Contacts of the helix formed by residues 4 - 35 (chain Q) in PDB entry 3IS7
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 ASP 4 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q GLY* 1.3 68.4 - - - -
5Q LYS* 1.3 66.2 + - - +
6Q LYS* 2.8 11.5 + - - +
7Q VAL* 2.7 47.0 + - + +
8Q ILE* 3.0 23.3 + - - +
65Q LEU* 5.5 0.4 - - - +
107Q HIS* 3.2 15.5 + - - -
111Q VAL* 3.5 26.3 - - + +
113Q ASP* 5.9 1.5 + - + +
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Residues in contact with LYS 5 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q GLY 3.4 5.0 + - - -
4Q ASP* 1.3 72.6 + - - +
6Q LYS* 1.3 60.3 + - + +
8Q ILE* 3.5 9.6 + - + +
9Q GLN* 3.1 52.2 + - + +
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Residues in contact with LYS 6 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q ASP* 2.8 7.0 + - - +
5Q LYS* 1.3 72.9 - - + +
7Q VAL* 1.3 61.5 + - - +
9Q GLN* 3.6 20.2 - - - +
10Q HIS* 2.8 43.0 + - + +
107Q HIS* 3.4 28.9 - - + +
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Residues in contact with VAL 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q ASP* 2.7 32.5 + - + +
6Q LYS* 1.3 71.6 - - - +
8Q ILE* 1.3 57.9 + - - +
10Q HIS* 3.0 9.1 + - - +
11Q LEU* 2.9 36.6 + - + +
65Q LEU* 4.0 18.8 - - + -
107Q HIS* 3.7 10.5 - - + -
108Q CYS* 4.2 15.3 - - - -
111Q VAL* 3.7 26.0 - - + -
113Q ASP* 3.5 25.1 - - + +
116Q SER* 4.2 5.4 - - - +
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Residues in contact with ILE 8 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q GLY 4.0 14.8 - - - +
4Q ASP 3.0 11.9 + - - +
5Q LYS* 3.6 11.0 - - + +
7Q VAL* 1.3 76.3 - - - +
9Q GLN* 1.3 60.1 + - + +
11Q LEU* 3.8 7.4 - - + +
12Q ASN* 2.9 42.5 + - - +
62Q ILE* 4.4 9.6 - - + +
65Q LEU* 4.0 29.6 - - + +
66Q GLU 4.4 1.3 - - - +
67Q GLY* 3.7 37.5 - - - +
68Q LEU 4.9 1.1 - - - +
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Residues in contact with GLN 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q LYS* 3.1 43.9 + - + +
6Q LYS* 3.6 23.8 - - - +
7Q VAL 3.2 0.2 - - - -
8Q ILE* 1.3 79.2 - - + +
10Q HIS* 1.3 58.5 + - + +
12Q ASN* 3.3 6.1 + - - +
13Q LYS* 2.9 27.6 + - - +
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Residues in contact with HIS 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q LYS* 2.8 31.6 + - + +
7Q VAL* 3.4 8.3 - - - +
9Q GLN* 1.3 74.4 - - + +
11Q LEU* 1.3 60.4 + - + +
13Q LYS* 3.1 16.0 + - + +
14Q ILE* 2.9 34.3 + - - +
100Q ASP 4.8 1.8 + - - -
103Q GLU* 3.9 28.7 - - + +
104Q ALA* 3.5 27.0 + - + +
107Q HIS* 3.8 26.5 + + + +
108Q CYS* 6.0 2.0 - - - -
120Q LEU* 6.0 0.4 - - + -
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Residues in contact with LEU 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q VAL* 2.9 26.9 + - + +
