Contacts of the helix formed by residues 50 - 77 (chain R) in PDB entry 6Y5D
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 50 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121Q MET* 6.1 4.3 - - + -
122Q PRO* 3.6 25.3 - - + +
48R SER* 3.1 9.0 + - - +
49R GLY* 1.3 81.4 - - - +
51R ILE* 1.3 63.8 + - - +
52R TYR 3.3 2.0 - - - -
53R GLU* 3.6 12.9 + - + +
54R GLU* 3.3 20.1 + - - +
84U C 5.6 1.3 - - - +
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Residues in contact with ILE 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Q PHE* 3.9 17.5 - - + -
120Q ILE* 3.4 25.8 - - + +
121Q MET 3.4 34.3 - - - +
122Q PRO 3.5 3.8 - - - -
125Q ILE* 3.7 15.0 - - + -
35R ILE* 4.3 5.4 - - + -
47R ILE* 3.6 18.6 - - + -
48R SER* 3.0 23.1 + - - +
50R LEU* 1.3 78.6 - - - +
52R TYR* 1.3 55.7 + - - +
54R GLU* 3.6 2.8 - - - +
55R THR* 2.7 55.9 + - - +
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Residues in contact with TYR 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R LYS* 3.5 47.2 - - + -
35R ILE* 3.4 32.6 - - + +
36R ARG* 3.6 25.0 - - + +
47R ILE* 3.6 30.5 + - + +
48R SER 3.7 0.7 - - - -
49R GLY* 3.3 37.2 - - - -
50R LEU 3.3 0.8 - - - -
51R ILE* 1.3 74.8 - - - +
53R GLU* 1.3 61.6 + - - +
56R ARG* 3.0 54.5 + - - +
84U C 5.3 0.3 - - - -
85U C 3.6 16.1 + - - -
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Residues in contact with GLU 53 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R GLN* 6.1 2.7 - - - +
49R GLY 3.5 21.2 - - - +
50R LEU* 3.8 12.8 - - + +
51R ILE 3.2 0.2 - - - -
52R TYR* 1.3 76.0 - - - +
54R GLU* 1.3 66.1 + - - +
56R ARG* 3.3 27.6 + - - +
57R GLY* 3.1 19.1 + - - -
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Residues in contact with GLU 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Q PRO* 4.0 18.8 - - + +
125Q ILE* 3.9 28.8 - - + +
126Q GLN* 3.3 32.8 + - - +
129Q ARG* 5.7 2.3 - - - -
50R LEU 3.3 12.6 + - - +
51R ILE* 3.1 8.4 + - - +
53R GLU* 1.3 77.7 - - - +
55R THR* 1.3 63.6 + - - +
57R GLY* 3.3 10.7 + - - -
58R VAL* 3.3 22.3 + - + +
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Residues in contact with THR 55 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q LEU* 4.1 24.2 - - + +
104Q LEU* 6.4 1.1 - - - -
105Q PHE* 3.5 20.2 - - + -
125Q ILE* 4.4 5.4 - - - +
30R ILE* 6.3 0.2 - - + -
35R ILE* 3.7 26.9 - - + +
51R ILE* 2.7 43.2 + - - +
52R TYR 3.5 5.2 - - - -
54R GLU* 1.3 71.1 - - - +
56R ARG* 1.3 65.9 + - - +
58R VAL* 3.0 8.7 + - - +
59R LEU* 3.0 21.7 + - + +
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Residues in contact with ARG 56 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ILE* 3.6 43.4 + - + +
28R GLN* 4.4 28.5 + - - +
30R ILE* 2.7 33.5 + - + +
31R THR* 3.7 1.8 - - - +
32R LYS* 3.7 22.4 - - - +
35R ILE* 4.0 14.7 - - + +
52R TYR* 3.0 33.2 + - - +
53R GLU* 3.3 33.8 + - - +
55R THR* 1.3 75.6 - - - +
57R GLY* 1.3 62.6 + - - +
58R VAL 3.0 1.2 + - - -
59R LEU* 3.3 4.9 + - - +
