Contacts of the helix formed by residues 10 - 41 (chain I) in PDB entry 1VEQ
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 SER 10 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LEU* 1.3 72.5 - - - +
11I ASP* 1.3 55.7 + - - +
12I LYS* 2.6 22.4 + - - +
13I LYS* 2.9 53.6 + - - +
14I ALA* 2.9 10.1 + - - +
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Residues in contact with ASP 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I SER 4.7 9.0 - - - +
4I PHE 5.0 1.6 - - - +
5I THR* 4.0 25.0 - - - +
9I LEU 3.4 2.6 + - - +
10I SER* 1.3 69.4 - - - +
12I LYS* 1.3 57.1 + - - +
14I ALA* 4.2 9.0 - - - +
15I SER* 3.5 20.1 + - - -
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Residues in contact with LYS 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I SER* 2.6 11.8 + - - +
11I ASP* 1.3 74.4 - - - +
13I LYS* 1.3 75.7 + - + +
14I ALA 3.1 0.9 - - - -
15I SER* 3.1 6.3 + - - -
16I ASP* 2.6 55.8 + - - +
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Residues in contact with LYS 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LEU* 4.6 14.4 - - + -
10I SER* 2.9 33.5 + - - +
12I LYS* 1.3 84.3 - - + +
14I ALA* 1.3 63.3 + - - +
16I ASP* 3.1 7.2 + - - +
17I VAL* 3.0 29.3 + - - +
129I ASP 4.1 16.2 + - - +
130I LEU* 4.4 32.9 + - + +
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I THR* 3.6 23.6 - - - +
9I LEU* 4.3 22.1 - - + +
10I SER 2.9 14.5 + - - +
11I ASP* 4.2 7.2 - - - +
13I LYS* 1.3 77.4 - - - +
15I SER* 1.3 63.3 + - - +
17I VAL* 3.2 6.6 + - - +
18I ALA* 3.1 20.8 + - - +
75I LEU* 3.8 17.0 - - + +
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Residues in contact with SER 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ASP 3.5 16.4 + - - -
12I LYS* 3.1 7.0 + - - -
14I ALA* 1.3 79.0 - - - +
16I ASP* 1.3 63.0 + - - +
18I ALA* 3.5 9.6 - - - +
19I ASP* 3.1 31.6 + - - +
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Residues in contact with ASP 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LYS* 2.6 46.4 + - - +
13I LYS* 3.1 11.4 + - - +
15I SER* 1.3 76.4 - - - +
17I VAL* 1.3 64.0 + - - +
19I ASP* 3.7 11.9 + - - +
20I LEU* 3.3 23.7 + - - +
130I LEU* 4.6 16.2 - - + +
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LEU* 5.4 2.0 - - + -
13I LYS* 3.0 17.1 + - + +
14I ALA* 3.2 8.3 + - - +
16I ASP* 1.3 73.4 - - - +
18I ALA* 1.3 70.5 + - - +
20I LEU* 2.8 18.1 + - - +
21I LEU* 3.0 18.3 + - + +
75I LEU* 3.7 17.9 - - + -
127I LEU* 4.0 15.5 - - + -
130I LEU* 3.7 31.0 - - + -
131I ASP* 4.3 11.7 - - + -
134I SER* 3.9 20.0 - - - +
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Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA 3.1 9.9 + - - +
15I SER* 3.5 13.7 - - - +
17I VAL* 1.3 77.5 - - - +
19I ASP* 1.3 65.3 + - - +
20I LEU 2.9 1.2 + - - -
21I LEU* 2.9 7.2 + - - +
22I GLN* 2.9 25.9 + - - +
72I ILE* 4.4 11.2 - - + +
75I LEU* 3.9 14.7 - - + +
77I LYS* 3.8 29.2 - - + -
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Residues in contact with ASP 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I SER* 3.1 24.7 + - - +
16I ASP* 3.7 13.3 - - - +
17I VAL 3.3 0.2 - - - -
18I ALA* 1.3 79.4 - - - +
20I LEU* 1.3 62.3 + - + +
22I GLN* 3.8 8.2 + - - +
23I LYS* 3.6 16.8 + - - +
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ASP 3.3 13.0 + - - +
17I VAL* 2.8 12.2 + - - +
