Contacts of the helix formed by residues 76 - 105 (chain P) in PDB entry 3L73
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 TYR 76 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P VAL 2.9 2.8 + - - -
75P GLN* 1.3 79.9 - - + +
77P GLY* 1.3 65.2 + - - +
78P TRP* 3.1 22.5 - + - +
79P LEU* 3.0 16.5 + - + +
80P ILE* 3.0 29.9 + - + +
200Q GLN* 3.8 20.6 + - - -
204Q MET* 4.6 5.8 - - - -
3009Q BOG 3.6 26.8 + - - -
3091Q BOG 3.6 26.3 + - - -
56R THR* 5.9 2.7 - - + +
57R GLN* 3.8 50.2 - - + +
58R PHE* 5.7 0.2 - - + -
60R SER* 3.8 19.7 - - - -
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Residues in contact with GLY 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 4.5 1.9 - - - +
70P THR* 3.2 28.9 - - - -
71P CYS* 4.2 2.0 - - - -
74P VAL* 2.7 26.9 + - - -
75P GLN 3.1 2.4 + - - -
76P TYR* 1.3 71.7 - - - +
78P TRP* 1.3 51.7 + - - +
80P ILE* 3.2 8.8 + - - +
81P ARG* 2.7 37.1 + - - +
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Residues in contact with TRP 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P CYS* 3.6 38.1 + - + +
74P VAL 5.1 0.7 - - - -
76P TYR* 4.1 20.7 - + - +
77P GLY* 1.3 76.8 - - - +
79P LEU* 1.3 91.7 + - + +
81P ARG* 3.6 2.8 - - - +
82P ASN* 3.0 50.0 + - - +
245P LEU* 4.4 5.8 - - + -
197Q GLU* 3.8 40.4 - - + +
200Q GLN* 3.3 31.4 + - + -
201Q ARG* 3.4 39.7 - - + -
204Q MET* 4.0 24.2 - - - -
3091Q BOG 4.4 5.6 + - - -
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Residues in contact with LEU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P TYR* 3.0 18.7 + - + +
78P TRP* 1.3 100.3 - - + +
80P ILE* 1.3 56.3 + - - +
82P ASN* 3.0 6.0 + - + +
83P LEU* 2.8 60.9 + - + +
245P LEU* 4.3 23.6 - - + -
204Q MET* 3.8 18.6 - - + -
57R GLN* 3.0 33.9 - - - +
58R PHE* 4.9 3.8 - - + -
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Residues in contact with ILE 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P THR* 3.8 25.8 - - + +
51P LEU* 4.0 22.7 - - + +
52P LEU* 3.4 22.4 - - + -
74P VAL* 5.7 0.7 - - + -
75P GLN 4.5 0.2 - - - +
76P TYR* 3.0 20.9 + - + +
77P GLY* 3.6 6.3 - - - +
79P LEU* 1.3 75.4 - - - +
81P ARG* 1.3 63.0 + - - +
83P LEU* 3.5 8.4 + - - +
84P HIS* 3.0 24.6 + - - +
58R PHE* 3.8 26.0 - - + -
61R SER* 3.6 34.8 - - - +
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Residues in contact with ARG 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 3.8 15.7 - - + +
67P VAL* 3.6 25.6 - - + +
70P THR* 5.6 1.8 - - + -
71P CYS* 3.5 32.2 - - - -
77P GLY 2.7 20.8 + - - +
78P TRP 3.6 4.7 - - - +
80P ILE* 1.3 76.1 - - - +
82P ASN* 1.3 69.3 + - - +
84P HIS* 3.8 1.7 - - - +
85P ALA* 3.0 26.8 + - - +
135P PRO* 4.2 0.6 - - - +
257P PHE* 6.2 0.6 - - - -
501P HEM 2.8 51.8 + - - +
3011P GOL 3.7 31.9 + - - -
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Residues in contact with ASN 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P CYS* 6.2 1.0 - - - -
78P TRP* 3.0 36.5 + - - +
79P LEU* 3.0 11.9 + - + +
81P ARG* 1.3 86.6 - - - +
83P LEU* 1.3 64.6 + - - +
85P ALA* 3.7 2.5 - - - -
86P ASN* 2.8 35.8 + - - +
244P ALA* 3.4 26.4 - - + +
248P PRO* 3.9 23.8 + - - +
249P ASN* 5.7 1.6 + - - -
197Q GLU* 5.5 3.0 + - - +
201Q ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P THR* 6.1 3.0 - - + +
45P GLN* 4.1 1.7 - - - +
48P THR* 4.4 11.7 - - + -
