Contacts of the helix formed by residues 38 - 67 (chain B) in PDB entry 4IF8
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 GLY 38 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.3 11.4 + - - +
36B VAL 3.2 1.0 - - - -
37B GLN* 1.3 77.8 - - - +
39B TRP* 1.4 60.9 + - - +
40B LYS 3.4 2.2 - - - -
41B GLN* 3.3 23.8 + - - +
42B ARG* 3.2 36.9 + - - +
118B TYR* 5.6 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.0 22.4 + - + +
37B GLN 3.3 1.4 - - - -
38B GLY* 1.4 74.4 - - - +
40B LYS* 1.3 92.0 + - + +
42B ARG* 3.3 25.3 + - - +
43B MET* 3.0 63.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN 4.7 4.3 + - - +
38B GLY 3.4 0.6 - - - -
39B TRP* 1.3 99.6 - - + +
41B GLN* 1.4 57.1 + - - +
43B MET* 3.3 5.1 + - + +
44B ALA* 2.9 35.2 + - + +
110B LYS* 3.9 17.2 - - - +
111B ASP* 3.2 27.5 + - - +
114B GLU* 2.7 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN 5.6 0.2 + - - -
38B GLY* 3.3 22.8 + - - +
40B LYS* 1.4 79.3 - - - +
42B ARG* 1.4 56.7 + - - +
44B ALA* 3.4 8.0 + - - +
45B ALA* 3.0 27.0 + - - +
114B GLU* 4.0 23.3 - - + +
115B GLY* 4.3 4.6 - - - +
117B HIS* 4.2 12.1 - - - -
118B TYR* 3.4 48.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU 2.9 35.9 + - - +
36B VAL* 4.7 2.2 + - - +
38B GLY* 3.2 23.7 + - - +
39B TRP* 3.3 33.4 + - - +
41B GLN* 1.4 76.9 - - - +
43B MET* 1.3 69.8 + - + +
45B ALA* 3.4 2.6 + - - +
46B LYS* 3.1 35.9 + - - +
118B TYR* 3.3 35.7 - - + +
398B LYS 6.2 0.2 - - - -
400B PRO* 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 3.0 62.0 + - + +
40B LYS* 3.6 9.4 - - + +
42B ARG* 1.3 80.4 - - + +
44B ALA* 1.3 66.5 + - - +
46B LYS* 3.3 40.7 + - - +
47B GLU* 3.1 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 2.9 19.6 + - + +
41B GLN* 3.5 7.2 - - - +
43B MET* 1.3 75.1 - - - +
45B ALA* 1.4 55.2 + - - +
47B GLU* 3.4 4.2 + - - +
48B LEU* 2.9 35.9 + - - +
107B MET* 3.7 15.2 - - - +
111B ASP* 3.7 28.5 - - + +
114B GLU* 5.9 0.7 - - + -
115B GLY* 3.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN 3.0 14.7 + - - +
42B ARG* 3.6 7.6 - - - +
43B MET 3.2 0.4 - - - -
44B ALA* 1.4 72.9 - - - +
46B LYS* 1.3 60.0 + - - +
48B LEU* 3.3 1.7 + - - +
49B ALA* 2.9 31.5 + - - +
115B GLY* 4.6 1.7 - - - +
118B TYR* 3.8 17.7 - - + -
119B ILE* 3.7 32.5 - - + -
400B PRO* 3.6 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.1 18.3 + - - +
43B MET* 3.3 43.0 + - + +
45B ALA* 1.3 75.5 - - - +
47B GLU* 1.3 65.0 + - - +
49B ALA* 3.7 2.6 - - - +
50B ARG* 3.3 27.4 + - - +
400B PRO* 4.0 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MET* 3.1 17.8 + - + +
44B ALA* 3.6 2.2 - - - +
46B LYS* 1.3 78.6 - - - +
48B LEU* 1.3 59.1 + - - +
50B ARG* 3.3 18.6 + - - +
51B GLN* 3.0 45.8 + - - +
106B LYS* 5.0 9.4 + - - +
107B MET* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 2.9 20.8 + - - +
45B ALA 3.3 4.2 + - - +
47B GLU* 1.3 74.8 - - - +
49B ALA* 1.4 51.6 + - - +
51B GLN* 3.2 20.6 + - + +
52B ASN* 2.8 37.8 + - - +
104B PHE* 4.4 5.2 - - + -
107B MET* 3.9 9.2 - - + -
112B LEU* 3.7 22.9 - - + +
115B GLY* 3.7 12.1 - - - -
116B PHE* 3.6 63.1 - - + +