8Q ILE* 3.8 4.9 - - - +
10Q HIS* 1.3 72.5 - - + +
12Q ASN* 1.3 59.2 + - - +
14Q ILE* 3.2 6.4 + - - +
15Q LEU* 2.9 28.9 + - - +
58Q LEU* 4.0 14.6 - - + +
61Q ARG* 3.9 17.0 - - + -
62Q ILE* 3.7 30.5 - - + +
65Q LEU* 3.9 27.4 - - + -
108Q CYS* 5.4 0.7 - - - -
116Q SER* 4.3 10.3 - - - +
119Q LEU* 5.5 1.3 - - + -
120Q LEU* 4.0 36.8 - - + -
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Residues in contact with ASN 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q ILE* 2.9 28.5 + - - +
9Q GLN* 3.6 6.7 - - - +
11Q LEU* 1.3 77.5 - - - +
13Q LYS* 1.3 60.9 + - - +
15Q LEU* 3.5 14.3 + - - +
16Q GLY* 3.0 18.4 + - - -
62Q ILE* 3.8 6.7 - - - +
68Q LEU 2.9 23.4 + - - -
69Q PRO* 3.6 4.7 - - - +
70Q ASN* 2.9 40.2 + - + +
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Residues in contact with LYS 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q GLN 2.9 14.6 + - - +
10Q HIS* 3.4 17.7 - - + +
12Q ASN* 1.3 75.0 - - - +
14Q ILE* 1.3 67.9 + - + +
16Q GLY* 3.1 10.8 + - - +
17Q ASN* 3.1 17.1 + - - +
96Q LYS* 5.0 8.6 - - - +
100Q ASP* 3.3 40.1 + - + +
103Q GLU* 4.9 6.1 + - - -
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Residues in contact with ILE 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q HIS* 2.9 17.5 + - - +
11Q LEU* 3.2 6.3 + - - +
13Q LYS* 1.3 73.9 - - + +
15Q LEU* 1.3 66.2 + - - +
17Q ASN* 3.0 12.0 + - + +
18Q GLU* 2.9 30.5 + - - +
58Q LEU* 3.8 23.1 - - + -
97Q ALA 4.8 0.9 - - - +
100Q ASP* 3.7 37.9 - - + +
101Q LEU* 3.3 37.7 - - + -
104Q ALA* 4.3 5.4 - - + -
120Q LEU* 4.3 12.1 - - + -
123Q ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q LEU 2.9 16.4 + - - +
12Q ASN* 3.5 24.2 - - - +
14Q ILE* 1.3 77.6 - - - +
16Q GLY* 1.4 56.1 + - - +
18Q GLU* 3.1 4.2 + - - +
19Q LEU* 2.9 47.3 + - + +
55Q ALA* 3.8 31.6 - - + +
58Q LEU* 3.8 14.0 - - + +
59Q ILE* 4.0 28.7 - - + -
62Q ILE* 4.2 8.3 - - + -
69Q PRO* 4.2 0.7 - - + -
70Q ASN 3.7 24.5 - - - +
71Q LEU* 4.1 4.7 - - + -
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Residues in contact with GLY 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q ASN 3.0 14.9 + - - -
13Q LYS* 3.1 5.7 + - - -
15Q LEU* 1.4 76.5 - - - +
17Q ASN* 1.3 62.7 + - - +
19Q LEU* 3.3 12.6 + - - +
20Q ILE* 3.3 29.0 + - - +
70Q ASN 5.5 2.2 - - - -
73Q ASP 5.0 8.1 - - - +
75Q GLY 5.2 1.0 + - - -
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Residues in contact with ASN 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q LYS* 3.1 15.5 + - - +
14Q ILE* 3.0 14.1 + - + +
16Q GLY* 1.3 79.9 - - - +
18Q GLU* 1.3 58.3 + - + +
20Q ILE* 3.5 16.5 + - - +
21Q ALA* 3.1 27.0 + - - +
93Q LEU* 4.7 8.5 - - + +
