Contacts of the helix formed by residues 5 - 35 (chain T) in PDB entry 1BFR
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 THR 5 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3T GLY 3.4 5.4 + - - -
4T ASP* 1.3 72.2 + - - +
6T LYS* 1.3 59.1 + - - +
8T ILE* 3.4 10.9 + - - +
9T ASN* 3.0 40.7 + - - +
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Residues in contact with LYS 6 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4T ASP* 3.2 2.8 + - - +
5T THR* 1.3 77.3 - - + +
7T VAL* 1.3 59.8 + - - +
9T ASN* 3.3 12.3 + - + +
10T TYR* 3.0 61.4 + - + -
107T TYR* 3.3 42.6 - - + +
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Residues in contact with VAL 7 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4T ASP* 3.1 18.6 + - + +
6T LYS* 1.3 73.4 - - - +
8T ILE* 1.3 61.5 + - - +
10T TYR* 3.2 7.5 + - + +
11T LEU* 2.9 36.4 + - + +
65T LEU* 4.5 4.3 - - + -
107T TYR* 3.6 14.5 - - + -
108T ALA* 4.1 12.6 - - + -
111T VAL* 3.5 31.9 - - + -
113T ASP* 3.4 24.0 - - - +
116T SER* 4.0 14.8 - - - +
120T MET* 5.3 1.6 - - + -
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Residues in contact with ILE 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2T LYS* 5.9 1.8 - - + -
3T GLY* 4.4 8.7 - - - +
4T ASP 3.0 14.9 + - - +
5T THR* 3.7 10.5 - - - +
7T VAL* 1.3 74.8 - - - +
9T ASN* 1.3 61.3 + - - +
11T LEU* 3.5 7.6 + - + +
12T ASN* 3.0 34.3 + - - +
62T ILE* 4.0 14.8 - - + +
65T LEU* 3.4 46.9 - - + +
66T GLU 4.4 1.1 - - - +
67T GLY* 3.8 28.7 - - - +
68T LEU 4.7 0.7 - - - +
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Residues in contact with ASN 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T THR* 3.0 29.7 + - - +
6T LYS* 3.3 13.9 + - + +
8T ILE* 1.3 79.3 - - - +
10T TYR* 1.3 60.0 + - + +
12T ASN* 3.2 10.4 + - - +
13T LYS* 2.9 29.8 + - - +
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Residues in contact with TYR 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6T LYS* 3.0 51.4 + - + -
7T VAL* 3.6 7.4 - - + +
9T ASN* 1.3 73.3 - - + +
11T LEU* 1.3 60.0 + - + +
13T LYS* 3.2 24.9 + - + +
14T LEU* 2.9 38.5 + - + +
100T ASN 5.2 0.2 - - - -
103T GLU* 2.8 39.6 + - + +
104T ALA* 3.8 30.3 - - + +
107T TYR* 3.6 43.6 - + + +
120T MET* 5.5 0.9 - - + -
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Residues in contact with LEU 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T VAL* 2.9 31.4 + - + +
8T ILE* 3.7 3.4 - - - +
10T TYR* 1.3 71.6 - - + +
12T ASN* 1.3 59.5 + - - +
14T LEU* 3.4 4.8 + - - +
15T LEU* 2.8 28.9 + - - +
58T TYR* 4.2 21.9 - - + -
61T ARG* 3.9 24.9 - - + -
62T ILE* 3.7 27.1 - - + +
65T LEU* 4.0 18.2 - - + -
116T SER* 4.3 3.1 - - - +
119T MET* 4.3 9.4 - - + -
120T MET* 3.9 33.7 - - + -
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Residues in contact with ASN 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8T ILE* 3.0 28.4 + - - +
9T ASN* 3.2 12.8 + - - +
11T LEU* 1.3 75.0 - - - +
13T LYS* 1.3 55.9 + - - +
15T LEU* 3.7 5.9 - - - +
16T GLY* 2.9 26.2 + - - -
62T ILE* 3.6 11.6 - - - +
68T LEU 3.0 21.6 + - - +
69T PRO* 3.5 4.3 - - - +
70T ASN* 2.7 42.4 + - + +
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Residues in contact with LYS 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T ASN 2.9 16.1 + - - +
10T TYR* 3.5 32.7 - - + +
12T ASN* 1.3 70.5 - - - +