119B ILE* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA 2.9 18.1 + - - +
46B LYS 3.7 5.8 - - - +
47B GLU 3.3 0.2 - - - -
48B LEU* 1.4 73.9 - - - +
50B ARG* 1.4 63.0 + - - +
52B ASN* 3.2 16.3 - - - +
53B MET* 3.2 22.7 + - - +
119B ILE* 5.2 0.2 - - - +
395B TYR* 4.6 8.3 - - + +
400B PRO* 3.4 38.1 + - + -
401B SER* 3.6 4.0 - - - +
402B VAL* 4.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS 3.3 12.2 + - - +
47B GLU* 3.3 24.3 + - - +
49B ALA* 1.4 76.7 - - - +
51B GLN* 1.3 64.5 + - + +
53B MET* 3.3 16.5 + - - +
54B ASP* 3.4 10.2 + - - +
106B LYS* 5.8 3.6 - - - +
289B VAL* 3.9 37.8 + - + +
290B ASP* 4.8 10.1 + - - -
293B SER* 5.6 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 3.0 35.6 + - - +
48B LEU* 3.2 29.3 + - + +
50B ARG* 1.3 75.9 - - + +
52B ASN* 1.4 56.8 + - - +
54B ASP* 3.6 1.1 + - - -
55B LEU* 3.2 22.2 + - - +
102B PHE 4.1 7.8 - - - +
103B ASN* 3.2 52.8 + - + +
104B PHE* 4.5 6.7 - - + -
106B LYS* 3.9 33.3 - - - +
107B MET* 3.8 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 2.8 24.4 + - - +
49B ALA* 3.2 11.3 - - - +
51B GLN* 1.4 69.1 - - - +
53B MET* 1.3 59.9 + - - +
54B ASP 3.4 0.2 - - - -
55B LEU* 3.8 5.8 - - - -
56B GLY* 2.9 24.3 + - - -
76B PRO* 3.3 19.5 - - - +
77B LEU* 3.6 37.0 - - - +
80B SER* 3.8 20.6 + - - +
116B PHE* 5.0 5.2 - - + -
119B ILE* 5.7 0.6 - - - +
401B SER* 4.0 9.1 - - - -
402B VAL* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.2 12.8 + - - +
50B ARG* 3.4 13.5 - - - +
51B GLN 3.3 0.2 - - - -
52B ASN* 1.3 77.6 + - - +
54B ASP* 1.4 57.1 + - - +
56B GLY* 3.4 2.0 + - - -
57B PHE* 3.1 66.3 + - + -
288B GLN 5.2 0.4 - - - +
289B VAL* 4.7 10.1 - - + +
292B PHE* 3.5 48.9 - - + -
393B LEU* 4.2 10.3 - - + -
395B TYR* 4.2 8.3 - - + -
402B VAL* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG 3.4 5.0 + - - +
51B GLN* 4.0 2.9 - - - +
52B ASN 3.4 0.2 - - - -
53B MET* 1.4 75.8 - - - +
55B LEU* 1.3 60.3 - - - +
57B PHE* 3.5 6.7 + - - +
58B LYS* 2.9 43.2 + - - +
103B ASN* 2.8 33.7 + - - +
288B GLN* 5.5 1.9 - - - -
289B VAL* 3.5 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN 3.2 15.3 + - - +
52B ASN* 3.8 4.0 - - - +
53B MET 3.3 0.2 - - - -
54B ASP* 1.3 76.5 + - - +
56B GLY* 1.3 59.1 - - - +
58B LYS* 3.1 8.7 + - - +
59B LEU* 2.9 45.2 + - + +
76B PRO* 3.9 14.1 - - + +
79B ILE* 4.8 1.3 - - + -
80B SER* 3.3 26.0 - - - +
101B GLY 3.6 23.6 - - - +
102B PHE* 3.6 29.6 - - + +
103B ASN* 3.9 5.6 - - - +
326B ILE* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN 2.9 17.9 + - - -
53B MET* 3.8 2.0 - - - -
55B LEU* 1.3 76.0 - - - +
57B PHE* 1.3 56.5 + - - +
59B LEU* 3.3 6.3 + - - +
60B LEU 2.8 26.2 + - - -
74B LEU* 5.1 3.1 - - - +
76B PRO* 3.7 23.7 - - - +
402B VAL* 6.0 0.4 - - - -
405B LEU* 3.4 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 3.1 50.6 + - + +
54B ASP* 3.9 6.3 - - - +
56B GLY* 1.3 73.4 - - - +
58B LYS* 1.4 62.5 + - - +
60B LEU* 3.5 2.6 + - - +
61B LYS* 3.1 32.8 + - - +
287B LEU* 3.8 48.0 - - + +
288B GLN* 3.3 32.3 - - - -
291B THR* 4.7 6.1 - - + -
292B PHE* 5.0 5.2 - - + -
295B TRP* 4.7 10.5 - + - -
391B LEU* 6.3 0.4 - - + -