96Q LYS* 4.3 10.9 + - - +
97Q ALA* 3.9 26.3 - - + +
100Q ASP* 2.8 40.7 + - - +
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Residues in contact with GLU 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q ILE* 2.9 22.9 + - - +
15Q LEU 3.1 7.6 + - - +
17Q ASN* 1.3 74.5 - - - +
19Q LEU* 1.3 65.4 + - - +
21Q ALA* 3.2 3.7 + - - +
22Q ILE* 2.9 28.0 + - - +
51Q GLU* 2.7 41.3 - - - +
54Q HIS* 3.7 12.1 - - + -
55Q ALA* 4.1 18.2 - - + +
58Q LEU* 3.9 18.4 - - + -
97Q ALA* 6.0 1.2 - - - +
101Q LEU* 5.5 0.9 - - - +
123Q ILE* 3.6 16.3 - - - +
127Q GLU* 3.0 19.9 - - - +
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Residues in contact with LEU 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q LEU* 2.9 43.7 + - + +
16Q GLY* 3.3 6.7 + - - +
18Q GLU* 1.3 72.7 - - - +
20Q ILE* 1.3 62.6 + - - +
22Q ILE* 3.6 10.2 + - + +
23Q ASN* 3.4 25.6 + - - +
55Q ALA* 4.6 3.4 - - + -
59Q ILE* 5.9 0.2 - - + -
70Q ASN 3.9 8.7 - - - +
71Q LEU* 3.9 37.0 - - + +
73Q ASP 4.6 9.4 - - - +
74Q LEU* 3.8 14.1 - - + +
159Q HEM 3.9 28.0 - - + -
23R ASN* 4.8 7.9 - - - +
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Residues in contact with ILE 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q GLY 3.3 14.6 + - - +
17Q ASN* 3.7 18.6 - - - +
18Q GLU 3.2 0.4 - - - -
19Q LEU* 1.3 76.7 - - - +
21Q ALA* 1.3 59.4 + - - +
23Q ASN* 3.3 3.5 + - - +
24Q GLN* 2.9 32.2 + - - +
74Q LEU* 3.9 9.0 - - + -
75Q GLY* 3.4 43.5 - - - +
76Q LYS 3.6 24.5 - - - +
77Q LEU* 4.1 5.9 - - + +
93Q LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q ASN 3.1 16.3 + - - +
18Q GLU* 3.2 5.4 + - - +
20Q ILE* 1.3 77.0 - - - +
22Q ILE* 1.3 59.2 + - - +
24Q GLN* 4.3 1.3 - - - -
25Q TYR* 2.8 49.3 + - + +
51Q GLU* 3.7 27.4 - - + +
93Q LEU* 3.8 19.3 - - + -
94Q GLU* 6.2 0.2 - - - -
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Residues in contact with ILE 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q GLU 2.9 21.4 + - - +
19Q LEU* 3.8 16.2 - - + +
20Q ILE 3.3 0.2 - - - -
21Q ALA* 1.3 74.0 - - - +
23Q ASN* 1.3 70.6 + - - +
26Q PHE* 2.9 17.2 + - + +
48Q SER* 2.9 27.1 + - - +
51Q GLU* 3.7 11.0 - - + +
52Q MET* 3.6 48.5 - - + +
55Q ALA* 4.3 4.3 - - + -
159Q HEM 3.6 47.3 - - + -
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Residues in contact with ASN 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q LEU 3.4 11.3 + - - +
20Q ILE 3.3 7.2 + - - +
21Q ALA 3.3 0.4 - - - -
22Q ILE* 1.3 77.0 - - - +
24Q GLN* 1.3 64.4 + - - +
26Q PHE* 4.5 0.7 - - - -
27Q LEU* 2.9 26.0 + - - +
74Q LEU* 3.9 11.9 - - - +
77Q LEU* 4.2 13.0 - - + -
159Q HEM 2.8 32.9 - - - +
19R LEU* 4.5 8.7 - - - +
71R LEU* 3.2 48.9 + - + +