60R LYS* 3.2 22.7 + - - +
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Residues in contact with GLY 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R GLU 3.1 13.7 + - - -
54R GLU* 3.3 4.7 + - - -
55R THR 3.2 0.6 - - - -
56R ARG* 1.3 75.7 - - - +
58R VAL* 1.3 59.4 + - - +
60R LYS* 4.5 3.1 - - - +
61R VAL* 3.2 25.9 - - - +
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Residues in contact with VAL 58 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100Q TYR* 3.6 32.8 - - + +
101Q LEU* 4.2 4.7 - - + -
104Q LEU* 3.9 21.3 - - + -
125Q ILE* 4.8 11.2 - - + -
129Q ARG* 5.6 8.3 - - - +
134Q GLU* 5.7 1.3 - - - +
54R GLU* 3.3 21.3 - - + +
55R THR* 3.0 8.8 + - - +
57R GLY* 1.3 80.8 - - - +
59R LEU* 1.3 66.9 + - - +
60R LYS 3.2 1.6 - - - -
61R VAL* 3.2 5.5 + - + +
62R PHE* 2.9 21.3 + - - +
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Residues in contact with LEU 59 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ILE* 4.2 18.6 - - + -
68Q PHE* 4.6 4.0 - - + -
71Q LEU* 4.0 18.8 - - + -
97Q SER* 3.7 29.8 - - - -
101Q LEU* 4.0 27.1 - - + +
27R ILE* 4.5 2.2 - - + -
30R ILE* 4.0 25.6 - - + -
55R THR* 3.0 15.4 + - + +
56R ARG* 3.9 6.3 - - - +
58R VAL* 1.3 76.8 - - - +
60R LYS* 1.3 65.0 + - - +
62R PHE* 3.2 6.1 + - + +
63R LEU* 3.0 37.1 + - + +
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Residues in contact with LYS 60 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Q LEU* 4.3 15.0 - - + -
74Q GLU* 4.7 16.7 + - - +
75Q ILE* 3.7 27.5 - - + +
78Q ASP* 4.6 12.3 + - - -
27R ILE* 4.0 21.0 - - + +
56R ARG 3.2 14.4 + - - +
57R GLY* 5.0 3.1 - - - +
59R LEU* 1.3 79.6 - - - +
61R VAL* 1.3 54.0 + - + +
63R LEU* 3.2 5.9 + - - +
64R GLU* 2.7 65.6 + - - +
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Residues in contact with VAL 61 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129Q ARG* 6.2 2.2 - - - +
57R GLY 3.2 19.7 - - - +
58R VAL* 3.2 9.5 + - + +
60R LYS* 1.3 75.0 - - + +
62R PHE* 1.3 67.6 + - - +
64R GLU* 3.6 18.2 - - - +
65R ASN* 3.0 38.1 + - - +
----------------------------------------------------------
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Residues in contact with PHE 62 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q LEU* 4.7 1.1 - - + -
96Q ALA* 3.7 18.4 - - + -
97Q SER* 3.4 42.8 - - - -
100Q TYR* 3.5 50.3 - + + -
58R VAL 2.9 13.5 + - - +
59R LEU* 3.2 9.8 + - + +
61R VAL* 1.3 78.4 - - - +
63R LEU* 1.3 65.8 + - + +
65R ASN* 3.2 6.0 + - - +
66R VAL* 3.1 45.0 + - + +
91R LEU* 4.0 11.7 - - + -
94R GLN* 4.9 4.9 - - - -
96R ARG* 3.9 18.4 - - - -
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Residues in contact with LEU 63 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q PHE* 3.6 28.5 - - + -
71Q LEU* 3.4 38.8 - - + -
72Q VAL* 4.5 3.6 - - + -
75Q ILE* 3.3 16.2 - - + -
93Q LEU* 4.1 15.3 - - + -
97Q SER* 3.1 27.4 - - - +
59R LEU* 3.0 21.5 + - + +
60R LYS 3.4 2.0 - - - +
62R PHE* 1.3 76.9 - - + +
