Contacts of the helix formed by residues 37 - 66 (chain w) in PDB entry 3J9X
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 VAL 37 (chain w).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 T 3.9 21.8 - - - +
537 A 3.9 4.3 - - - +
16v LYS* 4.7 11.2 - - + -
19v ALA* 3.7 18.6 - - + -
20v LYS* 3.6 30.1 - - + -
33w ILE 3.0 21.3 + - - +
34w LEU* 3.5 15.7 - - + +
36w ASN* 1.3 75.7 - - - +
38w SER* 1.3 68.6 + - - +
39w PRO* 3.5 1.6 - - - -
40w VAL* 3.9 7.9 - - + -
41w ALA* 2.9 21.2 + - + +
21x PHE* 4.5 8.7 - - + -
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Residues in contact with SER 38 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34w LEU 2.6 23.4 + - - -
35w SER* 3.3 16.0 - - - -
37w VAL* 1.3 80.6 - - - +
39w PRO* 1.4 72.5 - - - +
41w ALA* 2.9 10.6 + - - +
42w GLN* 2.9 27.0 + - - +
21x PHE* 3.5 21.0 - - - -
22x ASN* 5.5 1.9 + - - -
25x SER* 4.7 5.0 + - - -
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Residues in contact with PRO 39 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35w SER 4.0 3.4 - - - +
36w ASN 3.6 12.6 - - - +
37w VAL 3.5 1.6 - - - -
38w SER* 1.4 98.1 - - - +
40w VAL* 1.3 67.6 + - + +
42w GLN* 3.5 19.0 + - + +
43w GLN* 3.1 21.8 + - - +
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Residues in contact with VAL 40 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 T 4.8 1.6 - - - +
12v GLN* 5.0 1.8 - - - +
15v ALA* 4.1 30.3 - - + +
16v LYS* 3.9 31.6 - - + +
19v ALA* 4.5 3.8 - - + -
36w ASN 4.3 13.9 - - - +
37w VAL* 3.5 12.1 - - + +
38w SER 3.0 0.8 - - - -
39w PRO* 1.3 79.0 - - + +
41w ALA* 1.3 67.6 + - - +
43w GLN* 3.1 10.3 + - + +
44w ASN* 3.1 32.3 + - - +
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Residues in contact with ALA 41 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517 A 3.9 4.4 - - - +
527 T 3.5 39.0 - - - +
37w VAL 2.9 17.7 + - - +
38w SER 3.4 3.8 - - - +
40w VAL* 1.3 75.9 - - - +
42w GLN* 1.3 57.8 + - - +
44w ASN* 3.1 2.4 + - - +
45w PHE* 2.8 31.7 + - - +
17x TRP* 4.2 14.6 - - + -
21x PHE* 4.5 9.4 - - + -
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Residues in contact with GLN 42 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38w SER* 2.9 21.3 + - - +
39w PRO* 3.5 29.8 - - - +
40w VAL 3.1 0.2 - - - -
41w ALA* 1.3 76.2 - - - +
43w GLN* 1.3 63.1 + - - +
45w PHE* 3.7 1.0 - - - +
46w GLN* 2.9 35.2 + - - +
14x TYR* 3.9 9.5 + - - +
17x TRP* 4.2 13.0 - - + -
18x GLN* 3.2 43.6 - - - +
21x PHE* 5.8 1.1 - - + -
22x ASN* 4.6 2.0 + - - -
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Residues in contact with GLN 43 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12v GLN* 5.3 7.4 - - + +
39w PRO 3.1 10.6 + - - +
40w VAL* 3.1 11.2 + - - +
42w GLN* 1.3 80.0 - - - +
44w ASN* 1.3 60.5 + - - +
46w GLN* 3.7 12.5 + - - +
47w THR* 2.6 60.6 + - - +
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Residues in contact with ASN 44 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517 A 3.6 24.1 - - - +
527 T 2.9 20.0 + - - -
8v ARG* 3.7 24.9 - - - +
12v GLN* 2.9 34.7 + - - +
16v LYS* 5.5 3.6 - - - +
40w VAL* 3.1 20.6 + - - +
41w ALA 3.1 7.9 + - - +
43w GLN* 1.3 77.6 - - - +
45w PHE* 1.3 65.5 + - - +
47w THR* 3.7 4.6 - - - -
48w ASN* 3.1 24.5 + - - +
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Residues in contact with PHE 45 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 T 4.5 10.8 - - - -
517 A 3.5 27.3 - - - -
3008 T 5.3 5.8 - - + -
41w ALA 2.8 15.5 + - - +
42w GLN 3.7 4.0 - - - +
44w ASN* 1.3 78.3 - - - +
46w GLN* 1.3 58.6 + - - +
49w VAL* 2.9 69.0 + - + +
10x TYR* 5.1 1.8 - + - -
13x ARG* 4.4 5.8 - - + -
14x TYR* 3.5 43.5 - + + -
17x TRP* 3.5 56.5 - + + -
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Residues in contact with GLN 46 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42w GLN* 2.9 27.6 + - - +
43w GLN* 3.8 13.1 + - - +
45w PHE* 1.3 80.2 - - - +