79P LEU* 2.8 49.1 + - + +
80P ILE* 3.8 4.7 - - - +
82P ASN* 1.3 73.3 - - - +
84P HIS* 1.3 53.6 + - - +
86P ASN* 5.0 0.2 - - - -
87P GLY* 2.7 34.3 + - - -
240P PHE* 3.6 20.1 - - + -
241P LEU* 3.9 27.8 - - + -
244P ALA* 4.7 8.3 - - + -
245P LEU* 6.3 1.1 - - + -
54R VAL* 6.2 0.2 - - + -
58R PHE* 4.0 26.2 - - + -
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Residues in contact with HIS 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P GLN* 3.0 49.4 + - - -
48P THR* 2.6 27.0 + - - +
49P GLY* 3.4 5.7 + - - -
52P LEU* 3.9 18.4 - - + -
80P ILE 3.0 18.0 + - - +
81P ARG 3.8 3.4 - - - +
83P LEU* 1.3 74.3 - - - +
85P ALA* 1.3 65.2 + - - +
87P GLY 3.3 0.5 + - - -
88P ALA* 3.2 6.4 + - - +
501P HEM 2.0 88.4 + + + +
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Residues in contact with ALA 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P ARG* 3.0 23.3 + - - +
82P ASN* 3.7 3.6 - - - +
84P HIS* 1.3 78.3 - - - +
86P ASN* 1.3 65.1 + - - +
88P ALA* 3.3 20.1 - - - +
89P SER* 4.0 2.9 + - - -
501P HEM 3.9 38.2 + - + +
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Residues in contact with ASN 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82P ASN* 2.8 29.7 + - - +
85P ALA* 1.3 73.2 - - - +
87P GLY* 1.3 67.1 + - - +
88P ALA 3.0 2.0 - - - -
89P SER* 2.9 19.1 + - - -
90P PHE 3.2 8.7 + - - -
240P PHE* 3.6 22.4 - - + -
243P LEU* 3.7 28.7 - - + +
244P ALA* 3.7 21.4 - - + +
247P SER 5.4 0.2 + - - -
248P PRO 3.7 21.4 + - - +
251P LEU* 4.6 13.3 - - - +
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Residues in contact with GLY 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P CYS* 4.0 5.1 - - - -
44P THR* 6.5 0.7 - - - -
45P GLN* 3.7 16.8 - - - -
83P LEU 2.7 24.8 + - - -
84P HIS 3.3 0.2 + - - -
86P ASN* 1.3 73.0 - - - +
88P ALA* 1.3 63.0 + - - +
90P PHE* 3.3 5.6 + - - +
91P PHE* 2.9 23.9 + - - +
240P PHE* 3.5 15.4 - - - -
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Residues in contact with ALA 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P GLN* 3.3 14.5 - - - +
84P HIS 3.2 6.7 + - - +
85P ALA 3.3 14.6 - - - +
86P ASN 3.0 0.2 - - - -
87P GLY* 1.3 75.9 - - - +
89P SER* 1.3 61.1 + - - +
91P PHE* 3.0 21.4 - - - +
92P PHE* 3.1 17.6 + - + -
128P ALA* 5.5 0.2 - - + -
274P TYR* 4.3 18.6 - - + +
501P HEM 4.2 26.2 - - + -
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Residues in contact with SER 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ALA 4.0 1.9 + - - -
86P ASN* 2.9 12.9 + - - -
88P ALA* 1.3 74.2 - - - +
90P PHE* 1.3 68.1 + - - +
91P PHE 3.0 1.3 - - - -
92P PHE* 2.9 3.7 + - - +
93P ILE* 2.7 31.0 + - - +
251P LEU* 3.9 18.3 - - - +
272P GLU* 5.4 1.6 + - - -
273P TRP* 2.7 37.7 + - - -
274P TYR* 3.9 11.2 - - - -
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Residues in contact with PHE 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P LEU* 4.4 16.4 - - + -
41P CYS* 3.5 27.1 - - + -
86P ASN 3.2 8.7 + - - +
87P GLY* 3.5 11.9 - - - +
89P SER* 1.3 75.9 - - - +
91P PHE* 1.3 63.9 + - - +
93P ILE* 3.5 13.0 - - + +
94P CYS* 2.8 47.7 + - - +
233P LEU* 5.4 3.6 - - + -
236P MET* 3.4 55.9 - - + -
237P LEU* 4.2 9.0 - - + -
240P PHE* 3.9 33.0 - + + -
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Residues in contact with PHE 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LEU* 3.9 23.8 - - + -
