Contacts of the helix formed by residues 25 - 56 (chain C) in PDB entry 3OMA
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 ASN 25 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 3.3 2.6 + - - +
24C THR* 1.3 78.0 + - - +
26C HIS* 1.3 70.2 + - - +
27C LYS* 3.2 43.2 + - - +
28C ASP* 2.8 48.6 + - - +
29C ILE* 2.9 13.8 + - - +
131C PRO 4.8 2.8 + - - -
132C ASP* 3.4 16.2 + - - +
548C GLU* 4.1 12.0 + - - +
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Residues in contact with HIS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR 3.7 0.8 + - - -
25C ASN* 1.3 82.8 + - - +
27C LYS* 1.3 74.9 + - + +
29C ILE* 4.4 0.7 - - - -
30C GLY* 2.9 26.5 + - - -
121C ASN* 3.0 33.5 + - - +
122C TYR 3.3 19.2 + - - -
125C PRO* 3.7 14.8 - - + +
126C LEU* 3.6 21.0 - - + +
131C PRO 3.6 24.4 + - - -
132C ASP* 3.4 27.5 + - - +
133C MET* 4.2 15.3 - - + -
139C ASN* 4.1 11.4 - - - +
550C THR* 4.4 3.4 + - - -
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 3.1 27.7 + - - +
26C HIS* 1.3 102.9 + - + +
28C ASP* 1.3 60.2 + - - +
31C VAL* 3.2 23.4 + - - +
122C TYR* 3.3 51.5 - - + +
126C LEU* 4.8 3.6 - - + -
131C PRO 5.9 0.2 + - - -
546C PRO* 3.8 27.1 - - + -
547C PRO 3.4 25.9 + - - -
548C GLU* 3.5 12.2 + - - +
550C THR* 4.3 9.5 + - - +
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C DMU 4.6 11.6 + - - -
20C TRP* 4.5 7.3 - - - +
23C SER* 2.8 37.9 + - - +
25C ASN* 2.8 26.9 + - - +
27C LYS* 1.3 78.3 - - - +
29C ILE* 1.3 64.0 - - - +
31C VAL* 3.5 5.8 + - - +
32C LEU* 3.1 29.0 + - - +
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER 3.1 27.1 - - - +
24C THR 4.3 3.4 - - - -
25C ASN 2.9 20.2 + - - +
26C HIS 4.0 3.8 - - - +
28C ASP* 1.3 74.6 - - - +
30C GLY* 1.3 63.5 + - - +
32C LEU* 2.9 27.6 + - + +
33C TYR* 3.0 28.2 + - + -
121C ASN* 3.5 24.2 - - - +
139C ASN* 3.6 30.7 - - - +
140C ASN* 3.8 24.9 - - + +
143C TYR* 4.6 5.8 - - + -
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C HIS 2.9 19.4 + - - -
27C LYS 4.0 1.6 - - - -
29C ILE* 1.3 76.4 - - - +
31C VAL* 1.3 55.4 + - - +
34C LEU* 3.2 25.3 + - - +
117C GLY 3.6 8.7 - - - -
118C GLY* 3.3 32.9 - - - +
121C ASN* 3.8 2.7 - - - +
122C TYR* 4.2 6.1 - - - -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C DMU 4.1 22.4 - - - +
27C LYS 3.2 19.0 + - - +
28C ASP* 3.9 6.5 - - - +
29C ILE 3.2 0.2 - - - -
30C GLY* 1.3 72.4 - - - +
32C LEU* 1.3 67.7 + - + +
34C LEU* 3.8 7.6 - - + +
35C PHE* 3.1 48.6 + - + -
122C TYR* 3.7 20.4 - - + -
443C MET* 4.7 13.0 - - + -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TRP* 3.6 27.4 - - + +
21C PHE* 3.8 46.0 - - + +
28C ASP 3.1 17.4 + - - +
29C ILE* 2.9 20.5 + - + +
31C VAL* 1.3 78.0 - - + +
33C TYR* 1.3 59.0 + - - +
35C PHE* 3.3 5.3 + - + +
36C THR* 2.7 38.5 + - - +
143C TYR* 3.6 34.5 - - + +
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Residues in contact with TYR 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 3.0 30.1 + - + -
30C GLY 3.7 2.9 - - - +