47w THR* 1.3 63.3 - - - +
50w PRO* 3.1 25.2 - - - +
10x TYR* 5.2 12.4 + - - +
14x TYR* 3.4 48.3 + - + -
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Residues in contact with THR 47 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12v GLN* 4.9 12.6 + - - +
43w GLN* 2.6 47.1 + - - +
44w ASN* 3.7 7.0 - - - -
46w GLN* 1.3 79.7 - - - +
48w ASN* 1.3 72.3 + - - +
50w PRO* 4.3 2.4 - - - +
51w LYS* 3.4 23.1 - - - +
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Residues in contact with ASN 48 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 T 3.8 17.2 + - - +
517 A 3.0 20.8 + - - -
7v SER* 4.5 8.3 + - - -
8v ARG* 3.8 13.1 - - - +
12v GLN* 5.5 4.0 - - - +
44w ASN* 3.1 10.6 + - - +
47w THR* 1.3 87.2 - - - +
49w VAL* 1.3 67.7 + - - +
50w PRO* 3.4 1.8 - - - -
51w LYS* 2.9 49.9 + - + +
52w PHE* 3.4 12.3 - - + -
88w ASN* 4.9 5.2 + - - -
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Residues in contact with VAL 49 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 T 3.6 33.4 - - + +
45w PHE* 2.9 57.9 + - + +
48w ASN* 1.3 73.6 - - - +
50w PRO* 1.3 63.7 - - + +
52w PHE* 2.9 26.7 + - + +
53w THR* 3.0 12.5 + - - +
10x TYR* 4.6 6.5 - - + -
13x ARG* 3.8 29.4 - - + +
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Residues in contact with PRO 50 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45w PHE 3.8 1.3 - - - +
46w GLN 3.1 24.7 - - - +
47w THR 4.2 2.9 - - - +
48w ASN 3.4 3.6 - - - +
49w VAL* 1.3 97.0 - - + +
51w LYS* 1.3 60.5 + - + +
53w THR* 3.8 1.2 - - - -
54w SER* 3.2 23.7 + - - -
10x TYR* 3.7 48.7 - - + -
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Residues in contact with LYS 51 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47w THR* 3.4 24.0 + - - +
48w ASN* 2.9 37.4 + - - +
49w VAL 3.0 0.4 - - - -
50w PRO* 1.3 78.8 - - + +
52w PHE* 1.3 63.8 + - + +
54w SER* 2.9 19.1 + - - -
55w VAL* 3.3 12.5 - - - +
84w ALA* 5.5 0.9 - - - +
88w ASN* 3.9 27.2 + - - +
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Residues in contact with PHE 52 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497 A 3.7 16.6 - - + +
507 T 3.4 40.4 - - - +
48w ASN* 3.4 19.5 - - + -
49w VAL* 2.9 8.0 + - - +
51w LYS* 1.3 77.0 - - + +
53w THR* 1.3 65.9 + - - +
54w SER 3.2 1.3 - - - -
55w VAL* 3.1 7.0 + - - +
56w ASN* 2.9 27.4 + - - +
81w LEU* 3.7 28.9 - - + +
84w ALA* 3.6 27.1 - - + -
85w ARG* 3.6 14.8 - - - -
88w ASN* 3.3 30.7 - - + -
13x ARG* 4.5 6.3 - - - +
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Residues in contact with THR 53 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49w VAL* 3.0 7.5 + - - +
50w PRO 3.4 6.0 + - - -
52w PHE* 1.3 77.6 - - - +
54w SER* 1.3 63.7 + - - +
56w ASN* 3.1 8.3 + - + +
57w GLU* 3.0 23.4 + - + +
8x ARG 4.7 4.5 - - - +
9x SER* 4.2 6.3 - - - -
10x TYR* 3.1 46.4 - - + +
13x ARG* 2.7 30.3 + - - +
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Residues in contact with SER 54 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50w PRO 3.2 10.7 + - - -
51w LYS* 2.9 21.7 + - - -
53w THR* 1.3 79.2 - - - +
55w VAL* 1.3 57.7 + - - +
57w GLU* 3.4 6.4 + - - +
58w ASN* 3.0 41.2 + - - -
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Residues in contact with VAL 55 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51w LYS 3.3 18.2 - - - +
52w PHE* 3.1 10.3 + - - +
54w SER* 1.3 77.5 + - - +
56w ASN* 1.3 61.2 + - - +
58w ASN* 3.3 3.3 + - - +
59w VAL* 2.8 52.1 + - + +
77w GLN* 5.2 0.7 - - - +
80w GLY 4.1 13.2 - - - +
81w LEU* 4.3 10.3 - - + +
84w ALA* 4.0 20.6 - - + -
125w ILE* 3.9 26.5 - - + -
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Residues in contact with ASN 56 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3018 A 4.8 4.0 + - - +
3028 T 4.1 34.7 + - - +
52w PHE* 2.9 18.5 + - - +
53w THR* 3.4 8.8 - - + +
55w VAL* 1.3 75.3 - - - +
57w GLU* 1.3 58.3 + - - +
60w SER* 2.9 30.3 + - - -