64R GLU* 1.3 59.6 + - - +
66R VAL* 4.5 2.2 - - - +
67R ILE* 2.7 45.9 + - + +
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Residues in contact with GLU 64 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Q ILE* 3.7 27.4 - - + -
78Q ASP* 5.4 1.0 - - - +
79Q PHE* 3.9 7.1 - - + -
60R LYS* 2.7 56.5 + - - +
61R VAL* 3.2 20.3 + - - +
63R LEU* 1.3 70.9 - - - +
65R ASN* 1.3 59.0 + - - +
68R ARG* 2.9 42.3 + - - +
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Residues in contact with ASN 65 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R VAL* 3.0 32.5 + - - +
62R PHE* 3.7 7.9 - - - +
63R LEU 3.2 0.2 - - - -
64R GLU* 1.3 78.8 - - - +
66R VAL* 1.3 61.4 + - - +
68R ARG* 2.9 34.5 + - - +
69R ASP* 3.3 20.4 + - - +
94R GLN* 3.4 24.0 + - - +
96S LYS* 6.1 0.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q LEU* 3.4 27.6 - - + -
62R PHE* 3.1 30.0 + - + +
63R LEU* 4.0 3.1 - - - +
65R ASN* 1.3 74.1 - - - +
67R ILE* 1.3 65.6 + - - +
69R ASP 3.3 1.0 + - - -
70R ALA* 3.0 19.1 + - - +
87R VAL* 4.2 2.5 - - + +
90R ALA* 3.1 21.2 - - + +
91R LEU* 3.6 39.7 - - + -
94R GLN* 3.6 25.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q VAL* 3.8 32.3 - - + +
75Q ILE* 3.7 20.9 - - + -
76Q ALA* 4.3 11.4 - - + -
79Q PHE* 3.9 12.6 - - + -
85Q PHE* 4.5 8.5 - - + -
93Q LEU* 3.8 23.1 - - + -
63R LEU* 2.7 43.2 + - + +
64R GLU 4.1 1.3 - - - +
66R VAL* 1.3 69.4 - - - +
68R ARG* 1.3 61.1 + - - +
70R ALA* 2.9 7.9 + - - +
71R VAL* 2.7 43.9 + - + +
----------------------------------------------------------
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Residues in contact with ARG 68 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q PHE* 3.6 40.2 - - + -
64R GLU* 2.9 36.5 + - - +
65R ASN* 2.9 40.6 + - - +
67R ILE* 1.3 78.3 - - - +
69R ASP* 1.3 61.2 + - - +
71R VAL* 3.2 3.1 + - + +
72R THR* 2.7 43.0 + - - +
100T ARG 5.9 1.0 + - - -
104T PRO* 6.1 2.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 69 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R ASN 3.3 10.0 + - - +
66R VAL 3.3 2.2 + - - +
67R ILE 3.2 0.6 - - - -
68R ARG* 1.3 89.6 + - - +
70R ALA* 1.3 58.8 + - - +
72R THR* 3.0 9.6 + - - -
73R TYR* 2.8 40.5 + - + -
90R ALA* 3.5 20.3 - - + +
93R ARG* 3.1 36.1 + - - -
94R GLN* 3.1 20.8 + - - +
100T ARG 5.2 1.6 - - - +
101T LEU* 4.2 9.4 - - + +
----------------------------------------------------------
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Residues in contact with ALA 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R VAL 3.0 12.9 + - - +
67R ILE* 2.9 12.7 + - + +
69R ASP* 1.3 75.7 - - - +
71R VAL* 1.3 53.6 + - - +
73R TYR* 3.4 1.3 + - - -
74R THR* 2.6 37.1 + - - -
82R VAL* 3.8 18.2 - - + -
86R ASP* 3.6 35.5 - - - +
87R VAL* 3.9 11.4 - - + +
90R ALA* 3.6 0.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q PHE* 4.1 26.7 - - + -
80Q LYS* 5.2 6.1 - - + -
83Q LEU* 3.8 35.2 - - + -
67R ILE* 2.7 38.8 + - + +
68R ARG* 3.5 7.2 - - + +