32C LEU* 1.3 76.7 - - - +
34C LEU* 1.3 55.7 - - - +
36C THR* 4.1 0.8 - - - -
37C GLY* 2.8 29.3 + - - -
113C PRO* 3.4 38.3 - - + +
117C GLY* 3.2 31.6 - - - +
118C GLY 3.5 0.4 - - - +
121C ASN* 3.6 17.5 - - - -
142C SER* 3.1 35.1 + - - -
143C TYR* 3.8 18.6 - + + -
146C TYR* 3.6 34.1 + + + -
200C SER* 3.2 10.9 + - - -
204C GLY* 6.0 0.2 - - - -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.6 33.4 - - + +
30C GLY 3.2 17.2 + - - +
31C VAL* 3.8 9.6 - - + +
32C LEU 3.3 0.4 - - - -
33C TYR* 1.3 78.1 - - - +
35C PHE* 1.3 60.1 + - + +
38C GLY* 2.9 23.4 + - - -
114C ALA* 3.9 18.2 - - + +
118C GLY* 4.1 9.8 - - - +
119C PHE* 3.5 43.3 - - + -
122C TYR* 6.1 0.7 - - + -
432C ILE* 5.2 0.2 - - + -
436C ILE* 4.3 8.7 - - + -
443C MET* 4.0 22.4 - - + -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C DMU 5.5 5.2 - - - -
31C VAL* 3.1 41.5 + - + +
32C LEU* 3.9 5.2 - - + +
34C LEU* 1.3 77.5 - - + +
36C THR* 1.3 61.6 + - - +
38C GLY* 3.4 2.6 + - - -
39C LEU* 3.1 26.9 + - - +
515C ILE* 4.8 10.3 - - + -
519C LEU* 3.6 31.6 - - + -
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Residues in contact with THR 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU 2.7 17.2 + - - -
33C TYR 4.1 0.2 - - - -
35C PHE* 1.3 73.6 - - - +
37C GLY* 1.3 60.3 + - - +
39C LEU* 3.0 13.3 + - + +
40C VAL* 2.9 41.0 + - + +
143C TYR* 2.6 30.2 + - + +
146C TYR* 3.5 30.5 - - + +
147C VAL* 4.8 8.5 - - + -
150C THR* 5.5 3.1 - - + +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 4.0 7.0 - - - -
33C TYR 2.8 22.0 + - - -
34C LEU 3.9 0.9 - - - -
36C THR* 1.3 71.5 - - - +
38C GLY* 1.3 57.4 + - - +
40C VAL* 4.1 0.3 - - - +
41C GLY* 2.9 27.4 + - - -
109C PHE 4.4 2.0 - - - -
110C VAL* 3.6 24.8 - - - +
113C PRO* 5.0 0.9 - - - -
114C ALA* 4.9 3.1 - - - -
146C TYR* 3.2 13.7 + - - -
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.7 26.1 - - - +
34C LEU 2.9 16.6 + - - -
35C PHE* 3.7 2.7 - - - -
36C THR 3.2 0.2 - - - -
37C GLY* 1.3 74.6 - - - +
39C LEU* 1.3 56.3 + - - +
41C GLY* 3.6 1.6 + - - -
42C LEU* 3.0 25.6 + - - +
508C PHE* 4.3 8.6 - - - -
512C LEU* 5.4 6.5 - - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE 3.1 12.3 + - - +
36C THR* 3.0 17.7 + - + +
38C GLY* 1.3 73.4 - - - +
40C VAL* 1.3 69.6 + - + +
42C LEU* 3.0 30.4 + - + +
43C ILE* 3.1 29.4 + - + +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C THR* 2.9 30.1 + - + +
37C GLY 4.1 0.4 - - - +
39C LEU* 1.3 73.6 - - + +
41C GLY* 1.3 52.9 + - - +
43C ILE* 3.0 16.8 + - + +
44C SER* 2.8 32.2 + - - -
105C LEU* 3.9 30.5 - - + -
109C PHE* 3.4 29.6 - - + +
110C VAL* 3.6 10.3 - - + -
146C TYR* 3.7 7.0 - - - +
150C THR* 3.8 22.0 - - + -
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 4.3 9.9 - - - -
37C GLY 2.9 19.2 + - - -
38C GLY 3.7 2.7 - - - -
40C VAL* 1.3 75.6 - - - +
42C LEU* 1.3 55.2 + - - +
44C SER* 3.5 2.4 + - - -
45C VAL* 2.9 37.9 + - - +
110C VAL* 3.5 21.6 - - - +
508C PHE* 4.7 3.6 - - - -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLY 3.0 13.0 + - - +
