Contacts of the helix formed by residues 7 - 43 (chain B) in PDB entry 2VRZ
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 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LYS 3.5 3.4 + - - -
6B MSE 1.3 75.7 - - - +
8B PRO* 1.3 71.0 - - - +
9B GLU* 3.2 22.7 + - - +
10B GLU* 3.0 23.3 + - - +
11B ILE* 2.9 21.6 + - - +
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Residues in contact with PRO 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 1.3 81.6 - - - +
9B GLU* 1.3 71.0 + - - +
11B ILE* 3.3 4.4 + - + -
12B ARG* 3.0 33.1 + - - +
80B ALA* 3.6 28.5 - - + +
83B VAL* 3.8 28.3 - - + -
84B GLN* 3.5 35.7 - - + +
87B ASP* 4.4 8.3 - - - +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.2 23.4 - - - +
8B PRO* 1.3 86.4 - - - +
10B GLU* 1.3 61.9 + - - +
12B ARG* 3.7 7.3 + - - +
13B ALA* 3.3 21.0 + - - +
84B GLN* 4.4 12.2 + - - +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.4 1.9 - - - +
6B MSE 3.8 23.3 - - + +
7B SER* 3.0 18.4 + - - +
9B GLU* 1.3 79.1 - - - +
11B ILE* 1.3 60.4 + - - +
13B ALA* 3.2 6.8 + - + +
14B LYS* 2.9 42.9 + - - +
1090B ZN 2.0 37.6 - - - -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.6 32.1 - - + -
6B MSE 3.6 31.9 - - + +
7B SER 2.9 24.6 + - - +
8B PRO* 3.3 10.1 + - + +
10B GLU* 1.3 75.5 - - - +
12B ARG* 1.3 57.7 + - - +
14B LYS* 3.2 4.4 + - - +
15B SER* 2.9 28.2 + - - -
76B LEU* 3.3 48.2 - - + +
79B THR* 5.0 1.1 - - - -
80B ALA* 3.8 14.1 - - + +
83B VAL* 4.6 8.7 - - + -
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO 3.0 17.6 + - - +
9B GLU* 3.8 7.4 - - - +
11B ILE* 1.3 74.4 - - - +
13B ALA* 1.3 62.0 + - - +
15B SER* 3.3 15.2 - - - -
16B GLN* 3.4 8.5 + - - +
77B ASN* 3.7 30.3 + - - +
80B ALA* 3.4 32.3 + - + +
81B ASP* 3.4 17.1 - - - +
84B GLN* 2.9 42.7 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU 3.3 11.6 + - - +
10B GLU* 3.2 12.0 + - + +
12B ARG* 1.3 77.3 - - - +
14B LYS* 1.3 65.2 + - - +
16B GLN* 3.2 25.4 + - - +
17B SER* 3.6 5.5 + - - -
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 5.8 0.2 - - - -
35A ALA* 4.6 23.6 - - + +
38A GLU* 2.7 31.1 + - + +
39A ILE* 4.5 16.8 - - + -
6B MSE 3.7 20.0 - - + -
10B GLU* 2.9 28.5 + - - +
11B ILE* 3.2 4.2 + - - +
13B ALA* 1.3 77.2 - - - +
15B SER* 1.3 61.4 + - - +
17B SER* 2.5 31.6 + - - +
18B TYR* 3.3 10.4 - - + -
76B LEU* 4.5 2.9 - - + -
1090B ZN 3.7 1.8 - - - -
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE 2.9 13.6 + - - -
12B ARG 3.3 12.3 - - - -
14B LYS* 1.3 75.2 - - - +
16B GLN* 1.3 58.0 - - - +
18B TYR* 3.2 2.9 - - - -
19B GLY 3.0 22.7 - - - -
73B LYS* 2.6 52.4 + - - +
76B LEU* 4.0 16.3 - - - +
77B ASN* 3.2 18.1 + - - -
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG 3.4 6.8 + - - +
13B ALA* 3.2 17.3 + - - +