70R ALA* 1.3 70.5 - - + +
72R THR* 1.3 57.3 + - - +
74R THR* 3.1 7.2 + - - -
75R GLU* 2.7 40.7 + - + +
82R VAL* 4.2 5.6 - - + -
----------------------------------------------------------
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Residues in contact with THR 72 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R ARG* 2.7 29.1 + - - +
69R ASP* 3.0 10.6 + - - -
71R VAL* 1.3 76.8 - - - +
73R TYR* 1.3 56.4 + - - +
75R GLU* 3.4 6.4 + - - +
76R HIS* 2.9 28.4 + - - +
97T THR* 4.0 9.5 - - + +
100T ARG* 4.0 32.0 + - + +
101T LEU* 3.7 30.1 - - + +
----------------------------------------------------------
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Residues in contact with TYR 73 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ASP 2.8 26.8 + - - -
70R ALA 3.6 5.6 - - - +
72R THR* 1.3 76.5 - - - +
74R THR* 1.3 63.8 + - - +
76R HIS* 3.3 7.0 + - - +
77R ALA* 3.1 24.8 + - - +
79R ARG* 4.6 0.2 + - - -
86R ASP* 3.8 23.1 - - + +
89R TYR* 3.5 39.5 + + + +
90R ALA* 3.8 13.2 - - - -
93R ARG* 3.3 25.9 + - - +
77T GLU* 4.1 8.5 + - - -
80T ARG* 5.0 9.7 + - - -
81T LEU* 4.1 20.2 - - + -
84T TYR* 4.6 17.2 - + + -
101T LEU* 3.5 35.8 - - + +
----------------------------------------------------------
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Residues in contact with THR 74 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q LEU* 4.9 4.0 - - + -
70R ALA 2.6 18.9 + - - -
71R VAL* 3.3 13.0 - - + -
73R TYR* 1.3 78.2 - - - +
75R GLU* 1.3 58.9 + - - +
77R ALA* 3.3 2.3 + - - +
78R LYS 3.3 3.6 + - - -
79R ARG* 2.9 61.1 + - + +
80R LYS 4.0 4.0 - - - +
81R THR 3.5 26.2 - - - +
82R VAL* 3.5 15.6 - - + +
86R ASP* 3.3 15.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 75 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q LYS* 5.4 10.6 - - - +
71R VAL* 2.7 25.7 + - + +
72R THR* 3.7 7.9 - - - +
74R THR* 1.3 72.0 - - - +
76R HIS* 1.3 65.5 + - - +
78R LYS* 2.9 14.5 + - - +
79R ARG 4.3 8.5 - - - +
93T ARG* 2.8 18.4 + - - +
100T ARG* 4.5 18.6 - - - +
----------------------------------------------------------
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Residues in contact with HIS 76 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R THR 2.9 17.2 + - - +
73R TYR* 3.3 7.2 + - - +
75R GLU* 1.3 74.9 - - - +
77R ALA* 1.3 57.5 + - - +
78R LYS* 3.1 6.4 + - - +
81T LEU* 3.9 19.7 + - + +
84T TYR* 5.7 0.4 - + - -
85T ASN* 3.3 31.2 + - - +
87T ARG* 5.7 2.2 + - - -
93T ARG* 3.0 58.0 + - + +
94T GLU* 3.8 27.0 + - + +
97T THR* 2.6 39.7 + - + +
100T ARG* 5.5 1.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R TYR 3.1 13.3 + - - +
74R THR 3.7 3.6 - - - +
75R GLU 3.2 0.2 - - - -
76R HIS* 1.3 77.6 - - - +
78R LYS* 1.3 70.8 - - - +
79R ARG* 3.4 36.9 + - - +
84T TYR* 5.0 1.3 - - + -
85T ASN* 3.3 29.8 - - - +
----------------------------------------------------------
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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