14T LEU* 1.3 64.5 + - + +
16T GLY* 3.2 4.2 + - - -
17T ASN* 3.0 25.7 + - - +
100T ASN* 3.3 44.8 + - + +
103T GLU* 3.9 18.0 + - - -
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Residues in contact with LEU 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T TYR* 2.9 22.7 + - + +
11T LEU* 3.6 4.5 - - - +
13T LYS* 1.3 79.6 - - + +
15T LEU* 1.4 64.9 + - - +
17T ASN* 3.0 20.9 + - - +
18T GLU* 3.1 15.2 + - - +
58T TYR* 3.8 30.3 - - + +
97T GLY 5.2 0.2 - - - +
100T ASN* 3.7 39.9 - - + +
101T LEU* 4.2 11.2 - - + +
104T ALA* 3.7 12.3 - - + -
120T MET* 3.6 30.3 - - - -
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Residues in contact with LEU 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T LEU 2.8 21.9 + - - +
12T ASN* 3.7 17.9 - - - +
14T LEU* 1.4 68.3 - - - +
16T GLY* 1.3 64.0 + - - +
18T GLU* 3.0 6.1 + - - +
19T LEU* 3.0 28.4 + - + +
55T ALA* 3.8 39.3 - - + +
58T TYR* 4.0 14.8 - - + -
59T ILE* 4.0 12.3 - - + +
62T ILE* 4.2 6.3 - - + -
69T PRO* 4.2 5.2 - - + -
70T ASN 3.9 23.8 - - - +
71T LEU* 3.9 25.8 - - + -
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Residues in contact with GLY 16 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T ASN 2.9 14.8 + - - -
13T LYS* 3.5 6.3 - - - -
14T LEU 3.2 0.2 - - - -
15T LEU* 1.3 76.5 - - - +
17T ASN* 1.3 61.1 + - - +
19T LEU* 3.4 21.6 + - - +
20T VAL* 3.5 15.8 + - - +
70T ASN 5.1 2.9 + - - -
73T ASP 4.7 11.0 - - - +
75T GLY 5.2 0.5 + - - -
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Residues in contact with ASN 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13T LYS* 3.0 21.9 + - - +
14T LEU* 3.0 14.8 + - - +
16T GLY* 1.3 74.2 - - - +
18T GLU* 1.3 66.2 + - + +
20T VAL* 3.2 11.5 + - - +
21T ALA* 3.2 20.4 + - - +
93T LEU* 4.9 9.8 - - + +
96T ASP* 6.5 0.2 - - - -
97T GLY* 4.1 15.3 - - - -
100T ASN* 2.9 37.3 + - - +
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Residues in contact with GLU 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T LEU 3.1 12.5 + - - +
15T LEU 3.0 7.6 + - - +
17T ASN* 1.3 75.9 - - - +
19T LEU* 1.3 59.0 + - - +
21T ALA* 3.2 5.2 + - - +
22T ILE* 2.8 34.4 + - - +
51T GLU* 2.8 18.2 - - - +
54T HIS* 3.6 15.3 - - + +
55T ALA* 4.2 18.4 - - + +
58T TYR* 3.7 26.5 + - + -
101T LEU* 5.9 1.0 - - - +
123T ILE* 4.0 5.0 - - - +
127T GLU* 5.3 0.2 - - - +
202T MN 2.1 37.8 + - - -
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Residues in contact with LEU 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S ASN* 4.6 6.3 - - - +
74S LEU* 5.8 0.9 - - + -
15T LEU* 3.0 27.8 + - + +
16T GLY* 3.7 8.7 - - - +
17T ASN 3.3 0.2 - - - -
18T GLU* 1.3 77.3 - - - +
20T VAL* 1.3 59.3 + - - +
22T ILE* 3.8 8.5 + - + +
23T ASN* 3.5 26.3 + - - +
55T ALA* 4.6 1.6 - - + -
70T ASN 4.1 6.3 - - - +
71T LEU* 3.9 44.9 - - + +
73T ASP 4.4 14.6 - - - +
74T LEU* 3.9 14.2 - - + +
200T HEM 3.9 31.6 - - + -
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Residues in contact with VAL 20 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T GLY 3.8 12.6 - - - +
17T ASN* 3.2 7.7 + - - +
19T LEU* 1.3 72.5 - - - +
21T ALA* 1.3 62.3 + - - +
23T ASN* 3.2 2.5 + - - +
24T GLN* 2.8 36.5 + - - +
74T LEU* 3.8 11.0 - - + -
75T GLY* 3.5 36.8 - - - +
76T LYS 4.4 13.2 - - - +
77T LEU* 4.1 9.9 - - + +
93T LEU* 3.7 30.5 - - + -
