Contacts of the helix formed by residues 23 - 55 (chain L) in PDB entry 6XXD
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 23 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 5.1 1.9 - - - +
22L PRO* 1.3 73.3 - - - +
24L LEU* 1.3 61.7 + - - +
25L LEU* 3.4 4.3 + - - +
26L ALA* 2.9 36.2 + - + +
27L ALA* 3.5 19.4 + - - +
42O ASP* 5.2 2.8 + - - -
46O PHE* 3.7 20.4 - - + -
68O GLY* 2.8 34.6 + - - -
70O LYS* 4.8 6.9 - - - +
106P ASP* 3.1 37.2 + - - +
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Residues in contact with LEU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ILE* 4.0 19.5 - - + -
8I ILE* 3.4 35.4 - - + +
21L ILE* 5.4 4.7 - - + -
22L PRO* 3.2 20.2 + - + +
23L ASN* 1.3 70.3 - - - +
25L LEU* 1.3 66.4 + - - +
27L ALA* 3.2 4.6 + - - +
28L ARG* 3.1 28.1 + - + +
44P VAL* 3.5 21.1 - - + -
48P GLU* 3.8 18.2 - - + +
57P TYR* 5.5 0.2 - - - +
88P TYR* 3.5 24.5 - - - +
104P THR 5.4 0.7 - - - +
105P PRO* 3.1 20.0 + - + +
108P GLY* 6.2 0.7 - - - -
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ASN* 3.4 0.8 + - - -
24L LEU* 1.3 79.0 - - - +
26L ALA* 1.3 62.4 + - - +
28L ARG* 3.5 9.6 + - + +
29L LYS* 3.3 45.5 + - + +
96L GLY* 5.9 2.5 - - - +
57P TYR* 6.2 0.2 - - + -
86P ASN* 3.1 30.5 - - + +
87P SER* 4.9 6.1 - - - +
105P PRO* 3.7 17.8 + - + +
106P ASP* 3.8 39.5 - - + +
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Residues in contact with ALA 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ASN* 2.9 26.9 + - + +
25L LEU* 1.3 74.2 - - - +
27L ALA* 1.3 66.4 + - - +
29L LYS* 3.4 27.0 + - - +
30L ARG* 3.8 5.2 + - - +
46O PHE* 3.7 25.1 - - + -
49O MET* 3.8 22.0 - - + +
67O LEU 4.4 7.4 - - - +
68O GLY* 4.9 0.9 - - - -
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Residues in contact with ALA 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.4 26.7 - - + -
7A LEU* 5.6 7.4 - - + +
10A ILE* 5.2 3.6 - - - +
8I ILE* 4.2 15.5 - - + -
12I ILE* 4.8 4.7 - - + +
23L ASN 3.5 13.6 + - - +
24L LEU 3.2 9.5 + - - +
26L ALA* 1.3 79.5 - - - +
28L ARG* 1.3 61.1 + - - +
30L ARG* 3.8 6.3 + - - +
31L ALA* 3.6 16.8 + - - +
49O MET* 5.2 3.1 - - - -
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Residues in contact with ARG 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ILE* 3.7 19.4 - - + +
11I ALA* 4.1 15.6 - - - +
12I ILE* 4.2 8.6 - - + +
15I ILE* 3.4 29.9 - - - +
24L LEU 3.1 16.7 + - - +
25L LEU* 3.9 8.1 - - + +
26L ALA 3.3 0.2 - - - -
27L ALA* 1.3 76.0 - - - +
29L LYS* 1.3 54.5 + - - +
31L ALA* 3.2 8.3 + - - +
32L ASN* 2.7 53.0 + - - +
48P GLU* 3.0 23.5 + - - -
51P GLN* 3.5 37.9 + - - +
52P ILE* 5.6 0.8 - - - +
57P TYR* 3.6 22.9 - - - -
86P ASN* 6.3 1.1 - - - +
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Residues in contact with LYS 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L LEU* 3.3 45.1 + - + +