41P CYS* 3.3 22.1 - - - -
42P LEU* 3.6 40.2 - - + -
45P GLN* 3.9 15.9 - - + -
87P GLY 2.9 11.2 + - - +
88P ALA* 3.0 17.0 - - - +
90P PHE* 1.3 77.8 - - - +
92P PHE* 1.3 56.1 + - + +
94P CYS* 3.2 3.8 + - - +
95P ILE* 2.8 22.9 + - - +
124P LEU* 3.4 38.6 - - + -
190P ILE* 5.0 2.5 - - + -
501P HEM 4.2 10.5 - - + -
502P HEM 3.9 26.9 - - + -
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Residues in contact with PHE 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ALA* 3.1 24.7 + - + -
89P SER 2.9 11.0 + - - +
91P PHE* 1.3 69.5 - - + +
93P ILE* 1.3 65.3 + - - +
95P ILE* 2.9 14.7 - - + +
96P PHE* 2.9 51.9 + + + -
121P LEU* 4.7 4.3 - - + -
124P LEU* 3.7 32.3 - - + -
125P MET* 4.1 20.4 - - + -
128P ALA* 3.9 13.2 - - + -
273P TRP* 4.1 2.2 - - + -
274P TYR* 3.7 50.0 - + + -
275P PHE* 4.0 21.1 - + - -
501P HEM 5.4 1.6 - - + -
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Residues in contact with ILE 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P SER* 2.7 23.8 + - - +
90P PHE* 3.5 16.8 - - + +
92P PHE* 1.3 73.9 - - - +
94P CYS* 1.3 65.8 + - - +
96P PHE* 3.1 11.8 + - - +
97P LEU* 3.1 32.2 + - + +
236P MET* 4.5 18.2 - - + -
251P LEU* 6.3 2.2 - - + -
273P TRP* 3.5 26.4 - - + -
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Residues in contact with CYS 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P PHE* 4.0 16.4 - - + +
37P LEU* 4.0 23.3 - - + -
38P LEU* 3.6 18.6 - - + +
90P PHE* 2.8 52.7 + - - +
91P PHE* 3.4 5.4 - - - +
93P ILE* 1.3 78.7 - - - +
95P ILE* 1.3 57.1 + - - +
97P LEU* 3.3 3.2 + - - +
98P HIS* 2.9 29.1 + - - +
236P MET* 4.6 8.1 - - - -
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Residues in contact with ILE 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LEU* 3.6 17.2 - - + +
91P PHE 2.8 13.0 + - - +
92P PHE* 2.9 37.6 + - + +
94P CYS* 1.3 75.7 - - - +
96P PHE* 1.3 72.2 + - + +
98P HIS* 3.4 3.3 + - + +
99P ILE* 2.9 35.7 + - + +
121P LEU* 3.7 38.4 - - + +
124P LEU* 3.7 19.5 - - + -
502P HEM 4.1 29.8 - - + -
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Residues in contact with PHE 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P PHE* 2.9 47.0 + + + +
93P ILE* 3.7 4.9 - - - +
95P ILE* 1.3 86.5 - - + +
97P LEU* 1.3 62.6 + - + +
99P ILE* 3.3 11.4 + - + +
100P GLY* 2.8 24.9 + - - -
121P LEU* 4.9 8.7 - - + -
273P TRP* 3.6 30.5 - + - -
274P TYR* 3.9 17.7 - - + -
277P PHE* 4.6 4.7 - + - -
3007P PEE 3.5 79.1 - - + +
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Residues in contact with LEU 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P TRP* 4.4 10.9 - - + -
34P PHE* 3.5 44.0 - - + -
93P ILE* 3.1 29.0 + - + +
94P CYS 3.8 4.9 - - - +
96P PHE* 1.3 78.9 - - + +
98P HIS* 1.3 57.7 + - - +
100P GLY 4.4 0.2 - - - +
101P ARG* 2.9 33.1 + - - +
236P MET* 5.2 3.1 - - + -
3007P PEE 3.8 49.3 - - + +
3004T CDL 4.3 17.3 - - + -
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Residues in contact with HIS 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P TRP 5.4 0.2 - - - -
34P PHE* 4.0 9.5 - - + +
35P GLY* 3.7 12.7 + - - -
38P LEU* 3.4 10.8 - - + -
94P CYS 2.9 17.7 + - - +
95P ILE 3.5 5.2 - - - +
97P LEU* 1.3 77.1 - - - +
99P ILE* 1.3 62.5 + - - +
101P ARG* 3.0 38.3 + - - +
