Contacts of the helix formed by residues 48 - 77 (chain L) in PDB entry 5JKL
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 LEU 48 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L PHE* 3.0 32.2 + - + +
46L VAL* 3.4 13.4 - - + +
47L ALA* 1.3 81.1 - - - +
49L LYS* 1.3 59.2 + - - +
51L PHE* 3.3 26.5 + - + +
52L ALA* 3.1 22.3 + - - +
167L GLU* 4.1 24.7 - - + +
168L TYR* 4.0 25.1 - - + +
171L ASP* 3.2 31.4 - - + +
172L LYS* 4.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L PHE 5.0 0.9 - - - -
42L ASP* 6.1 0.7 - - - +
47L ALA 3.8 3.1 + - - +
48L LEU* 1.3 73.2 - - - +
50L ASN* 1.3 81.6 + - - +
52L ALA* 3.4 8.2 + - - +
53L LYS* 3.0 52.0 + - + +
171L ASP* 3.5 4.4 + - - -
172L LYS* 5.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L LYS* 1.3 95.8 + - - +
51L PHE* 1.3 59.4 + - - +
53L LYS* 3.8 18.5 + - - +
54L TYR* 2.9 31.5 + - - +
171L ASP* 2.9 44.0 + - - +
172L LYS* 4.3 8.9 - - - +
175L LEU* 3.7 19.2 - - + +
176L GLY* 3.5 19.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L PHE* 3.5 20.0 - + + -
48L LEU* 3.5 20.9 - - + +
50L ASN* 1.3 74.2 - - - +
52L ALA* 1.3 62.8 + - - +
54L TYR* 3.3 1.9 + - - +
55L PHE* 3.0 49.0 + + - -
96L GLY* 3.5 38.1 - - - -
100L MET* 3.9 16.4 - - + -
155L LEU* 4.1 9.9 - - + -
167L GLU* 3.8 22.2 - - + -
170L PHE* 3.6 22.4 - + - -
171L ASP* 3.0 24.4 + - + -
175L LEU* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L SER* 2.7 48.9 + - - +
41L PHE* 3.7 6.0 - - + +
42L ASP* 4.1 15.5 - - + +
48L LEU 3.1 13.5 + - - +
49L LYS* 3.5 11.9 - - - +
50L ASN 3.3 0.2 - - - -
51L PHE* 1.3 75.8 - - - +
53L LYS* 1.3 63.1 + - - +
55L PHE 3.5 0.2 + - - -
56L LEU* 3.0 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L LYS* 3.0 42.8 + - + +
50L ASN* 3.8 20.1 + - - +
52L ALA* 1.3 75.5 - - + +
54L TYR* 1.3 63.5 + - - +
56L LEU* 3.3 6.2 + - - +
57L HIS* 3.0 25.1 + - - +
175L LEU 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ASN 2.9 18.2 + - - +
51L PHE 3.6 4.0 - - - +
52L ALA 3.2 0.2 - - - -
53L LYS* 1.3 78.9 - - - +
55L PHE* 1.4 86.2 + + - +
57L HIS* 3.3 8.1 + + - +
58L GLN* 3.0 50.3 + - + +
100L MET* 3.7 28.3 - - + -
147L GLU* 2.8 32.4 + - - +
148L LEU* 3.7 19.8 - - + +
151L HIS* 3.8 17.1 - + - -
175L LEU* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.5 53.0 - + + +
37L MET* 3.9 17.7 - - + -
38L SER* 3.7 7.9 - - - +
41L PHE* 3.5 34.8 - + - -
51L PHE* 3.0 36.6 + + - +
54L TYR* 1.4 98.8 - + - +
56L LEU* 1.3 56.6 + - - +
58L GLN* 3.2 2.9 + - + -
59L SER* 2.9 24.3 + - - -
99L ALA* 4.0 18.2 - - + -
100L MET* 3.8 23.6 - - + -
103L ALA* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K GLU* 3.7 27.6 - - - +
35L LEU* 3.8 21.5 - - + -
38L SER* 3.4 19.2 - - - +
39L TYR* 4.2 17.3 - - + +
52L ALA 3.0 11.7 + - - +
53L LYS* 3.8 7.6 - - + +
55L PHE* 1.3 74.4 - - - +
57L HIS* 1.3 63.5 + - - +
59L SER* 3.1 9.1 + - - -
60L HIS* 2.9 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L LYS 3.0 13.6 + - - +
54L TYR* 3.5 11.0 - + - +
56L LEU* 1.3 76.7 - - - +
58L GLN* 1.3 71.6 + - - +
60L HIS* 3.2 10.3 + - - +
61L GLU* 2.6 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.7 30.8 + - + -
54L TYR* 3.0 58.4 + - + +
55L PHE* 3.2 6.7 + - - +
57L HIS* 1.3 94.4 - - - +
59L SER* 1.3 62.2 - - - +
61L GLU* 3.3 8.1 + - - +
62L GLU* 3.0 28.8 + - - +