393B LEU* 4.1 12.6 - - + -
405B LEU* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 2.9 36.1 + - - +
55B LEU* 3.4 12.8 - - - +
57B PHE* 1.4 74.9 - - - +
59B LEU* 1.3 61.6 + - - +
61B LYS* 3.5 8.2 + - - +
62B LYS* 3.3 32.5 + - - +
100B GLN 4.4 1.4 + - - -
101B GLY* 2.8 37.1 + - - -
103B ASN* 3.9 9.5 + - - +
326B ILE* 3.9 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 2.9 41.9 + - + +
56B GLY* 3.7 4.0 - - - +
58B LYS* 1.3 72.2 - - - +
60B LEU* 1.3 59.1 + - - +
62B LYS* 3.3 4.4 + - + +
63B LEU* 2.9 37.4 + - + +
74B LEU* 4.3 19.7 - - + -
76B PRO* 5.5 0.7 - - + -
79B ILE* 4.0 31.4 - - + -
322B THR* 3.8 28.0 - - + +
323B LEU* 4.9 2.7 - - + -
325B TYR* 5.8 1.3 - - + -
326B ILE* 3.8 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 2.8 21.6 + - - +
57B PHE 3.8 3.6 - - - +
59B LEU* 1.3 71.9 - - - +
61B LYS* 1.4 55.2 + - - +
63B LEU* 3.5 5.8 + - - +
64B ALA* 2.9 33.1 + - + +
72B ILE* 4.2 18.6 - - + +
74B LEU* 5.5 3.7 - - + +
284B GLU* 5.3 6.7 - - + +
287B LEU* 3.8 24.9 - - + -
391B LEU* 4.2 21.3 - - + -
405B LEU* 3.8 26.5 - - + +
406B GLY* 4.4 5.2 - - - +
407B LYS* 3.9 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE 3.1 23.0 + - - +
58B LYS* 3.7 7.2 - - - +
59B LEU 3.3 0.2 - - - -
60B LEU* 1.4 75.0 - - - +
62B LYS* 1.4 65.0 + - + +
64B ALA* 3.5 5.9 + - - +
65B PHE* 3.3 22.5 + - - +
284B GLU* 3.2 33.9 - - + +
285B LYS* 2.8 23.3 + - - +
287B LEU* 3.3 34.3 + - + +
288B GLN* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 3.3 24.0 + - - +
59B LEU* 3.8 4.7 - - - +
61B LYS* 1.4 76.4 - - + +
63B LEU* 1.3 58.1 + - - +
65B PHE* 3.3 6.2 + - + +
66B TYR* 3.0 47.4 + - + +
325B TYR* 3.4 52.2 + - + +
326B ILE* 4.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 2.9 23.5 + - + +
60B LEU 3.9 1.3 - - - +
62B LYS* 1.3 73.9 - - - +
64B ALA* 1.4 57.0 + - - +
66B TYR* 5.0 0.9 - - - -
67B ASN* 2.8 57.1 + - - +
72B ILE* 3.7 30.3 - - + -
74B LEU* 3.6 31.2 - - + -
317B PHE* 3.9 21.5 - - + -
322B THR* 4.3 19.3 - - + +
325B TYR* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 2.9 20.7 + - + +
61B LYS* 3.8 6.3 - - - +
62B LYS 3.4 0.4 - - - -
63B LEU* 1.4 76.3 - - - +
65B PHE* 1.4 60.3 + - - +
67B ASN 4.3 4.5 - - - -
68B PRO* 3.5 25.1 - - - +
72B ILE* 4.7 5.1 - - - +
284B GLU* 3.4 32.1 - - + +
407B LYS* 4.0 15.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS 3.3 13.1 + - - +
62B LYS* 3.6 8.7 - - + +
63B LEU 3.3 0.4 - - - -
64B ALA* 1.4 75.4 - - - +
66B TYR* 1.4 104.2 + + - +
68B PRO* 3.5 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.0 40.7 + - + +
65B PHE* 1.4 104.1 - + - +
67B ASN* 1.3 72.0 + - - +
68B PRO* 3.7 5.6 - - - +
325B TYR* 3.5 57.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 2.8 40.7 + - - +
64B ALA* 3.7 5.6 - - - +
66B TYR* 1.3 92.3 - - - +
68B PRO* 1.4 64.4 - - - +
69B GLY 3.9 0.2 + - - -
70B ARG* 3.9 24.5 + - + +
72B ILE* 4.1 15.1 - - + +
321B LYS* 6.2 1.0 - - - +
325B TYR* 4.8 4.6 + - - -
407B LYS* 4.9 0.7 + - - -
----------------------------------------------------------
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