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Residues in contact with GLN 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Q ILE* 2.9 20.3 + - - +
21Q ALA* 3.9 3.4 - - - +
23Q ASN* 1.3 77.6 - - - +
25Q TYR* 1.3 66.6 + - + +
27Q LEU* 3.5 1.4 + - - +
28Q HIS* 3.0 34.8 + - + +
77Q LEU* 3.9 8.9 - - + +
78Q LEU* 3.0 49.6 + - - +
79Q ILE* 4.3 11.7 - - + -
89Q CYS 3.3 21.0 + - - -
90Q ASP* 2.9 30.9 + - - +
93Q LEU* 3.6 18.6 - - - +
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Residues in contact with TYR 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ALA* 2.8 26.9 + - + +
24Q GLN* 1.3 87.3 - - + +
26Q PHE* 1.3 57.6 + - - +
28Q HIS 3.4 0.3 + - - -
29Q SER* 2.8 27.0 + - - -
44Q GLU* 2.9 28.1 - - + +
47Q GLU* 3.9 13.9 - - + -
48Q SER* 3.8 18.4 - - - +
51Q GLU* 3.5 34.6 + - + -
90Q ASP* 3.2 38.5 + - + -
93Q LEU* 3.9 11.2 - - + +
94Q GLU* 2.7 31.0 + - - +
130Q HIS* 3.4 18.2 - + - -
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Residues in contact with PHE 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q ILE* 2.9 21.7 + - + +
23Q ASN* 3.9 5.2 - - - +
25Q TYR* 1.3 76.1 - - - +
27Q LEU* 1.3 62.8 + - - +
29Q SER* 3.2 6.7 + - - -
30Q ARG* 2.9 45.0 + - + -
45Q TYR* 4.1 19.1 - + - -
48Q SER* 3.5 18.8 + - - +
52Q MET* 4.2 2.5 - - + -
159Q HEM 3.5 53.2 - + + -
56R ASP* 3.4 35.7 - - + -
59R ILE* 4.0 20.9 - - + -
71R LEU* 4.8 3.4 - - + -
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Residues in contact with LEU 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q ASN 2.9 18.1 + - - +
24Q GLN 4.0 2.7 - - - +
26Q PHE* 1.3 76.9 - - - +
28Q HIS* 1.3 58.2 + - - +
30Q ARG* 3.0 4.6 + - - -
31Q MET* 2.9 54.0 + - + +
77Q LEU* 5.6 2.2 - - + -
79Q ILE* 3.9 35.0 - - + -
59R ILE* 4.4 9.2 - - + -
63R LEU* 4.5 1.8 - - + -
69R PRO* 3.7 50.3 - - + +
71R LEU* 4.5 17.0 - - + +
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Residues in contact with HIS 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q GLN* 3.0 21.6 + - + +
25Q TYR 3.6 0.4 - - - +
27Q LEU* 1.3 78.3 - - - +
29Q SER* 1.3 60.7 + - - +
31Q MET* 3.4 10.9 + - - -
32Q TRP* 3.0 34.1 + - + -
44Q GLU* 3.6 16.5 + - + +
78Q LEU 3.5 16.8 - - - -
79Q ILE* 3.5 11.3 - - + +
80Q GLY 3.0 24.4 + - - -
86Q MET* 3.5 49.9 - - + +
89Q CYS* 4.2 0.4 - - + -
90Q ASP* 3.0 27.9 + - - -
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Residues in contact with SER 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q TYR 2.8 16.7 + - - -
26Q PHE* 3.2 12.1 + - - -
28Q HIS* 1.3 72.4 - - - +
30Q ARG* 1.3 82.0 + - - -
32Q TRP* 3.2 4.3 + - - +
33Q ASN* 2.9 29.1 + - - -
41Q GLY* 2.7 27.1 + - - -
44Q GLU* 3.5 10.2 - - - +
45Q TYR* 3.5 16.7 + - - +
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Residues in contact with ARG 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q PHE* 2.9 35.8 + - + +