26L ALA* 3.4 16.3 + - - +
28L ARG* 1.3 78.3 - - - +
30L ARG* 1.3 59.6 + - + +
32L ASN* 3.4 3.7 + - - +
33L ASP* 3.1 33.8 + - - +
96L GLY* 3.6 22.9 - - - +
97L GLY* 3.6 18.1 - - - +
98L THR* 4.1 18.8 - - + +
49O MET* 5.8 1.1 - - + -
67O LEU 5.5 4.4 + - - +
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Residues in contact with ARG 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.3 20.6 - - + -
10A ILE* 3.5 20.9 - - + +
26L ALA 3.8 10.9 + - - +
27L ALA 3.8 6.1 + - - +
28L ARG 3.2 0.6 - - - -
29L LYS* 1.3 74.3 - - - +
31L ALA* 1.3 62.5 + - - +
33L ASP* 3.4 16.1 + - - +
34L THR* 2.9 26.0 + - - -
98L THR* 3.7 26.7 + - - +
111L LYS* 5.2 3.4 - - - +
49O MET* 3.5 39.7 + - + +
52O ILE* 4.3 20.9 - - + +
53O ASP* 2.7 41.7 + - - -
67O LEU* 4.2 10.9 - - - +
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Residues in contact with ALA 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 4.5 8.1 - - + +
12I ILE* 3.3 46.4 - - + -
15I ILE* 5.2 5.4 - - + -
16I LEU* 4.7 5.8 - - + +
27L ALA 3.6 7.1 + - - +
28L ARG 3.2 7.3 + - - +
30L ARG* 1.3 78.3 - - - +
32L ASN* 1.3 62.8 + - - +
34L THR* 3.3 11.1 + - - -
35L VAL* 3.2 25.1 + - - +
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Residues in contact with ASN 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ILE* 5.7 4.3 - - - +
28L ARG* 2.7 39.5 + - - +
29L LYS 3.5 5.6 - - - +
31L ALA* 1.3 72.9 - - - +
33L ASP* 1.3 64.4 + - - +
35L VAL* 3.4 8.6 + - - +
36L VAL* 3.2 26.5 + - - +
94L HIS* 3.2 43.4 + - + -
96L GLY 2.9 23.9 + - - +
97L GLY* 4.3 1.3 - - - -
86P ASN* 3.5 14.2 + - - +
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Residues in contact with ASP 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LYS 3.1 18.0 + - - +
30L ARG* 3.6 19.2 + - - +
31L ALA 3.3 0.4 - - - -
32L ASN* 1.3 73.2 - - - +
34L THR* 1.3 57.0 + - - +
36L VAL* 3.3 4.0 + - - +
37L THR* 2.7 40.0 + - - +
94L HIS* 5.5 0.7 - - - +
97L GLY* 3.8 3.8 - - - -
98L THR* 2.7 50.1 + - - +
99L VAL 4.7 0.5 - - - +
101L PHE* 3.8 27.5 - - + -
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Residues in contact with THR 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.2 20.4 + - + +
13A ILE* 4.3 20.6 - - + -
16I LEU* 4.4 19.3 - - + -
19I VAL* 4.8 1.6 - - + -
20I LEU* 3.8 24.5 - - + -
30L ARG 2.9 16.0 + - - -
31L ALA* 3.3 11.2 + - - -
33L ASP* 1.3 77.2 - - - +
35L VAL* 1.3 55.5 + - - +
37L THR* 3.8 5.7 - - - -
38L ALA* 2.8 32.6 + - - +
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Residues in contact with VAL 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE* 3.3 33.9 - - + -
16I LEU* 5.6 0.2 - - + -
19I VAL* 4.0 25.3 - - + +
31L ALA 3.2 11.6 + - - +
32L ASN* 3.6 13.0 - - - +
33L ASP 3.3 0.2 - - - -
34L THR* 1.3 77.2 - - - +
36L VAL* 1.3 57.3 + - - +