147L GLU* 4.1 5.9 + - - -
203L MG 1.9 35.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K ARG* 3.0 24.7 + - - -
31L SER* 2.7 47.9 + - - +
34L TYR* 3.6 7.7 - - - +
35L LEU* 3.6 16.3 - - - +
55L PHE 2.9 13.2 + - - -
56L LEU* 3.3 13.0 - - - -
58L GLN* 1.3 76.3 - - - +
60L HIS* 1.3 62.8 + - - +
62L GLU 3.3 1.4 + - - -
63L ARG* 3.1 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K ARG* 3.6 22.3 - - + +
64K GLU* 3.8 12.1 + - - -
67K GLU* 2.7 34.1 + - - -
56L LEU* 2.9 33.4 + - + +
57L HIS* 3.2 10.1 + - - +
59L SER* 1.3 76.7 - - - +
61L GLU* 1.3 61.9 + - - +
63L ARG* 3.3 9.6 + - + +
64L GLU* 3.2 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L HIS* 2.6 52.6 + - + +
58L GLN* 3.3 14.8 + - - +
60L HIS* 1.3 76.8 - - - +
62L GLU* 1.3 56.8 + - - +
64L GLU* 3.1 9.9 + - - +
65L HIS* 3.0 46.9 + - + +
140L GLU* 5.0 7.1 - - - +
203L MG 4.1 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L GLU* 2.7 15.4 - - - +
30L ALA* 3.9 18.0 - - + +
31L SER* 3.6 25.1 - - - +
34L TYR* 3.8 19.5 - - + -
58L GLN 3.0 18.3 + - - +
60L HIS 3.3 0.2 - - - -
61L GLU* 1.3 71.9 - - - +
63L ARG* 1.3 67.2 + - - +
65L HIS* 3.2 15.7 + - - +
66L ALA* 3.0 21.8 + - - +
107L GLU* 3.4 22.9 - - - +
110L VAL* 5.4 0.6 - - - +
201L FE 2.0 32.1 - - - -
203L MG 4.1 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K SER* 2.9 31.5 + - - -
32K TYR* 4.8 2.0 - - - +
35K LEU* 3.9 17.5 - - - +
59K SER* 3.0 20.0 + - - -
60K HIS* 3.6 16.7 - - + +
63K ARG* 5.0 21.2 - - - +
28L LEU* 4.0 21.3 - - - +
31L SER* 3.8 11.7 + - - +
59L SER 3.1 12.9 + - - +
60L HIS* 3.6 12.6 - - + +
61L GLU 3.3 0.2 - - - -
62L GLU* 1.3 76.8 - - - +
64L GLU* 1.3 62.1 + - - +
66L ALA* 3.2 5.0 + - - +
67L GLU* 2.9 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K HIS* 3.9 14.2 + - - -
60L HIS 3.2 15.3 + - - +
61L GLU* 3.1 9.9 + - - +
63L ARG* 1.3 77.1 - - - +
65L HIS* 1.3 68.5 + - + +
67L GLU* 2.8 33.1 + - - +
68L LYS* 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L GLU* 3.3 16.8 - - - +
61L GLU* 3.0 35.3 + - + -
62L GLU* 3.2 20.6 + - - +
64L GLU* 1.3 79.9 - - + +
66L ALA* 1.3 60.8 + - - +
68L LYS* 4.7 4.5 - - + -
69L LEU* 3.3 11.3 + - - +
136L HIS 5.4 3.8 + - - -
137L TYR* 2.7 43.2 + + + -
140L GLU* 4.9 21.1 + - + +
141L GLN* 4.8 7.2 - - - -
201L FE 2.3 27.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ILE* 4.1 9.3 - - + +
27L GLU* 3.9 19.0 - - + +
28L LEU* 3.6 36.6 - - + +
62L GLU 3.0 9.6 + - - +
63L ARG* 3.2 8.3 + - - +
65L HIS* 1.3 72.5 - - - +
67L GLU* 1.3 65.2 + - + +
69L LEU* 3.2 7.7 + - - +
70L MET* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K LEU* 4.0 13.0 - - + +
39K TYR* 3.4 25.3 + - - +
56K LEU* 3.6 15.8 - - - +
60K HIS* 2.8 31.4 + - - -
63L ARG* 2.9 42.0 + - - +
64L GLU* 2.8 32.3 + - - +
66L ALA* 1.3 74.8 - - + +
68L LYS* 1.3 58.0 + - - +
70L MET* 3.3 6.0 + - - +
71L LYS* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L GLU 3.0 15.4 + - - +
65L HIS* 4.7 4.4 - - + -
66L ALA 3.2 0.2 - - - -
67L GLU* 1.3 78.7 - - - +
69L LEU* 1.3 55.0 + - - +
71L LYS* 3.4 13.5 + - + +
72L LEU* 2.9 26.3 + - - +
132L PHE* 3.8 12.9 - - + -
136L HIS* 3.4 48.9 + - + +
137L TYR* 3.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L ILE* 3.8 31.7 - - + +
23L GLN* 3.6 36.1 - - + -
24L ILE* 3.6 14.8 - - + +
27L GLU* 3.7 16.4 - - + -
