEU* 4.1 15.3 - - + -
44I SER* 3.9 25.1 - - - +
47I THR* 3.8 11.0 - - - +
69I PHE 2.7 23.8 + - - +
70I ARG* 3.3 5.6 + - - +
72I ALA* 1.3 73.8 - - - +
74I ILE* 1.3 57.0 + - - +
76I HIS* 3.4 4.7 + - + +
77I LEU* 2.9 31.7 + - - +
125I TYR* 3.5 23.8 - - - +
155I LEU* 4.2 25.4 - - + -
158I PHE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I SER* 4.6 10.3 - - - +
70I ARG* 2.9 46.0 + - - +
71I THR* 3.6 6.5 - - - +
73I LEU* 1.3 77.4 - - - +
75I ASP* 1.3 63.2 + - - +
77I LEU* 3.3 15.2 - - + +
78I ASP* 2.8 34.3 + - - +
70J ARG* 2.9 44.4 - - - +
74J ILE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I THR* 3.1 27.9 + - - +
72I ALA* 3.1 10.2 + - - +
74I ILE* 1.3 78.2 - - - +
76I HIS* 1.3 65.2 + - + +
78I ASP* 3.5 7.7 + - - +
79I THR* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I PHE* 4.0 10.5 - + + -
72I ALA* 3.1 29.0 + - + +
73I LEU* 3.8 7.6 - - + +
75I ASP* 1.3 76.7 - - + +
77I LEU* 1.3 63.9 + - - +
79I THR* 3.1 9.3 + - - -
80I MET* 2.9 29.5 + - + +
147I ILE* 4.7 3.6 + - + +
150I ALA* 3.4 19.7 - - + +
151I ALA* 3.3 45.0 + - + +
154I ASP* 2.7 36.1 + - + +
155I LEU* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 4.0 7.9 - - + +
40I PHE* 4.1 13.2 - - + +
41I ILE* 3.3 44.9 - - + +
44I SER* 4.7 2.5 - - - +
73I LEU 2.9 15.5 + - - +
74I ILE* 3.3 23.6 - - + +
76I HIS* 1.3 76.6 - - - +
78I ASP* 1.3 79.0 + - - +
80I MET* 3.1 17.7 + - - +
81I ALA* 2.9 20.6 + - - +
52J TRP* 3.5 23.8 - - + -
70J ARG* 5.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I ILE* 2.8 24.1 + - - +
75I ASP* 3.9 7.6 - - - +
77I LEU* 1.3 90.3 - - - +
79I THR* 1.3 57.9 + - - +
81I ALA* 3.4 1.4 + - - +
82I GLU* 2.9 43.0 + - - +
48J LYS* 2.7 32.8 + - - +
52J TRP* 3.3 17.6 + - - +
67J ASP* 4.4 0.3 - - - +
70J ARG* 3.5 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ASP 2.8 20.1 + - - -
76I HIS* 3.1 12.8 + - - -
78I ASP* 1.3 76.3 - - - +
80I MET* 1.3 61.4 + - - +
82I GLU* 3.3 10.8 + - - +
83I ARG* 3.0 21.3 + - - +
147I ILE* 3.8 20.4 - - + -
153K ARG* 3.6 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 3.6 23.9 - - + +
36I GLN* 3.6 28.9 - - + -
37I VAL* 4.0 11.7 - - + +
40I PHE* 3.6 39.3 - - + -
76I HIS* 2.9 14.3 + - + +
77I LEU* 3.6 26.0 - - - +
79I THR* 1.3 72.5 - - - +
81I ALA* 1.3 66.4 + - - +
83I ARG* 3.1 6.5 + - - +
84I ALA* 3.0 20.4 + - - +
147I ILE* 3.6 20.0 - - + -
148I LEU* 3.8 17.5 - - - -
151I ALA* 5.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 3.8 12.7 - - + +
77I LEU 2.9 12.2 + - - +
78I ASP 3.6 3.1 - - - +