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Residues in contact with ALA 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17T ASN 3.2 12.0 + - - +
18T GLU* 3.2 10.2 + - - +
20T VAL* 1.3 76.8 - - - +
22T ILE* 1.3 56.6 + - - +
25T TYR* 2.8 47.5 + - + -
51T GLU* 3.9 24.2 - - + +
93T LEU* 4.0 18.8 - - + -
94T GLU* 4.9 2.7 - - - +
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Residues in contact with ILE 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T GLU 2.8 25.9 + - - +
19T LEU* 3.9 7.9 - - - +
21T ALA* 1.3 69.5 - - - +
23T ASN* 1.3 65.5 + - - +
26T PHE* 2.9 27.7 + - - +
48T SER* 3.2 12.2 + - - +
51T GLU* 3.6 12.9 - - + +
52T MET* 3.6 56.1 - - + +
55T ALA* 4.0 10.5 - - + -
200T HEM 3.8 47.6 - - + -
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Residues in contact with ASN 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S LEU* 4.5 10.3 - - - +
71S LEU* 2.9 53.7 + - + +
19T LEU 3.5 12.6 + - - +
20T VAL 3.2 7.1 + - - +
22T ILE* 1.3 77.9 - - - +
24T GLN* 1.3 62.7 + - - +
26T PHE* 3.9 2.0 - - - -
27T LEU* 3.0 22.7 + - - +
74T LEU* 3.7 16.3 - - - +
77T LEU* 4.3 9.4 - - + -
200T HEM 3.8 21.0 - - - +
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Residues in contact with GLN 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T VAL* 2.8 22.9 + - - +
21T ALA* 4.0 1.3 - - - +
23T ASN* 1.3 73.8 - - - +
25T TYR* 1.3 60.9 + - + +
27T LEU* 4.1 2.8 - - - +
28T HIS* 3.0 37.8 + - + +
76T LYS 4.8 0.8 + - - -
77T LEU* 3.8 15.0 - - + +
78T ASN* 3.0 37.9 + - - +
79T ILE* 4.5 7.8 - - + +
89T SER* 3.4 21.0 + - - -
90T ASP* 3.0 23.0 - - - +
93T LEU* 3.6 26.1 - - + +
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Residues in contact with TYR 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21T ALA* 2.8 38.2 + - + +
24T GLN* 1.3 72.2 - - + +
26T PHE* 1.3 57.2 + - - +
28T HIS* 3.4 1.8 + - - +
29T ALA* 2.9 29.3 + - - +
44T GLU* 3.5 32.6 - - - +
47T GLU* 3.2 39.7 + - + -
48T SER* 3.9 18.8 - - - +
51T GLU* 3.6 20.4 - - + -
90T ASP* 3.8 22.0 - - + -
93T LEU* 5.9 3.4 - - + -
94T GLU* 3.0 44.3 + - + +
130T HIS* 3.6 7.4 + - - +
134T LEU* 3.8 3.1 - - + +
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Residues in contact with PHE 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ASP* 3.4 36.1 - - + -
59S ILE* 3.8 16.6 - - + -
71S LEU* 5.1 1.8 - - + -
22T ILE 2.9 21.1 + - - +
23T ASN* 3.9 3.8 - - - +
25T TYR* 1.3 73.9 - - - +
27T LEU* 1.3 63.4 + - - +
29T ALA* 3.2 6.5 + - + +
30T ARG* 3.1 38.2 + - + +
45T TYR* 3.6 27.4 - + - -
48T SER* 3.4 21.6 + - - +
52T MET* 4.1 4.5 - - + -
200T HEM 3.6 52.3 - + + -
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Residues in contact with LEU 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59S ILE* 4.0 12.6 - - + -
63S LEU* 4.5 1.3 - - + -
68S LEU* 5.5 3.6 - - + -
69S PRO* 3.7 50.7 - - + +
71S LEU* 3.8 19.2 - - + +
23T ASN 3.0 18.0 + - - +
24T GLN 4.1 2.0 - - - +
26T PHE* 1.3 76.8 - - - +
28T HIS* 1.3 62.4 + - - +
30T ARG* 3.3 3.1 + - - +
31T MET* 2.9 42.1 + - + +
77T LEU* 5.1 1.3 - - + -
79T ILE* 3.5 35.9 - - + -
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Residues in contact with HIS 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T GLN* 3.0 31.0 + - + +
25T TYR 3.7 0.7 - - - +
27T LEU* 1.3 72.2 - - - +
29T ALA* 1.3 63.6 + - - +
31T MET* 3.3 1.2 + - - +
32T PHE* 2.9 34.9 + + + -