14B LYS 3.2 0.8 - - - -
15B SER* 1.3 78.8 + - - +
17B SER* 1.3 57.3 + - - +
19B GLY* 3.2 2.8 + - - +
20B GLN* 2.9 51.3 + - + +
73B LYS* 5.2 4.9 - - - +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 6.4 0.9 - - - -
32A LEU* 3.5 23.2 - - - +
35A ALA* 4.9 1.9 - - - +
13B ALA 3.6 5.4 + - - -
14B LYS* 2.5 29.7 + - - +
16B GLN* 1.3 76.5 - - - +
18B TYR* 1.3 67.1 + - - +
20B GLN* 3.5 12.6 + - - +
21B GLY* 3.0 21.1 - - - -
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Residues in contact with TYR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.1 18.6 - - + -
35A ALA* 3.3 23.2 + - + +
36A GLN* 2.6 53.9 + - + +
39A ILE* 3.7 7.1 - - + +
55A PHE* 4.6 0.4 - + - -
14B LYS* 3.3 23.3 + - + -
15B SER 3.2 7.2 - - - -
17B SER* 1.3 83.5 + - - +
19B GLY* 1.3 56.7 + - - +
21B GLY* 3.4 0.7 + - - -
22B SER* 3.0 28.9 + - - -
69B LEU* 3.6 41.2 - - + +
72B ILE* 3.7 26.9 - - + -
73B LYS* 4.0 5.8 - - + +
76B LEU* 3.9 20.6 - - + -
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER 3.0 11.7 - - - -
16B GLN 3.2 4.0 + - - -
18B TYR* 1.3 75.9 - - - +
20B GLN* 1.3 62.3 + - - +
22B SER* 3.4 4.0 + - - -
23B ASP* 3.1 31.0 + - - +
69B LEU 5.3 0.2 - - - -
70B GLU* 4.0 9.0 - - - +
73B LYS* 3.8 28.4 - - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 2.9 47.9 + - + +
17B SER* 3.9 10.3 + - - +
19B GLY* 1.3 74.1 - - - +
21B GLY* 1.3 60.2 + - - +
23B ASP* 3.4 8.5 + - - +
24B GLN* 2.9 50.7 + - - +
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.9 28.3 - - - +
32A LEU* 4.4 2.9 - - - -
17B SER 3.0 16.5 - - - -
18B TYR 3.7 2.2 - - - -
20B GLN* 1.3 73.9 - - - +
22B SER* 1.3 63.4 + - - +
24B GLN* 5.2 0.2 - - - -
25B ILE* 3.1 29.6 + - - +
69B LEU* 3.8 7.2 - - - -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR 3.0 14.1 + - - -
19B GLY 3.5 9.4 - - - -
21B GLY* 1.3 75.9 - - - +
23B ASP* 1.3 64.6 + - - +
25B ILE* 3.4 1.6 + - - +
26B ARG* 3.1 46.4 + - - +
66B ALA* 2.7 30.4 + - - +
69B LEU* 3.7 13.9 - - - +
70B GLU* 3.7 15.8 + - - +
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Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.1 19.7 + - - +
20B GLN* 3.7 8.7 - - - +
22B SER* 1.3 82.6 + - - +
24B GLN* 1.3 60.8 + - + +
26B ARG* 3.4 11.2 + - - +
27B GLN* 3.0 29.2 + - - +
70B GLU* 5.1 3.9 - - - +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 5.4 10.3 - - - +
28A ILE* 3.4 30.7 - - + +
20B GLN* 2.9 34.7 + - - +
21B GLY* 5.2 0.2 - - - -
23B ASP* 1.3 79.3 - - + +
25B ILE* 1.3 60.0 + - - +
27B GLN* 3.3 7.2 + - - +
28B ILE* 3.0 40.9 + - + +
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.5 17.1 - - + +
28A ILE* 3.9 24.0 - - + -
29A LEU* 6.5 0.4 - - + -
62A VAL* 4.9 7.9 - - + -
21B GLY 3.1 18.6 + - - +
22B SER 3.9 2.7 - - - +
24B GLN* 1.3 73.7 - - - +
26B ARG* 1.3 59.3 + - - +