80I MET* 1.3 75.3 - - - +
82I GLU* 1.3 63.9 + - - +
84I ALA* 3.1 7.2 + - - +
85I VAL* 3.1 25.2 + - - +
91I ALA* 3.8 12.8 - - + +
52J TRP* 3.3 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ASP* 2.9 30.3 + - - +
79I THR* 3.6 7.8 - - - +
81I ALA* 1.3 74.6 - - - +
83I ARG* 1.3 58.4 + - - +
85I VAL* 3.3 5.7 + - - +
86I GLN* 2.9 44.8 + - - +
48J LYS* 5.5 0.7 + - - -
51J HIS* 4.7 6.9 + - - -
52J TRP* 4.3 12.3 - - + -
63J HIS* 4.6 9.8 + - - -
157K LYS* 4.0 28.5 + - - +
160K TRP* 3.9 26.5 - - + -
161K PHE* 5.7 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 3.5 16.6 - - + -
79I THR 3.0 13.8 + - - +
80I MET 3.1 8.9 + - - +
82I GLU* 1.3 77.1 - - - +
84I ALA* 1.3 63.8 + - - +
86I GLN* 3.2 20.1 + - - +
87I LEU* 3.1 42.1 + - + +
141I ASP* 2.7 38.2 + - - -
143I ASP* 3.3 26.2 + - - +
144I THR* 3.7 9.3 + - - +
147I ILE* 3.6 25.1 - - + -
133K ARG* 4.1 4.2 - - - +
153K ARG* 5.1 4.1 + - - +
156K ASP* 2.8 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I VAL* 3.6 27.0 - - + +
33I LEU* 3.4 23.3 - - + +
34I ASN* 4.5 9.2 - - - +
37I VAL* 6.2 0.2 - - + -
80I MET 3.0 11.6 + - - +
81I ALA* 3.1 12.5 + - - +
83I ARG* 1.3 76.9 - - - +
85I VAL* 1.3 64.1 + - - +
87I LEU* 3.1 8.4 + - - -
88I GLY 3.5 0.2 + - - -
89I GLY* 3.0 20.0 + - - -
91I ALA* 4.9 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 6.3 0.4 - - + -
81I ALA 3.1 12.4 + - - +
82I GLU* 3.7 7.2 - - - +
84I ALA* 1.3 72.4 - - - +
86I GLN* 1.3 65.9 + - - +
88I GLY* 2.9 14.7 + - - -
89I GLY 3.7 12.7 - - - +
91I ALA* 3.9 13.7 - - + +
52J TRP* 3.5 22.4 - - + +
53J ASN* 3.4 28.0 - - - +
54J MET 6.0 0.7 - - - +
55J ARG* 3.8 19.0 + - + +
160K TRP* 3.2 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I THR* 4.0 19.4 + - - +
19I ASN* 4.2 9.0 + - - +
82I GLU* 2.9 37.3 + - - +
83I ARG* 3.2 38.0 + - - +
85I VAL* 1.3 76.5 - - - +
87I LEU* 1.3 60.1 + - - +
88I GLY 3.3 3.3 + - - -
55J ARG* 5.7 0.2 + - - -
153K ARG* 4.3 4.9 - - - +
156K ASP* 3.7 8.7 - - + +
157K LYS* 3.7 27.5 + - - +
160K TRP* 3.5 48.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 4.1 2.6 - - - +
17I THR* 4.6 1.8 - - - -
19I ASN* 4.1 11.7 - - - +
21I VAL* 3.8 34.5 - - + -
26I LYS* 3.1 41.1 - - + +
29I THR* 3.3 41.5 - - + +
30I VAL* 4.2 9.2 - - + +
33I LEU* 4.8 0.9 - - + -
83I ARG* 3.1 39.7 + - + +
84I ALA 3.1 9.4 + - - +
86I GLN* 1.3 75.5 - - - +
88I GLY* 1.3 58.3 + - - +
89I GLY 3.4 1.4 + - - -
141I ASP* 4.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
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