38L ALA* 3.9 1.0 - - - +
39L TYR* 3.0 28.6 + - - +
73L PRO* 3.9 29.8 - - + -
76L VAL* 4.3 10.3 - - + -
94L HIS* 4.6 7.2 - - + +
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ASN 3.2 14.4 + - - +
33L ASP* 3.7 7.9 - - - +
35L VAL* 1.3 76.0 - - - +
37L THR* 1.3 59.2 + - - +
39L TYR* 3.5 4.1 + - - +
40L LEU* 3.0 32.1 + - + +
76L VAL* 4.5 11.2 - - + -
92L ALA* 3.5 32.7 - - + +
93L GLY* 3.7 3.4 - - - +
94L HIS* 3.4 35.9 - - + +
101L PHE* 3.6 26.7 - - + -
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Residues in contact with THR 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 6.1 3.4 - - + -
14A ALA* 5.6 8.1 - - - +
17A ALA* 4.0 26.7 - - + -
33L ASP* 2.7 28.5 + - - +
34L THR* 4.0 6.7 - - - -
36L VAL* 1.3 75.1 - - - +
38L ALA* 1.3 55.7 + - - +
40L LEU* 3.8 1.8 - - - +
41L ASN* 2.9 30.9 + - + +
101L PHE* 3.3 23.2 - - + -
109L VAL* 4.3 22.5 - - + +
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Residues in contact with ALA 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I VAL* 3.9 33.2 - - + +
20I LEU* 4.0 14.6 - - + -
34L THR 2.8 20.5 + - - +
35L VAL 3.9 3.1 - - - +
37L THR* 1.3 76.6 - - - +
39L TYR* 1.3 57.6 + - - +
41L ASN* 3.3 7.9 + - - +
42L ASP* 2.8 36.1 + - - +
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Residues in contact with TYR 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I VAL* 5.7 0.6 - - - +
35L VAL 3.0 19.0 + - - +
36L VAL* 4.0 4.9 - - - +
37L THR 3.4 0.2 - - - -
38L ALA* 1.3 73.4 - - - +
40L LEU* 1.3 57.1 + - + +
42L ASP* 3.4 8.8 + - - +
43L ALA* 2.8 33.4 + - - +
61L GLN* 3.1 21.0 + - - -
69L LEU* 3.8 24.3 - - + +
70L LYS* 2.9 29.1 + - + -
71L SER 3.4 19.5 - - - -
72L THR* 3.5 6.9 + - - -
73L PRO* 3.7 26.2 - - + -
76L VAL* 5.4 3.6 - - + -
78L PHE* 3.6 44.6 - + + -
92L ALA* 5.7 1.1 - - + -
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Residues in contact with LEU 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L VAL* 3.0 24.7 + - + +
37L THR 3.9 0.2 - - - +
39L TYR* 1.3 73.2 - - - +
41L ASN* 1.3 60.7 + - - +
43L ALA* 3.3 3.8 + - - +
44L VAL* 2.9 34.3 + - - +
78L PHE* 3.9 17.9 - - + -
90L MET* 3.8 21.2 - - + +
92L ALA* 3.6 22.4 - - + -
101L PHE* 3.3 43.5 - - + +
102L ALA 3.9 1.3 - - - +
103L ALA* 3.8 8.7 - - + -
109L VAL* 3.8 25.8 - - + -
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Residues in contact with ASN 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 5.8 7.0 - - + +
21A ILE* 3.8 29.7 - - - +
4F ILE* 5.0 3.6 - - - +
5G GLU* 5.9 1.0 + - - -
37L THR* 2.9 21.5 + - + +
38L ALA* 3.5 8.7 + - - +
40L LEU* 1.3 75.9 - - - +
42L ASP* 1.3 62.8 + - - +
44L VAL* 3.7 6.0 + - - +
45L LYS* 3.5 47.3 + - - +
109L VAL* 4.0 11.5 - - + +
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Residues in contact with ASP 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I VAL 3.7 17.6 - - - +