44T GLU* 3.3 14.1 - - - +
78T ASN 4.2 1.5 + - - -
79T ILE* 2.7 48.9 + - + +
86T MET* 3.3 40.0 + - + +
90T ASP* 3.0 40.8 + - - -
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Residues in contact with ALA 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T TYR 2.9 15.2 + - - +
26T PHE* 3.4 10.3 - - - +
28T HIS* 1.3 70.6 - - - +
30T ARG* 1.3 63.6 + - + +
32T PHE* 3.2 3.3 + - - +
33T LYS 2.8 24.1 + - - -
41T ASN* 3.1 26.4 - - - +
44T GLU* 3.9 9.3 - - + +
45T TYR* 3.5 35.9 - - + +
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Residues in contact with ARG 30 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ASP* 2.9 37.2 + - - +
59S ILE* 3.9 24.7 - - + -
60S GLU* 3.2 24.5 + - + +
63S LEU* 3.9 9.1 - - + +
26T PHE* 3.1 30.9 + - + +
27T LEU 4.1 0.9 - - - +
29T ALA* 1.3 78.1 - - - +
31T MET* 1.3 55.8 + - - +
33T LYS* 3.5 13.1 - - - +
34T ASN* 2.9 30.1 + - - +
41T ASN* 2.9 29.1 + - - +
45T TYR* 3.7 38.3 - - - +
----------------------------------------------------------
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Residues in contact with MET 31 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S LEU* 4.2 23.1 - - + -
68S LEU* 5.6 8.5 - - + -
27T LEU* 2.9 34.0 + - + +
28T HIS* 3.5 4.0 - - - +
30T ARG* 1.3 71.8 - - - +
32T PHE* 1.3 65.3 + - - +
34T ASN* 3.2 7.7 + - - +
35T TRP* 3.1 48.7 + - + -
79T ILE* 3.8 22.2 - - + -
80T GLY 4.2 14.1 - - - +
81T GLU* 5.5 0.9 - - - +
86T MET* 3.6 28.0 - - + -
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Residues in contact with PHE 32 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T HIS* 2.9 28.5 + - + -
29T ALA* 3.6 4.9 - - - +
31T MET* 1.3 69.9 - - - +
33T LYS* 1.3 60.9 + - - +
35T TRP* 3.2 21.0 + + - -
37T LEU* 2.9 38.8 + - + +
40T LEU* 3.7 33.7 - - + -
41T ASN 3.7 12.3 - - - +
44T GLU* 3.8 27.6 - - + -
83T VAL* 4.1 20.2 - - + -
86T MET* 3.7 34.1 - - + -
87T LEU* 3.7 23.6 - - + -
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Residues in contact with LYS 33 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S GLU* 3.4 37.5 + - - -
29T ALA 2.8 11.0 + - - +
30T ARG* 3.5 19.3 - - - +
31T MET 3.2 0.2 - - - -
32T PHE* 1.3 70.8 - - - +
34T ASN* 1.3 64.3 + - - +
36T GLY* 2.9 15.8 + - - -
37T LEU 4.8 2.9 - - - +
38T LYS* 5.4 5.4 - - + +
41T ASN* 3.4 42.1 - - + +
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Residues in contact with ASN 34 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R ASP* 4.2 12.2 - - - +
136R THR* 3.5 17.0 + - - +
63S LEU* 3.9 34.6 + - + +
64S PHE* 4.2 16.3 + - - +
30T ARG 2.9 17.2 + - - +
31T MET* 3.6 6.0 - - - +
33T LYS* 1.3 75.4 - - - +
35T TRP* 1.3 70.3 + - - +
36T GLY 3.2 1.1 + - - -
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Residues in contact with TRP 35 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R THR* 3.6 7.4 - - - +
139R ASP* 5.7 3.7 - - - +
140R LEU* 3.4 24.3 - - - +
143R LYS* 3.6 27.8 + - - +
31T MET* 3.1 34.0 + - + -
32T PHE* 3.7 14.6 - + - +
33T LYS 3.2 0.6 - - - -
34T ASN* 1.3 87.8 - - - +
36T GLY* 1.3 58.7 + - - +
37T LEU* 3.6 26.0 + - + +
81T GLU 3.9 18.2 - - - -
82T ASP* 4.6 2.0 - - - -
83T VAL* 4.1 15.7 - - + -
86T MET* 3.4 38.1 - - + -
----------------------------------------------------------
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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