19I ASP* 1.3 78.0 - - + +
21I LEU* 1.3 69.3 + - + +
23I LYS* 3.3 16.0 + - + +
24I GLN* 3.2 17.7 + - - +
123I SER* 3.3 36.6 + - - +
126I LYS* 4.5 25.1 - - + +
127I LEU* 4.1 29.8 - - + -
130I LEU* 4.1 11.7 - - + -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 3.4 31.0 - - + +
18I ALA 2.9 2.3 + - - +
20I LEU* 1.3 74.2 - - + +
22I GLN* 1.3 55.0 + - - +
23I LYS 2.9 4.7 - - - -
24I GLN* 2.6 28.8 + - + +
25I LEU* 2.6 18.2 + - - +
68I VAL* 3.6 18.3 - - + +
71I ARG* 3.8 29.6 - - + -
72I ILE* 3.6 20.0 - - + -
75I LEU* 4.5 5.8 - - + -
127I LEU* 4.9 8.7 - - + -
134I SER* 4.5 6.5 - - - +
137I LEU* 6.1 0.4 - - + -
138I LEU* 4.0 27.1 - - + -
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ALA 2.9 15.9 + - - +
19I ASP* 3.9 10.3 - - - +
21I LEU* 1.3 76.2 - - - +
23I LYS* 1.3 60.2 + - - +
25I LEU* 3.8 5.7 - - - +
26I SER* 3.4 18.0 + - - -
72I ILE* 3.5 13.5 - - + +
78I SER 4.3 2.6 - - - +
79I PRO* 3.6 9.5 - - - +
80I LYS* 3.0 54.1 + - - +
85I ALA* 4.8 0.2 - - - +
89I ASP* 3.2 26.2 + - - +
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Residues in contact with LYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ASP 3.6 9.8 + - - +
20I LEU* 3.3 17.7 + - + +
21I LEU 2.7 1.4 + - - -
22I GLN* 1.3 76.7 - - - +
24I GLN* 1.3 69.0 + - - +
26I SER* 3.1 5.7 + - - -
27I THR* 2.9 29.4 + - - +
89I ASP* 4.6 27.6 - - + +
91I THR* 5.2 14.0 + - - +
119I ASP* 3.4 27.2 + - + -
123I SER* 5.7 3.4 - - - +
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Residues in contact with GLN 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I LEU 3.2 4.6 + - - +
21I LEU* 2.6 24.0 + - + +
23I LYS* 1.3 76.8 - - - +
25I LEU* 1.3 57.8 + - - +
27I THR* 2.9 15.1 + - - +
28I TYR* 2.8 59.9 + - + +
68I VAL* 4.8 4.9 - - + -
116I VAL* 4.8 1.0 + - - +
119I ASP* 4.6 6.5 - - - +
120I THR* 2.7 35.4 + - - -
123I SER* 4.3 14.4 + - - -
138I LEU* 3.1 32.2 - - + +
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Residues in contact with LEU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TRP* 4.3 9.2 - - + -
21I LEU 2.6 16.4 + - - +
22I GLN* 3.8 11.2 - - - +
24I GLN* 1.3 74.5 - - - +
26I SER* 1.3 66.7 + - - +
28I TYR* 3.1 12.7 + - - +
29I ASN* 2.9 55.3 + - - +
65I ALA* 4.3 9.2 - - - +
68I VAL* 4.3 8.2 - - + +
69I ALA* 3.2 43.7 - - + +
72I ILE* 4.5 7.0 - - + -
79I PRO* 4.7 5.6 - - + -
80I LYS 3.3 26.2 - - - +
81I GLY* 4.3 2.0 - - - -
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Residues in contact with SER 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLN* 3.4 11.9 + - - -
23I LYS 3.1 9.0 + - - -
25I LEU* 1.3 82.5 - - - +
27I THR* 1.3 63.0 + - - +
29I ASN* 3.8 7.2 - - - +
30I ASP* 3.1 23.6 + - - +
80I LYS 4.4 1.0 + - - -
85I ALA 4.0 0.3 + - - -
86I ILE* 3.8 27.9 + - - +
89I ASP* 3.1 38.2 + - - +
90I ARG* 5.0 4.8 - - - +
92I TRP* 5.6 0.2 - - - -
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Residues in contact with THR 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I LYS* 2.9 25.4 + - - +
24I GLN* 2.9 21.8 + - - +
26I SER* 1.3 79.3 - - - +
28I TYR* 1.3 63.5 + - + +
30I ASP* 3.3 3.3 + - - +
31I LEU* 3.0 21.0 + - - +
90I ARG* 6.2 0.4 - - - -
92I TRP* 3.4 36.6 - - + -
115I GLY 5.5 0.2 - - - +
116I VAL* 4.0 32.3 - - + +
119I ASP* 5.2 9.4 + - + +
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Residues in contact with TYR 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLN* 2.8 49.5 + - + +