20I LEU 6.1 0.2 - - - -
21I ILE 5.3 0.9 - - - +
22I PRO* 4.5 15.2 - - - +
23I ASN 5.2 1.4 + - - -
38L ALA* 2.8 23.9 + - - +
39L TYR* 3.6 10.4 - - + +
41L ASN* 1.3 75.7 + - - +
43L ALA* 1.3 63.2 + - - +
45L LYS* 3.2 34.5 + - - +
46L PHE* 3.2 24.8 + - + -
69L LEU* 3.7 18.8 - - + -
70L LYS* 5.4 5.6 + - - -
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Residues in contact with ALA 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L TYR* 2.8 21.7 + - + +
40L LEU* 3.3 9.4 + - - +
42L ASP* 1.3 73.8 - - - +
44L VAL* 1.3 56.9 + - - +
46L PHE* 3.6 2.0 + - - +
47L GLN* 3.1 33.1 + - - +
64L LEU* 4.5 2.6 - - + +
69L LEU* 4.0 18.3 - - + +
78L PHE* 3.9 21.5 - - + -
90L MET* 3.5 19.3 - - + -
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Residues in contact with VAL 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.6 7.0 - - + -
24A LEU* 3.5 20.6 - - + -
4F ILE* 4.1 12.3 - - + -
40L LEU 2.9 21.4 + - - +
41L ASN* 3.8 9.4 - - - +
42L ASP 3.3 0.2 - - - -
43L ALA* 1.3 74.3 - - - +
45L LYS* 1.3 62.6 + - - +
47L GLN* 3.5 5.9 + - - +
48L GLU* 3.2 22.2 + - - +
88L TYR* 3.4 25.3 + - + +
90L MET* 4.0 14.6 - - + -
103L ALA* 4.3 6.3 - - + -
104L THR 5.3 2.0 - - - +
108L GLY* 5.6 1.3 - - - -
109L VAL* 3.9 20.6 - - + +
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Residues in contact with LYS 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 4.1 38.7 - - + +
4F ILE* 3.8 30.5 - - + +
7F LEU* 3.4 24.6 - - + +
5G GLU* 4.5 8.7 - - - +
22I PRO* 4.2 11.0 - - + +
41L ASN* 3.5 40.7 + - - +
42L ASP* 3.2 25.9 + - - +
44L VAL* 1.3 77.4 - - - +
46L PHE* 1.3 63.7 + - + +
48L GLU* 3.1 3.6 + - - +
49L MET* 3.0 24.6 + - - +
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Residues in contact with PHE 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ASN* 3.7 28.7 - - + -
26I ALA* 3.7 10.1 - - + -
42L ASP* 3.2 28.1 + - + +
43L ALA 4.3 2.0 - - - +
45L LYS* 1.3 80.9 - - + +
47L GLN* 1.3 60.1 + - - +
49L MET* 3.5 28.1 - - - +
50L TYR* 3.2 21.5 + - - +
64L LEU* 3.4 28.3 - - + +
67L LEU* 3.9 20.0 - - + +
68L GLY* 3.3 24.0 - - - -
69L LEU* 3.3 43.3 - - + -
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Residues in contact with GLN 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ALA 3.1 24.1 + - - +
44L VAL* 3.6 8.3 - - - +
45L LYS 3.2 0.2 - - - -
46L PHE* 1.3 76.8 - - - +
48L GLU* 1.3 57.8 + - - +
50L TYR* 3.5 3.9 + - - +
51L GLN* 3.1 25.6 + - - +
57L TYR* 3.5 30.1 - - + -
58L THR* 2.9 52.0 + - - +
64L LEU* 3.8 6.5 - - + +
80L ILE* 4.3 3.4 - - - +
88L TYR* 4.0 22.2 - - + +
90L MET* 3.4 32.9 - - + +
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Residues in contact with GLU 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.8 21.7 - - + +
28A ARG* 3.0 28.2 + - - -
