Contacts of the helix formed by residues 49 - 72 (chain d) in PDB entry 5GJQ
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 GLU 49 (chain d).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2d GLU* 5.4 0.3 - - - +
48d GLY* 1.3 77.2 - - - +
50d ALA* 1.3 71.1 + - + +
51d GLY 3.6 0.8 + - - +
52d ASP* 3.5 25.2 - - + +
53d THR* 3.1 18.0 + - - +
99d HIS* 3.0 38.1 + - + +
91e LYS* 3.5 30.6 + - - +
117e GLU* 5.6 2.3 - - - +
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Residues in contact with ALA 50 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48d GLY 3.8 0.4 + - - -
49d GLU* 1.3 83.9 + - + +
51d GLY* 1.3 59.7 + - - +
53d THR* 3.4 13.0 + - - -
54d VAL* 4.6 5.2 + - - +
117e GLU* 3.5 22.2 - - + -
118e GLY 4.5 0.7 - - - -
119e ASN* 2.8 47.5 + - - +
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Residues in contact with GLY 51 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49d GLU* 4.1 2.8 - - - +
50d ALA* 1.3 80.1 - - - +
52d ASP* 1.3 69.4 + - - +
53d THR 3.3 0.7 - - - -
54d VAL* 3.6 4.1 + - - +
55d GLN* 3.2 28.3 + - - +
88e TYR* 4.2 7.0 - - - -
91e LYS* 4.6 0.2 - - - -
117e GLU 3.6 18.0 + - - -
118e GLY* 3.6 16.9 - - - +
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Residues in contact with ASP 52 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49d GLU* 3.5 21.6 + - + +
50d ALA 3.5 0.2 - - - -
51d GLY* 1.3 77.4 - - - +
53d THR* 1.3 59.0 + - - +
55d GLN* 4.6 0.4 - - - -
56d PHE* 2.8 33.8 + - - +
97d PRO 3.8 6.0 - - - +
98d TYR* 3.7 19.9 - - + -
99d HIS* 3.1 34.0 + - - +
100d VAL* 3.6 4.5 - - + -
88e TYR* 3.1 28.0 + - - -
91e LYS* 3.4 15.9 - - - +
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Residues in contact with THR 53 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2d GLU* 5.0 3.1 - - - +
36d PHE* 5.6 1.8 - - - -
46d CYS* 3.7 16.6 - - - +
47d VAL* 3.3 14.6 - - - +
48d GLY* 3.3 28.5 - - - +
49d GLU 3.1 17.4 + - - +
50d ALA 3.4 14.2 + - - -
52d ASP* 1.3 77.3 - - - +
54d VAL* 1.3 72.5 + - - +
57d ALA* 2.9 32.5 + - - +
100d VAL* 3.5 12.1 - - + -
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Residues in contact with VAL 54 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32d HIS* 5.8 7.4 - - + +
36d PHE* 4.3 15.9 - - + -
50d ALA 5.0 4.5 - - - +
51d GLY* 3.6 5.7 + - - +
52d ASP 3.4 0.2 - - - -
53d THR* 1.3 88.0 + - - +
55d GLN* 1.3 68.7 + - - +
57d ALA* 4.4 4.3 - - - -
58d GLU* 2.8 63.3 + - + +
81e LYS* 4.7 7.9 - - - -
118e GLY 5.7 3.6 - - - +
120e ARG* 5.8 12.1 - - + +
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Residues in contact with GLN 55 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51d GLY 3.2 19.5 + - - +
52d ASP 4.0 1.8 - - - +
54d VAL* 1.3 86.3 - - - +
56d PHE* 1.3 57.3 + - - +
58d GLU* 4.0 2.7 + - - +
59d TYR* 3.0 31.8 + - - +
98d TYR* 4.3 8.3 - - + +
81e LYS* 5.1 3.8 - - - +
84e ALA* 4.7 6.9 + - - +
85e ASN* 3.0 30.3 + - - +
88e TYR* 3.6 53.1 - - + +
118e GLY* 5.2 5.7 + - - -
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Residues in contact with PHE 56 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44d LEU* 5.3 1.8 - - + -
46d CYS* 4.6 6.5 - - - -
52d ASP 2.8 23.0 + - - +
53d THR 4.0 1.6 - - - +
55d GLN* 1.3 71.5 - - - +
57d ALA* 1.3 69.6 + - - +
59d TYR* 3.3 8.0 + + - +
60d ILE* 2.9 51.1 + - + +
84d THR* 3.4 24.0 - - - -
87d ASN* 4.5 4.3 - - + -
88d LEU* 3.7 37.0 - - + -
98d TYR* 4.0 25.0 - + + -