39C LEU* 3.0 24.7 + - + +
41C GLY* 1.3 72.9 - - - +
43C ILE* 1.3 62.6 + - + +
45C VAL* 3.5 1.7 + - - -
46C ALA* 2.9 29.8 + - + +
505C PHE* 4.3 11.4 - - + -
508C PHE* 4.0 21.0 - - + -
509C LEU* 4.2 14.8 - - + -
512C LEU* 3.9 30.1 - - + -
----------------------------------------------------------
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.1 30.7 + - + +
40C VAL* 3.0 17.5 + - + +
42C LEU* 1.3 75.3 - - + +
44C SER* 1.3 65.1 + - - +
46C ALA* 3.1 10.0 + - + +
47C PHE* 3.1 49.7 + - + -
105C LEU* 4.3 9.4 - - + -
154C VAL* 5.5 14.8 - - + -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL 2.8 18.4 + - - -
41C GLY* 3.9 1.3 - - - -
43C ILE* 1.3 74.8 - - - +
45C VAL* 1.3 61.6 + - - +
47C PHE* 3.2 23.1 - - - +
48C THR* 3.3 10.0 + - - +
102C HIS* 2.9 42.3 + - - -
105C LEU* 3.9 21.0 - - - +
106C MET* 3.4 20.9 - - - +
110C VAL* 4.7 0.2 - - - -
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.8 60.6 - - + +
41C GLY 2.9 25.5 + - - +
42C LEU* 4.0 5.6 - - - +
44C SER* 1.3 68.7 - - - +
46C ALA* 1.3 65.8 + - - +
48C THR* 2.8 24.6 + - - +
49C VAL* 3.0 10.3 + - + +
106C MET* 3.9 11.9 - - + -
505C PHE* 3.5 27.8 - - + -
508C PHE* 5.0 6.3 - - + -
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 2.9 17.1 + - + +
43C ILE* 3.1 13.0 + - - +
45C VAL* 1.3 77.4 - - - +
47C PHE* 1.3 64.5 + - + +
49C VAL* 3.2 10.8 + - - +
50C TYR* 3.2 20.3 + - - +
505C PHE* 4.5 13.2 - - + -
552C TRD 6.0 1.7 - - - +
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Residues in contact with PHE 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.1 34.4 + - + -
44C SER* 3.2 11.2 - - - +
46C ALA* 1.3 77.6 - - + +
48C THR* 1.3 50.3 + - - +
50C TYR* 3.1 6.6 + - - +
51C MET* 2.7 39.4 + - - +
98C MET* 3.7 38.7 - - + +
101C GLY* 4.1 11.0 - - - -
102C HIS* 3.7 28.7 - - + -
105C LEU* 4.1 14.4 - - + -
157C LEU* 3.7 33.2 - - + -
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 2.9 47.0 + - + +
44C SER 3.4 4.9 - - - +
45C VAL* 2.8 18.7 + - - +
47C PHE* 1.3 71.9 - - - +
49C VAL* 1.3 61.6 + - - +
51C MET* 3.5 9.5 - - - +
52C ARG* 2.8 35.0 + - - +
102C HIS* 3.0 50.0 - - + +
501C ALA* 5.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 5.7 0.2 - - - +
10C DMU 3.8 28.9 - - + -
45C VAL* 3.0 17.6 + - + +
46C ALA* 3.2 9.4 + - - +
48C THR* 1.3 76.3 - - - +
50C TYR* 1.3 59.3 + - - +
52C ARG* 3.2 5.8 + - - -
53C MET* 3.0 37.3 + - - +
501C ALA* 4.6 7.9 - - + +
502C PHE* 3.8 7.7 - - + -
505C PHE* 3.4 43.5 - - + -
552C TRD 4.6 12.1 - - + -
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Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA 3.2 10.2 + - - +
47C PHE* 3.1 11.0 + - - +
49C VAL* 1.3 76.3 - - - +
51C MET* 1.3 64.1 + - - +
53C MET* 3.3 14.1 + - + -
54C GLU* 3.3 20.6 + - - +
62C PHE* 3.5 32.7 + + + +
63C MET* 3.7 32.0 - - + +
79C SER* 2.6 47.5 + - - -
80C LEU* 3.9 26.0 - - + -
94C LEU* 4.5 11.4 - - + +
98C MET* 4.1 18.8 - - + -
552C TRD 6.2 2.0 - - + -