28B ILE* 3.4 8.3 + - - +
29B LEU* 2.9 30.1 + - + +
62B VAL* 3.4 40.8 - - + +
65B PHE* 3.8 31.9 - - + -
66B ALA* 4.1 7.6 - - + -
69B LEU* 3.9 8.3 - - + -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.1 36.3 + - - +
23B ASP* 3.6 11.2 + - - +
25B ILE* 1.3 76.8 - - - +
27B GLN* 1.3 56.2 + - - +
29B LEU* 3.5 6.8 + - - +
30B SER* 2.9 32.8 + - - -
63B GLU* 2.8 38.1 + - - +
66B ALA* 3.6 13.2 + - + +
67B GLN* 2.8 47.8 - - - +
70B GLU* 4.6 7.9 - - - +
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP 3.0 17.3 + - - +
24B GLN* 3.6 7.4 - - - +
26B ARG* 1.3 73.2 - - - +
28B ILE* 1.3 61.6 + - + +
30B SER* 3.3 6.7 + - - -
31B ASP* 2.9 52.4 + - - +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 3.9 13.2 - - - +
24A GLN* 3.4 43.5 - - + +
25A ILE* 3.8 33.7 - - + +
28A ILE* 5.0 1.6 - - + -
65A PHE* 5.1 1.1 - - + -
69A LEU* 4.3 1.1 - - + -
24B GLN* 3.0 28.2 + - + +
25B ILE* 3.7 4.3 - - - +
27B GLN* 1.3 74.8 - - + +
29B LEU* 1.3 61.2 + - - +
31B ASP* 3.4 5.1 + - - -
32B LEU* 2.8 56.3 + - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.7 30.5 - - + -
25B ILE* 2.9 18.5 + - + +
26B ARG* 3.7 7.2 - - - +
28B ILE* 1.3 76.8 - - - +
30B SER* 1.3 55.9 + - - +
32B LEU* 3.8 1.7 - - - -
33B THR* 2.6 46.0 + - - +
55B PHE* 4.3 2.7 - - + -
59B SER* 3.8 40.8 - - - +
62B VAL* 4.4 8.5 - - + -
63B GLU* 3.9 30.7 - - + +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG 2.9 18.9 + - - -
27B GLN* 3.5 10.5 - - - -
28B ILE 3.2 0.2 - - - -
29B LEU* 1.3 74.1 - - - +
31B ASP* 1.3 71.1 - - - +
33B THR* 3.8 5.1 - - - -
34B ARG* 3.2 27.6 - - - +
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 6.4 1.1 - - - -
27B GLN* 2.9 41.2 + - - +
28B ILE* 3.9 4.9 - - - +
30B SER* 1.3 76.2 + - - +
32B LEU* 1.3 64.9 + - + +
34B ARG* 2.9 51.2 + - - +
35B ALA* 3.1 12.6 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.4 47.1 - - - +
18A TYR* 3.7 26.4 + - + +
21A GLY* 4.4 0.2 - - - -
65A PHE* 5.6 0.7 - - + -
69A LEU* 3.6 37.7 - - + -
28B ILE* 2.8 34.7 + - + +
29B LEU* 5.1 0.4 - - - -
31B ASP* 1.3 77.3 - - + +
33B THR* 1.3 60.5 + - - +
35B ALA* 3.7 5.7 - - + +
36B GLN* 2.9 32.9 + - - +
55B PHE* 3.9 12.6 - - + -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.6 33.3 + - - +
30B SER* 3.8 6.3 - - - -
32B LEU* 1.3 76.7 - - - +
34B ARG* 1.3 62.8 + - + +
36B GLN* 3.3 4.0 + - + +
37B GLY* 3.1 19.9 + - - -
55B PHE* 3.6 23.3 - - + -
59B SER* 5.4 1.2 - - - -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 3.2 12.9 - - - +
31B ASP* 2.9 50.7 + - - +
33B THR* 1.3 79.5 - - + +
35B ALA* 1.3 61.2 + - - +
37B GLY* 3.3 3.0 + - - -
38B GLU* 3.1 23.2 + - - +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 3.8 31.9 - - + +
17A SER* 5.1 1.1 - - - +
18A TYR* 3.6 22.2 - - + +