100d VAL* 3.9 23.6 - - + -
102d LEU* 4.0 26.7 - - + -
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Residues in contact with ALA 57 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36d PHE* 3.9 41.6 - - + +
38d MET* 4.6 0.5 - - - +
44d LEU* 4.2 19.4 - - + +
46d CYS* 4.5 8.3 - - + -
53d THR 2.9 23.2 + - - +
54d VAL 3.9 2.9 - - - +
56d PHE* 1.3 75.1 - - - +
58d GLU* 1.3 51.9 + - - +
60d ILE* 3.3 2.1 + - - +
61d GLN* 2.8 34.4 + - - +
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Residues in contact with GLU 58 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 3.9 15.5 - - + +
99E GLU* 3.9 20.7 - - - +
36d PHE* 4.4 19.0 - - + -
54d VAL* 2.8 41.5 + - + +
55d GLN* 4.1 3.0 + - - +
57d ALA* 1.3 68.6 - - - +
59d TYR* 1.3 67.4 + - - +
61d GLN* 3.5 13.2 - - - +
62d LYS* 2.9 33.5 + - + +
81e LYS* 2.3 38.2 + - - +
120e ARG* 5.0 1.7 + - - -
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Residues in contact with TYR 59 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 4.4 12.6 - - + +
55d GLN 3.0 18.8 + - - +
56d PHE* 3.5 9.4 - + - +
58d GLU* 1.3 77.4 - - - +
60d ILE* 1.3 75.7 + - + +
62d LYS* 3.3 2.5 + - - +
63d ASN* 3.1 52.8 + - - -
83d PHE* 5.0 1.4 - + - -
87d ASN* 3.8 39.0 + - + -
98d TYR* 5.6 8.3 - + - +
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Residues in contact with ILE 60 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38d MET* 3.6 28.7 - - + -
44d LEU* 4.3 6.3 - - + -
56d PHE* 2.9 47.7 + - + +
57d ALA 3.6 6.5 - - - +
59d TYR* 1.3 87.4 - - + +
61d GLN* 1.3 64.2 + - - +
63d ASN* 3.2 4.7 + - - +
64d VAL* 3.0 32.6 + - + +
83d PHE* 4.1 7.0 - - + -
84d THR* 3.8 37.9 - - + -
87d ASN* 3.9 13.0 - - - +
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Residues in contact with GLN 61 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36d PHE* 5.1 13.6 - - + -
37d LYS* 2.8 32.6 + - - +
38d MET* 3.8 17.4 - - + +
57d ALA 2.8 20.4 + - - +
58d GLU* 3.5 14.1 - - + +
59d TYR 3.3 0.2 - - - -
60d ILE* 1.3 72.4 - - - +
62d LYS* 1.3 95.2 + - - +
64d VAL* 3.2 4.4 + - - +
65d GLN* 2.9 32.1 + - + +
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Residues in contact with LYS 62 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLN* 3.6 26.3 + - + +
95E ARG* 3.5 27.6 - - - +
96E LEU* 3.1 60.8 - - + +
58d GLU* 2.9 29.2 + - - +
59d TYR* 3.9 3.8 - - - +
61d GLN* 1.3 104.0 + - - +
63d ASN* 1.3 60.9 + - - +
65d GLN* 3.5 9.4 + - - +
66d LEU* 2.9 28.8 + - - +
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Residues in contact with ASN 63 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 5.4 1.8 + - - -
59d TYR* 3.1 57.0 + - - +
60d ILE 3.8 0.4 - - - +
61d GLN 3.2 0.2 - - - -
62d LYS* 1.3 77.5 - - - +
64d VAL* 1.3 59.8 + - - +
66d LEU* 3.3 14.9 + - - +
67d TYR* 3.0 27.4 + - - +
75d LEU* 5.3 1.0 - - - +
83d PHE* 3.7 33.5 - - + -
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Residues in contact with VAL 64 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38d MET* 3.3 48.0 - - + +
39d SER* 3.4 16.2 - - - +
42d ILE* 5.4 1.3 - - + -
60d ILE* 3.0 20.2 + - + +
61d GLN* 3.5 6.7 - - - +
63d ASN* 1.3 74.1 - - - +
65d GLN* 1.3 66.6 + - - +
67d TYR* 3.1 6.6 + - - +
68d LYS* 3.0 21.0 + - + +
74d GLU* 5.9 0.4 - - + -
75d LEU* 3.9 36.1 + - + +
80d ALA* 5.1 3.8 - - + -
83d PHE* 5.1 5.2 - - + -
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Residues in contact with GLN 65 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ASP* 5.2 4.2 - - - +