27Q LEU 3.0 6.7 + - - +
29Q SER* 1.3 97.0 + - - +
31Q MET* 1.3 53.0 + - - +
33Q ASN* 3.3 19.3 + - + +
34Q ASP* 2.7 36.3 + - - +
41Q GLY 4.9 0.2 + - - -
45Q TYR* 3.4 29.0 - - - +
159Q HEM 5.3 0.2 - - - +
56R ASP* 2.8 43.0 + - - +
59R ILE* 3.9 24.0 - - + -
60R GLU* 3.3 23.7 + - + +
63R LEU* 4.6 8.3 - - + +
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Residues in contact with MET 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q LEU* 2.9 44.5 + - + +
28Q HIS* 3.5 13.7 - - - +
30Q ARG* 1.3 73.6 - - - +
32Q TRP* 1.3 65.5 + - - +
34Q ASP* 3.3 9.2 + - - +
35Q TRP* 3.0 52.2 + - + -
79Q ILE* 4.1 14.6 - - + -
80Q GLY 3.5 23.3 - - - +
81Q GLU* 4.9 2.2 - - - -
86Q MET* 3.6 15.5 - - + -
63R LEU* 4.3 14.6 - - + -
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Residues in contact with TRP 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q HIS* 3.0 31.7 + - + +
29Q SER* 3.6 3.1 - - - +
31Q MET* 1.3 75.8 - - - +
33Q ASN* 1.3 64.1 + - - +
35Q TRP* 3.3 19.5 + + - +
36Q GLY 3.1 4.0 + - - -
37Q LEU* 3.0 39.8 + - + +
40Q LEU* 3.7 36.3 - - + +
41Q GLY 3.8 12.6 - - - +
44Q GLU* 3.7 35.9 - - + -
83Q THR* 2.8 43.9 + - + -
86Q MET* 3.7 35.2 - - + -
87Q LEU* 4.0 22.0 - - + -
90Q ASP* 4.8 0.7 - - - -
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Residues in contact with ASN 33 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q SER* 2.9 16.4 + - - +
30Q ARG* 3.6 35.2 + - + +
32Q TRP* 1.3 74.6 - - - +
34Q ASP* 1.3 66.1 + - - +
36Q GLY* 3.0 14.0 + - - +
37Q LEU 4.9 1.6 - - - +
38Q LYS* 3.7 30.0 + - + +
41Q GLY* 3.4 23.4 - - - -
42Q ALA 4.2 0.4 - - - +
156Q GLU* 5.9 0.2 + - - -
60R GLU* 5.3 4.6 - - + +
136V THR* 5.0 1.4 + - - +
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Residues in contact with ASP 34 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ARG 2.7 21.2 + - - +
31Q MET* 3.6 4.3 - - - +
33Q ASN* 1.3 72.0 - - - +
35Q TRP* 1.3 75.1 + - - +
63R LEU* 3.8 47.6 - - + +
64R PHE* 4.7 3.5 + - - -
132V ASP* 4.6 11.0 - - - +
136V THR* 3.2 22.7 + - - +
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Residues in contact with TRP 35 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q MET* 3.0 33.9 + - + +
32Q TRP* 3.6 23.1 - + - +
33Q ASN 3.1 0.4 - - - -
34Q ASP* 1.3 96.6 + - - +
36Q GLY* 1.3 57.2 + - - +
37Q LEU* 3.6 10.0 + - + +
81Q GLU 3.3 26.5 - - - -
82Q ASN* 4.1 4.5 - - - -
83Q THR* 4.4 5.8 - - - -
86Q MET* 3.4 33.4 - - + -
136V THR* 3.7 7.9 - - - +
139V GLY* 5.5 0.5 - - - -
140V LEU* 3.3 26.2 + - - +
143V LYS* 3.8 40.2 + - - +
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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