77w GLN* 3.1 21.0 + - - +
81w LEU* 3.3 29.9 - - - +
13x ARG* 4.0 22.8 - - - +
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Residues in contact with GLU 57 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53w THR* 3.0 14.0 + - + +
54w SER* 3.5 11.9 - - - +
55w VAL 3.1 0.2 - - - -
56w ASN* 1.3 75.1 - - - +
58w ASN* 1.3 74.5 + - - +
60w SER* 3.2 8.6 + - - -
61w ALA* 3.0 22.9 + - + +
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Residues in contact with ASN 58 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54w SER* 3.0 23.6 + - - +
55w VAL* 4.1 3.7 - - - +
57w GLU* 1.3 88.7 - - - +
59w VAL* 1.3 63.7 + - - +
61w ALA* 3.2 10.4 + - - +
62w VAL* 3.2 25.4 + - - +
124w ILE* 3.7 27.8 - - + +
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Residues in contact with VAL 59 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55w VAL* 2.8 37.5 + - + +
58w ASN* 1.3 74.3 - - + +
60w SER* 1.3 65.7 + - - +
62w VAL* 3.1 9.0 + - - +
63w LEU* 2.9 34.1 + - + +
76w TYR 4.3 1.1 - - - +
77w GLN* 3.3 32.1 - - - +
80w GLY* 4.7 2.0 - - - -
121w VAL* 4.0 39.0 - - + +
124w ILE* 5.5 3.1 - - + -
125w ILE* 4.4 6.7 - - + -
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Residues in contact with SER 60 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3028 T 4.9 0.2 - - - -
3038 A 3.4 9.9 + - - -
56w ASN 2.9 21.3 + - - -
57w GLU* 3.4 9.4 - - - -
59w VAL* 1.3 76.9 - - - +
61w ALA* 1.3 63.1 + - - +
63w LEU* 3.1 2.9 + - - -
64w THR* 3.0 13.1 + - - -
73w ARG* 2.7 41.6 + - - +
77w GLN* 3.4 12.5 - - - +
89y ARG 4.7 2.8 + - - -
90y ILE 4.7 3.3 + - - -
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Residues in contact with ALA 61 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57w GLU* 3.0 15.7 + - + +
58w ASN* 3.4 13.2 - - - +
59w VAL 3.2 0.2 - - - -
60w SER* 1.3 76.1 - - - +
62w VAL* 1.3 62.7 + - + +
64w THR* 3.2 7.1 + - - -
65w GLN* 3.1 31.8 + - - +
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Residues in contact with VAL 62 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58w ASN 3.2 13.0 + - - +
59w VAL* 3.1 12.3 + - + +
61w ALA* 1.3 77.9 - - + +
63w LEU* 1.3 69.0 + - + +
65w GLN* 2.9 23.5 + - - +
66w TYR* 3.0 39.2 + - + -
117w VAL* 5.3 0.9 - - + +
120w ALA* 4.0 16.6 - - + +
121w VAL* 4.8 7.2 - - + +
124w ILE* 3.6 32.3 - - + -
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Residues in contact with LEU 63 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59w VAL* 2.9 34.3 + - + +
60w SER* 3.5 6.7 - - - +
62w VAL* 1.3 78.9 - - + +
64w THR* 1.3 61.1 + - - +
66w TYR* 3.2 2.5 + - - +
67w GLY 3.0 4.3 + - - -
68w ILE* 2.9 43.1 + - + -
73w ARG* 3.5 48.7 - - + +
76w TYR* 3.6 34.1 - - + -
77w GLN* 4.0 10.3 - - + +
117w VAL* 4.1 11.0 - - + -
121w VAL* 5.1 1.3 - - + -
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Residues in contact with THR 64 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60w SER 3.0 5.4 + - - -
61w ALA* 3.6 10.9 - - - -
62w VAL 3.2 0.2 - - - -
63w LEU* 1.3 76.4 - - - +
65w GLN* 1.3 61.7 + - + +
67w GLY 3.1 9.7 + - - -
73w ARG* 3.0 21.2 + - - +
90y ILE* 2.6 34.4 + - + +
91y GLY* 3.8 7.0 - - - +
92y SER 3.3 28.3 - - - +
93y GLY* 4.6 1.3 - - - -
94y PRO* 3.3 5.2 - - + +
95y ALA* 3.3 19.1 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61w ALA* 3.1 18.2 + - - +
62w VAL* 2.9 17.4 + - - +
64w THR* 1.3 78.2 - - + +
66w TYR* 1.3 65.9 + - + +
67w GLY 3.3 0.2 - - - -
94y PRO* 3.4 23.3 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62w VAL* 3.0 35.9 + - + +
63w LEU* 3.2 7.5 + - - +
65w GLN* 1.3 83.7 - - + +
67w GLY* 1.3 62.9 + - - +
68w ILE* 3.2 21.7 + - + +
116w GLN* 2.9 42.3 + - - -
117w VAL* 4.1 15.7 - - + -
120w ALA* 3.5 28.5 - - + +
94y PRO* 4.6 1.3 - - - -
----------------------------------------------------------
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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