31B ASP 3.1 12.6 + - - +
32B LEU* 3.7 12.6 - - + +
34B ARG* 1.3 77.4 - - - +
36B GLN* 1.3 63.4 + - - +
38B GLU* 3.2 2.8 + - - +
39B ILE* 3.0 29.2 + - - +
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 2.5 36.1 + - - -
72A ILE* 3.5 6.2 - - - +
32B LEU 2.9 25.7 + - - +
33B THR* 3.3 7.4 + - + +
35B ALA* 1.3 72.0 - - - +
37B GLY* 1.3 64.1 + - - +
39B ILE* 3.9 2.7 - - - +
40B ALA* 3.0 27.7 + - - +
48B PHE* 3.3 34.7 - - - -
51B PHE 4.1 1.7 - - - +
52B GLU* 3.9 13.6 - - + +
55B PHE* 3.5 47.6 - - + +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR 3.1 10.6 + - - -
34B ARG* 3.8 3.6 - - - -
35B ALA 3.3 0.4 - - - -
36B GLN* 1.3 80.5 - - - +
38B GLU* 1.3 56.3 + - - +
40B ALA* 3.9 4.1 - - - +
41B ALA* 3.0 31.6 + - - +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MSE 4.9 3.1 - - + +
10A GLU* 3.6 5.3 - - - +
14A LYS* 3.0 28.9 + - - -
1097A ZN 1.9 33.8 - - - -
34B ARG 3.1 15.7 + - - +
35B ALA* 3.2 4.1 + - - +
37B GLY* 1.3 73.2 - - - +
39B ILE* 1.3 64.2 + - - +
41B ALA* 3.4 5.2 + - - +
42B ASN* 3.0 43.6 + - - +
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.7 0.6 - - + +
6A MSE 3.6 28.5 - - + +
14A LYS* 4.3 14.6 - - + -
18A TYR* 3.8 22.0 - - + +
76A LEU* 3.8 32.5 - - + -
35B ALA 3.0 21.9 + - - +
36B GLN 3.9 2.5 - - - +
38B GLU* 1.3 72.9 - - - +
40B ALA* 1.3 67.3 + - - +
42B ASN* 3.2 5.0 + - - +
43B TRP* 3.2 50.6 + - + +
48B PHE* 3.7 18.6 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN 3.0 19.3 + - - +
37B GLY* 3.9 5.2 - - - +
39B ILE* 1.3 77.6 - - - +
41B ALA* 1.3 61.5 + - - +
42B ASN 3.4 0.5 + - - -
43B TRP* 3.5 20.0 + - - +
48B PHE* 4.3 8.1 - - + -
52B GLU* 3.4 36.2 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 4.7 8.1 + - - -
37B GLY 3.0 19.8 + - - +
38B GLU* 3.7 7.0 - - - +
39B ILE 3.2 0.6 - - - -
40B ALA* 1.3 76.7 - - - +
42B ASN* 1.3 62.1 + - - +
43B TRP 3.5 0.8 - - - +
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MSE 3.8 1.2 - - - +
4A ILE* 3.5 2.1 - - + -
5A LYS* 2.7 79.1 + - - +
6A MSE 4.1 13.2 - - + +
38B GLU* 3.0 36.7 + - - +
39B ILE 3.2 4.8 + - - +
41B ALA* 1.3 83.5 - - - +
43B TRP* 1.3 55.4 + - - +
44B GLU* 5.6 0.2 - - - -
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Residues in contact with TRP 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.9 5.9 - - + +
2A ALA* 4.1 10.3 + - - +
3A MSE 3.6 10.3 - - - -
4A ILE* 3.7 24.4 - - + +
75A GLN* 4.2 15.3 - - + -
76A LEU* 4.2 9.2 - - + -
79A THR* 3.3 35.9 - - + -
39B ILE* 3.2 31.3 + - + +
40B ALA* 3.5 15.1 + - - +
41B ALA 3.5 1.0 - - - -
42B ASN* 1.3 76.5 - - - +
44B GLU* 1.3 86.3 + - - +
45B GLY 3.8 7.6 - - - +
47B ALA* 3.7 31.5 - - + +
48B PHE* 3.4 42.6 - + + -
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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