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Residues in contact with MET 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.6 49.8 - - + +
47C PHE* 2.7 25.9 + - - +
48C THR* 3.5 13.9 - - - +
50C TYR* 1.3 72.7 - - - +
52C ARG* 1.3 58.5 + - + +
54C GLU 3.3 2.8 + - - -
55C LEU* 3.1 21.7 + - - +
63C MET* 4.7 1.6 - - + -
95C TRP* 3.4 28.0 - - + -
98C MET* 4.3 15.5 - - + +
99C ILE* 3.5 34.5 - - + -
102C HIS* 3.9 22.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 2.9 37.3 + - + -
48C THR 2.8 25.0 + - - +
49C VAL 3.8 3.6 - - - +
51C MET* 1.3 72.2 - - - +
53C MET* 1.3 61.3 + - - +
55C LEU* 3.4 26.2 - - - +
56C MET* 3.0 13.3 + - - +
414C TYR* 4.3 3.4 - - - -
467C THR* 5.0 0.7 - - - -
471C GLN* 3.4 14.1 - - - +
474C LEU* 5.8 0.2 - - - +
494C ASN* 2.9 46.5 + - - -
497C SER* 3.3 21.1 + - - -
498C SER* 2.6 43.5 + - - +
501C ALA* 3.5 29.8 - - + -
502C PHE* 4.2 5.8 - - + -
----------------------------------------------------------
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Residues in contact with MET 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C DMU 3.8 18.5 + - + -
49C VAL* 3.0 26.8 + - - +
50C TYR* 3.3 25.7 + - + +
52C ARG* 1.3 76.8 - - - +
54C GLU* 1.3 60.6 + - - +
56C MET* 3.2 20.1 - - - +
62C PHE* 3.5 49.3 - - + -
80C LEU* 3.6 16.4 - - + +
502C PHE* 3.8 22.2 - - + -
552C TRD 3.8 35.2 - - + -
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C CA 2.3 57.7 - - - -
50C TYR 3.3 8.3 + - - +
51C MET 3.7 7.4 - - - +
52C ARG 3.3 0.2 - - - -
53C MET* 1.3 79.8 - - - +
55C LEU* 1.3 57.2 + - - +
56C MET 3.3 0.6 + - - -
57C ALA 3.3 2.6 - - - +
60C VAL* 3.4 11.9 - - - +
61C GLN* 3.1 19.1 + - - +
62C PHE* 2.8 32.3 + - + +
63C MET* 2.9 25.1 + - + -
95C TRP* 3.9 14.4 - - + -
484C ILE* 3.9 25.6 - - + +
486C TYR* 5.0 0.9 - - - -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 4.5 3.8 - - - -
51C MET 3.1 11.5 + - - +
52C ARG* 3.4 37.2 + - - +
53C MET 3.4 0.2 - - - -
54C GLU* 1.3 72.8 - - - +
56C MET* 1.3 57.6 + - - +
57C ALA 3.2 3.1 - - - -
95C TRP* 3.3 29.8 - - + -
414C TYR* 3.4 20.2 - - + +
479C MET* 4.3 4.7 - - + -
483C TYR 3.5 23.1 - - - +
484C ILE 4.0 10.5 - - - +
486C TYR* 2.8 44.9 + - + -
494C ASN* 3.1 17.2 - - - +
498C SER* 3.9 2.2 - - - -
----------------------------------------------------------
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Residues in contact with MET 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C DMU 4.1 43.5 - - - +
52C ARG 3.0 10.1 + - - +
53C MET 3.2 15.9 - - - +
54C GLU 3.3 0.4 - - - -
55C LEU* 1.3 78.2 - - - +
57C ALA* 1.3 60.9 + - + +
58C PRO* 4.7 0.3 - - - +
486C TYR* 3.7 3.0 + - - -
491C ALA* 4.3 2.1 - - - +
494C ASN 4.1 1.6 - - - -
495C PHE* 3.4 55.2 + - + +
498C SER* 3.4 21.5 - - - -
499C LEU* 4.8 8.3 - - + -
502C PHE* 4.0 21.3 - - + -
----------------------------------------------------------
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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