25I LEU* 3.5 7.2 - - - +
27I THR* 1.3 77.1 - - + +
29I ASN* 1.3 60.1 + - - +
31I LEU* 2.9 11.4 + - + +
32I HIS* 2.7 36.7 + - - -
61I VAL* 3.7 23.2 - - + +
64I TYR* 3.6 28.5 - + + -
65I ALA* 4.3 8.1 - - + -
68I VAL* 3.7 18.6 - - + -
116I VAL* 4.7 10.5 - - + -
120I THR* 4.8 1.1 + - - +
138I LEU* 4.0 2.8 - - - +
141I HIS* 2.6 41.1 + - + +
145I LEU* 4.6 14.1 - - + +
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Residues in contact with ASN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.7 22.9 - - + +
40C TRP* 5.0 5.7 - - - -
25I LEU* 2.9 49.6 + - - +
26I SER* 3.8 6.7 - - - +
27I THR 3.4 0.2 - - - -
28I TYR* 1.3 75.7 - - - +
30I ASP* 1.3 63.9 + - - +
32I HIS* 3.4 22.5 + - - +
33I LEU* 3.1 27.9 + - - +
65I ALA* 4.2 12.3 - - - +
81I GLY* 4.4 10.9 + - - -
86I ILE* 4.0 15.4 - - + +
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Residues in contact with ASP 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PRO* 2.8 33.1 - - - +
26I SER 3.1 13.0 + - - +
27I THR 3.6 7.4 - - - +
29I ASN* 1.3 75.1 - - - +
31I LEU* 1.3 56.4 + - - +
33I LEU* 3.0 3.5 + - - +
34I THR* 2.7 46.7 + - - -
86I ILE* 3.5 15.4 - - + +
90I ARG* 3.3 10.5 + - + -
92I TRP* 3.5 32.5 + - + +
94I ASP* 4.4 4.2 - - - +
95I TYR 5.6 0.7 + - - -
112I VAL* 4.9 9.7 - - - +
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Residues in contact with LEU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I THR 3.0 11.8 + - - +
28I TYR* 2.9 13.1 + - + +
30I ASP* 1.3 80.4 + - - +
32I HIS* 1.3 52.4 + - - +
34I THR* 2.9 10.0 + - - -
35I LEU* 2.7 59.4 + - + +
61I VAL* 3.6 30.5 - - + -
109I LEU* 5.6 0.9 - - + -
112I VAL* 4.6 11.9 - - + -
113I TYR* 3.4 28.5 - - + +
116I VAL* 4.5 26.0 - - + -
145I LEU* 4.0 15.5 - - + -
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Residues in contact with HIS 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 4.3 19.7 - + - -
33C LEU* 4.6 5.2 - - + +
62C ARG* 3.3 27.1 + - - +
28I TYR 2.7 12.8 + - - -
29I ASN* 3.4 41.2 + - - +
31I LEU* 1.3 74.0 - - - +
33I LEU* 1.3 81.7 + - + +
35I LEU* 3.6 11.4 - - - +
36I LYS* 3.3 21.7 + - - +
58I VAL* 4.2 7.0 - - + +
61I VAL* 3.5 23.6 - - + -
62I ARG* 4.2 23.8 - - + +
65I ALA* 5.1 2.6 - - + +
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN* 3.7 30.3 - - + +
32C HIS* 4.5 6.3 - - - +
33C LEU* 3.7 28.5 - - + -
81C GLY 3.2 31.7 - - - +
82C THR* 5.1 0.7 - - - -
83C PRO* 4.7 21.5 - - + -
86C ILE* 5.2 5.4 - - + -
29I ASN 3.1 18.0 + - - +
30I ASP* 3.0 5.8 + - - +
32I HIS* 1.3 95.5 + - + +
34I THR* 1.3 58.5 + - - +
36I LYS* 3.6 9.7 + - + +
37I HIS 3.1 19.6 + - - -
40I TRP* 5.0 3.4 - - + -
86I ILE* 5.2 1.6 - - + -
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Residues in contact with THR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR* 4.4 5.9 - - - +
83C PRO* 4.2 6.2 - - - +
30I ASP* 2.7 37.2 + - - +
31I LEU* 3.3 10.8 - - - -
33I LEU* 1.3 76.4 - - - +
35I LEU* 1.3 66.4 + - - +
37I HIS* 2.8 24.5 + - + +
38I VAL* 3.0 13.3 + - + +
95I TYR* 3.5 45.2 + - + +
109I LEU* 4.7 8.1 - - + -
112I VAL* 5.2 7.9 - - + -
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Residues in contact with LEU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I LEU* 2.7 65.4 + - + +
32I HIS* 3.6 5.6 - - - +
33I LEU 3.4 0.2 - - - -