65L HIS 3.3 11.8 + - - +
66L ALA* 3.2 8.1 + - - +
68L LYS* 1.3 74.5 - - - +
70L MET* 1.3 59.4 + - - +
72L LEU* 3.5 4.4 - - + +
73L GLN* 2.9 29.3 + - - +
114L LEU* 6.0 0.9 - - + -
117L LEU* 5.2 2.2 - - + -
132L PHE* 3.6 23.3 - - + -
137L TYR* 3.4 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K LEU* 3.8 41.7 - - + +
36K SER* 5.0 0.9 - - - -
39K TYR* 3.4 42.2 - - + -
24L ILE* 3.7 31.4 - - + -
66L ALA* 3.0 20.1 + - - +
67L GLU* 3.3 7.6 + - - +
69L LEU* 1.3 71.3 - - - +
71L LYS* 1.3 67.6 + - - +
73L GLN* 3.4 1.5 + - - -
74L ASN* 3.2 19.6 + - - +
80L ILE* 3.7 33.8 - - + +
82L LEU* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K TYR* 3.6 14.5 - - + +
42K ASP* 4.2 16.1 + - - +
67L GLU 3.0 14.2 + - - +
68L LYS* 3.5 15.9 - - + +
70L MET* 1.3 78.1 - - - +
72L LEU* 1.3 56.2 + - - +
74L ASN* 3.2 3.8 + - - +
75L GLN* 2.8 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L TYR* 3.9 18.2 - - - +
20L ILE* 4.3 11.7 - - + -
68L LYS 2.9 15.1 + - - +
69L LEU* 3.3 7.2 + - - +
71L LYS* 1.3 72.8 - - - +
73L GLN* 1.3 71.0 + - - +
75L GLN* 3.1 17.3 + - + +
76L ARG* 3.0 30.5 + - + +
128L HIS* 3.7 30.1 - - + +
129L LEU* 4.0 19.7 - - + -
132L PHE* 3.7 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L TYR* 2.7 38.2 + - - -
17L GLU* 3.0 27.4 + - - +
20L ILE* 3.7 13.3 - - + +
21L ASN* 3.1 24.7 + - - +
24L ILE* 4.8 1.1 - - + -
69L LEU 2.9 17.2 + - - +
70L MET* 3.7 5.4 - - - +
71L LYS 3.3 0.2 - - - -
72L LEU* 1.3 81.3 - - - +
74L ASN* 1.3 59.8 + - - +
76L ARG* 3.4 1.2 + - - +
77L GLY 3.2 3.3 + - - -
78L GLY* 2.9 47.9 + - - +
79L ARG 3.9 3.1 - - - +
80L ILE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 74 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J LYS* 3.4 14.5 - - - +
39K TYR* 2.9 28.8 + - - +
42K ASP* 3.0 39.9 + - - +
43K ARG* 3.6 23.1 - - - +
44K ASP* 4.7 2.9 + - - +
8L VAL* 4.2 1.7 - - - +
70L MET 3.2 8.8 + - - +
71L LYS 3.2 2.9 + - - +
73L GLN* 1.3 72.9 - - - +
75L GLN* 1.3 66.7 + - - +
77L GLY* 3.2 12.1 + - - -
78L GLY 3.8 11.8 - - - +
79L ARG* 3.8 2.9 + - - +
80L ILE* 3.8 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J ASN* 4.5 9.0 + - - +
142J VAL* 3.8 27.3 - - + +
143J LYS* 4.0 26.7 - - - +
145J ILE* 5.7 0.5 - - - +
146J LYS* 4.1 28.0 - - + +
42K ASP* 6.1 0.2 - - - +
8L VAL* 3.6 13.7 - - - +
71L LYS* 2.8 46.1 + - + +
72L LEU* 3.1 30.6 + - + +
74L ASN* 1.3 72.8 - - - +
76L ARG* 1.3 62.4 + - + +
77L GLY 3.3 0.6 + - - -
128L HIS* 5.4 0.2 - - - -
132L PHE* 5.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J VAL* 3.9 18.7 - - - +
8L VAL* 3.9 4.4 - - - +
9L ARG* 3.5 25.7 - - - +
10L GLN 3.0 28.0 + - - +
11L ASN* 3.1 23.4 + - - +
12L TYR* 3.6 39.2 - - + +
72L LEU* 3.0 29.9 + - + +
73L GLN 4.2 0.2 - - - +
74L ASN 3.2 0.2 - - - -
75L GLN* 1.3 76.5 - - - +
77L GLY* 1.3 61.0 + - - +
78L GLY 3.3 0.8 + - - -
126L ASP* 2.9 31.0 + - - -
128L HIS* 3.1 38.6 + - - +
129L LEU* 3.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K ASP* 4.5 0.2 - - - -
6L SER* 3.5 25.3 + - - -
8L VAL* 3.5 19.2 - - - +
9L ARG* 3.9 14.1 + - - -
74L ASN 3.2 12.7 + - - -
75L GLN 3.3 1.0 - - - -
76L ARG* 1.3 78.5 - - - +
78L GLY* 1.3 63.8 + - - +
79L ARG* 4.0 11.0 + - - +
----------------------------------------------------------
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