92E GLN* 3.4 25.3 + - - +
95E ARG* 6.1 1.7 - - - -
37d LYS 5.5 0.8 + - - -
38d MET* 3.2 26.1 + - - +
39d SER* 4.6 5.1 - - - +
61d GLN* 2.9 30.9 + - + +
62d LYS* 3.8 11.4 - - - +
64d VAL* 1.3 77.0 - - - +
66d LEU* 1.3 56.8 + - - +
68d LYS* 3.2 32.3 + - - +
69d MET* 2.9 35.5 + - - +
74d GLU* 5.3 0.2 + - - -
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Residues in contact with LEU 66 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ARG* 4.1 6.7 - - + -
89E VAL* 3.7 42.0 - - + +
92E GLN* 3.9 21.3 - - + +
62d LYS 2.9 19.1 + - - +
63d ASN* 3.4 17.3 - - - +
64d VAL 3.1 0.2 - - - -
65d GLN* 1.3 76.6 - - - +
67d TYR* 1.3 65.2 + - - +
69d MET* 3.3 2.5 + - + +
70d ARG* 2.9 55.7 + - + +
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Residues in contact with TYR 67 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TYR* 2.4 39.6 + + - -
101D TYR* 4.2 17.0 - + - +
103D GLU* 5.1 2.9 + - - -
106D PRO* 4.2 1.9 - - - +
109D GLN* 3.0 13.6 + - - -
142D HIS* 5.2 1.2 + - - -
63d ASN 3.0 12.6 + - - +
64d VAL 3.1 8.2 + - - +
66d LEU* 1.3 76.6 - - - +
68d LYS* 1.3 57.7 + - - +
70d ARG* 3.3 6.4 + - - +
71d ASN* 2.9 53.2 + - - +
73d TYR* 3.9 28.4 - + - -
74d GLU 4.3 7.4 - - - -
75d LEU* 3.6 39.8 - - + +
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Residues in contact with LYS 68 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ASP* 4.0 28.0 + - - -
40d GLU* 5.2 9.3 + - - +
64d VAL* 3.0 12.7 + - + +
65d GLN* 3.3 33.1 + - - +
67d TYR* 1.3 76.9 - - - +
69d MET* 1.3 66.7 + - - +
72d GLY* 3.0 32.2 + - - +
73d TYR 3.7 13.5 - - - +
74d GLU* 4.0 41.2 + - + +
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Residues in contact with MET 69 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ALA* 3.9 18.6 - - + +
65E LEU 3.4 32.5 - - - +
66E ASP* 3.5 14.4 - - - +
67E ASP* 3.8 19.7 - - - +
88E ARG* 3.2 34.3 + - + -
92E GLN* 3.0 31.9 - - - +
65d GLN* 2.9 18.3 + - - +
66d LEU* 3.3 4.5 + - - +
68d LYS* 1.3 91.0 - - - +
70d ARG* 1.3 60.9 + - - +
72d GLY 4.7 0.7 + - - -
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Residues in contact with ARG 70 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ASP* 5.0 5.5 + - - -
85E ASN* 4.0 42.8 - - - +
88E ARG* 4.0 18.7 + - + +
89E VAL* 4.3 17.8 - - - +
66d LEU* 2.9 47.3 + - + +
67d TYR* 4.0 5.6 - - - +
69d MET* 1.3 79.5 - - - +
71d ASN* 1.3 70.3 + - - +
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Residues in contact with ASN 71 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLU* 5.3 3.1 - - - +
109D GLN* 3.1 41.7 + - - +
112D THR* 5.7 0.3 + - - -
143D TYR* 4.5 2.8 + - - -
67d TYR* 2.9 41.3 + - - +
70d ARG* 1.3 90.8 - - - +
72d GLY* 1.3 58.6 + - - +
73d TYR* 3.2 42.2 + - + +
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Residues in contact with GLY 72 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TYR* 5.6 1.1 - - - -
68d LYS* 3.0 20.9 + - - +
69d MET 4.7 1.0 - - - -
70d ARG 3.8 0.6 - - - -
71d ASN* 1.3 75.6 - - - +
73d TYR* 1.3 59.2 + - - +
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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
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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) + - + + + + + -
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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