34I THR* 1.3 73.5 - - - +
36I LYS* 1.3 59.6 + - - +
38I VAL* 3.1 11.9 + - - +
39I HIS* 2.9 24.9 + - - +
54I ILE* 3.5 24.5 - - + +
57I GLN* 4.6 5.4 - - + +
58I VAL* 3.3 23.3 - - + -
61I VAL* 5.1 1.1 - - + -
109I LEU* 3.9 28.0 - - + -
113I TYR* 3.6 16.8 - - + +
148I PHE* 4.1 8.7 - - + -
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Residues in contact with LYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 4.7 19.3 - - + +
65C ALA* 6.1 1.3 - - + -
66C ASP* 2.9 41.2 + - - +
32I HIS 3.3 8.2 + - - +
33I LEU* 3.7 12.8 - - + +
34I THR 3.2 0.2 - - - -
35I LEU* 1.3 77.1 - - - +
37I HIS* 1.3 66.5 + - - +
39I HIS* 3.0 30.9 + - + +
40I TRP* 3.0 48.2 + - + -
55I ASP* 3.2 20.3 + - - +
58I VAL* 3.6 27.6 - - + -
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Residues in contact with HIS 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PRO 3.4 15.6 + - - -
80C LYS* 3.4 12.7 - - + +
81C GLY 3.0 28.2 + - - +
82C THR* 3.9 17.6 - - + +
33I LEU 3.1 11.2 + - - +
34I THR* 2.8 22.1 + - - +
36I LYS* 1.3 79.0 - - - +
38I VAL* 1.3 59.4 + - - -
40I TRP* 3.2 16.4 + - - +
41I ASN* 2.8 44.5 + - - -
95I TYR* 3.5 30.1 + + + -
97I VAL 3.1 18.8 + - - -
98I GLU* 4.7 3.3 + - - -
105I HIS* 5.4 0.2 - + - -
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Residues in contact with VAL 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I THR 3.0 17.5 + - - +
35I LEU* 3.6 6.5 - - - +
37I HIS* 1.3 69.8 - - - +
39I HIS* 1.3 64.9 + - - +
40I TRP 2.7 6.9 + - - -
41I ASN 4.3 1.8 - - - +
42I VAL* 2.7 39.0 + - + +
50I VAL* 5.4 0.7 - - + -
54I ILE* 3.2 26.2 - - + -
95I TYR* 3.7 27.1 - - + +
105I HIS* 4.0 26.5 - - + +
106I LEU* 6.5 0.9 - - + -
109I LEU* 4.3 18.8 - - + -
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Residues in contact with HIS 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 4.8 0.7 - - - -
66C ASP* 3.0 8.5 + - - -
70C GLU* 3.3 1.8 + - - -
209C FE 2.3 27.5 - - - -
35I LEU 2.9 13.4 + - - +
36I LYS* 3.0 40.4 + - + +
38I VAL* 1.3 76.7 - - - +
40I TRP* 1.3 66.2 + + - +
42I VAL* 4.9 1.3 + - - +
47I PHE* 5.0 1.7 - - - -
51I HIS* 2.7 81.8 + + - +
52I GLU* 5.2 0.2 - - - -
54I ILE* 4.0 19.4 - - + +
55I ASP* 3.2 22.2 - - - -
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Residues in contact with TRP 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 3.6 24.9 - - - -
25C LEU* 4.4 10.8 - - + -
29C ASN* 5.0 6.3 - - - -
65C ALA* 4.1 9.4 - - + -
66C ASP* 3.2 36.3 + - - +
69C ALA* 3.2 33.5 - - + +
70C GLU* 3.6 25.1 - - + +
73C ALA* 4.2 7.8 - - + +
79C PRO* 4.5 15.9 - - + -
81C GLY* 4.3 20.9 - - - -
33I LEU* 5.0 2.2 - - + -
36I LYS* 3.0 47.3 + - + -
37I HIS* 3.5 18.2 - - - +
38I VAL 2.7 1.6 + - - -
39I HIS* 1.3 87.5 - + - +
41I ASN* 1.3 65.3 + - - +
42I VAL 3.4 8.5 + - - +
43I VAL* 5.7 0.5 - - - +
47I PHE* 5.7 0.2 - - - -
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Residues in contact with ASN 41 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C SER* 2.9 20.5 + - - -
79C PRO* 3.1 26.9 + - - +
37I HIS* 2.8 57.4 + - - +
38I VAL 3.2 2.8 + - - -
40I TRP* 1.3 76.0 - - - +
42I VAL* 1.3 60.9 + - - +
43I VAL* 4.7 2.5 - - - -
98I GLU 3.7 7.3 - - - +
99I ARG* 3.2 24.4 - - - +
100I ASP 3.1 23.6 + - - -
105I HIS* 3.1 9.2 + - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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