102P GLY* 3.2 17.7 + - - -
502P HEM 2.0 107.8 + + + +
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Residues in contact with ILE 99 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P ILE* 2.9 27.9 + - + +
96P PHE* 3.7 14.4 - - + +
98P HIS* 1.3 73.7 - - - +
100P GLY* 1.3 67.9 + - - +
102P GLY* 3.1 4.1 + - - -
103P LEU* 3.1 19.4 + - + +
114P TRP* 4.3 8.0 - - + -
121P LEU* 3.9 30.5 - - + -
302P LEU* 4.3 18.8 - - + -
502P HEM 3.8 36.8 - - + -
3007P PEE 4.0 30.5 - - + -
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Residues in contact with GLY 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P PHE 2.8 20.4 + - - -
97P LEU 3.7 1.1 - - - -
99P ILE* 1.3 72.0 - - - +
101P ARG* 1.3 64.0 + - - +
103P LEU* 2.7 18.1 + - - +
104P TYR* 2.9 13.4 + - - +
326P PHE* 4.2 5.0 - - - -
3007P PEE 4.3 36.3 - - - +
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Residues in contact with ARG 101 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P TRP* 3.2 48.2 + - + +
32P TRP* 3.2 38.9 - - + +
97P LEU 2.9 20.8 + - - +
98P HIS* 3.0 42.9 + - - +
100P GLY* 1.3 70.4 - - - +
102P GLY* 1.3 74.3 + - - +
104P TYR* 3.5 0.4 + - - -
105P TYR* 3.1 30.9 + - + +
107P SER* 3.9 7.1 + - - -
502P HEM 2.8 49.7 + - - +
3007P PEE 4.3 15.0 - - - +
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Residues in contact with GLY 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P HIS 3.2 5.8 + - - -
99P ILE 3.1 7.8 + - - -
100P GLY 3.0 1.0 - - - -
101P ARG* 1.3 84.8 - - - +
103P LEU* 1.3 61.4 + - - +
106P GLY 3.1 2.3 + - - -
107P SER* 2.8 47.9 + - - -
108P TYR* 3.4 7.3 - - - -
114P TRP* 4.3 10.1 - - - -
502P HEM 5.5 1.8 - - - -
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Residues in contact with LEU 103 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P ILE* 3.1 12.5 + - + +
100P GLY* 2.7 14.8 + - - +
102P GLY* 1.3 72.6 - - - +
104P TYR* 1.3 62.0 + - - +
105P TYR 3.4 0.3 + - - -
106P GLY* 3.5 2.1 + - - -
108P TYR* 3.4 31.1 + - + +
114P TRP* 4.5 6.0 - - + -
302P LEU* 6.5 1.1 - - + -
305P ILE* 3.9 24.9 - - + -
316P MET* 4.0 15.9 - - + +
326P PHE* 4.2 17.0 - - + -
329P LEU* 4.2 24.5 - - + -
363P LEU* 4.5 11.7 - - + -
367P PHE* 5.3 5.6 - - + -
3007P PEE 4.7 15.5 - - + -
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Residues in contact with TYR 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P GLY 2.9 13.6 + - - +
101P ARG 4.0 3.1 - - - +
103P LEU* 1.3 78.8 - - - +
105P TYR* 1.3 87.7 - + + +
106P GLY 3.5 0.4 - - - -
316P MET* 3.1 58.8 + - + +
323P GLN* 3.5 26.0 + - + -
326P PHE* 3.5 39.0 - + + -
327P TRP* 4.6 6.5 - - - -
3007P PEE 2.8 61.9 + - + -
44T GLN* 4.4 1.0 + - - -
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Residues in contact with TYR 105 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P SER* 4.4 1.7 + - - -
31P TRP* 3.8 11.6 - + - -
32P TRP* 3.7 27.6 - + + -
101P ARG* 3.1 30.7 + - + +
104P TYR* 1.3 99.7 - + + +
106P GLY* 1.3 66.1 + - - +
107P SER* 3.2 6.5 - - - +
207P ASN* 2.9 16.5 - - - +
208P ASN 5.1 0.2 - - - +
209P PRO* 3.4 48.6 - - + +
314P ARG* 3.7 2.9 - - - +
315P THR* 3.5 27.0 - - + +
317P THR* 4.1 0.7 - - - -
3007P PEE 3.1 35.9 + - + +
3004T CDL 3.6 17.8 + - - -
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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