4F ILE* 3.7 21.8 - - + -
7F LEU* 4.6 8.7 - - + +
8F ILE* 3.5 23.8 - - + +
11F ALA* 4.8 1.9 - - + +
44L VAL 3.2 13.0 + - - +
45L LYS 3.1 9.2 + - - +
47L GLN* 1.3 75.4 - - - +
49L MET* 1.3 62.2 + - - +
51L GLN* 3.4 6.1 + - - +
52L ILE* 3.2 28.6 + - + +
57L TYR* 3.0 28.2 + - + -
88L TYR* 4.5 2.4 - - - -
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Residues in contact with MET 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LEU* 4.0 26.9 - - + -
26I ALA* 3.8 36.1 - - + +
27I ALA* 5.3 1.6 - - - -
29I LYS* 5.9 1.6 - - + -
30I ARG* 3.5 31.8 + - + +
45L LYS* 3.0 17.0 + - - +
46L PHE* 3.5 33.4 - - + +
47L GLN 3.3 0.4 - - - -
48L GLU* 1.3 74.8 - - - +
50L TYR* 1.3 60.4 + - - +
52L ILE* 3.4 10.2 + - + +
53L ASP* 3.2 28.4 + - - +
67L LEU* 3.6 19.3 - - + +
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Residues in contact with TYR 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L PHE 3.2 17.0 + - - +
47L GLN* 3.7 7.0 - - - +
48L GLU 3.4 0.4 - - - -
49L MET* 1.3 74.1 - - - +
51L GLN* 1.3 59.7 + - - +
53L ASP* 4.5 2.5 - - - +
54L ASN* 2.8 70.2 + - + +
56L SER* 3.5 21.3 - - - +
57L TYR 4.8 1.8 - - - -
58L THR* 3.3 37.0 - - + -
63L ALA* 3.8 17.9 - - + +
64L LEU* 4.7 0.9 - - + -
67L LEU* 3.4 27.3 - - + +
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Residues in contact with GLN 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.4 40.8 + - - +
75A ASN* 4.7 3.0 - - - +
15F ILE* 6.1 0.3 - - - +
47L GLN 3.1 14.1 + - - +
48L GLU* 3.4 14.6 - - - +
49L MET 3.3 0.2 - - - -
50L TYR* 1.3 75.0 - - - +
52L ILE* 1.3 62.5 + - - +
55L ASN* 3.2 53.5 + - - +
56L SER 3.0 27.0 + - - +
57L TYR* 3.2 26.8 - - + +
85L ALA 3.4 9.1 + - - +
86L ASN* 5.6 3.6 - - - +
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Residues in contact with ILE 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 5.6 1.6 - - - +
7F LEU* 4.5 13.2 - - + +
10F ILE* 5.1 1.8 - - + -
11F ALA* 3.2 44.0 - - + +
14F ALA* 4.9 16.4 - - + -
15F ILE* 6.4 2.0 - - - -
30I ARG* 4.3 26.2 - - + +
111I LYS* 3.7 15.0 + - - +
48L GLU 3.2 15.0 + - - +
49L MET* 3.5 15.0 - - - +
50L TYR 3.3 0.4 - - - -
51L GLN* 1.3 77.8 - - - +
53L ASP* 1.3 69.9 + - - +
55L ASN* 4.0 8.6 + - - +
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Residues in contact with ASP 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ARG* 2.7 38.6 + - - -
111I LYS* 3.9 18.1 + - - +
49L MET 3.2 12.3 + - - +
50L TYR* 3.3 4.9 + - - +
52L ILE* 1.3 82.8 - - - +
54L ASN* 1.3 77.6 + - - +
55L ASN* 3.6 5.1 + - - +
67L LEU* 4.6 10.2 - - - +
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Residues in contact with ASN 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 5.4 0.3 - - - +
50L TYR* 2.8 63.2 + - + +
53L ASP* 1.3 88.6 + - - +
55L ASN* 1.3 73.4 + - - +
56L SER* 4.3 6.7 - - - +
67L LEU* 5.7 0.2 - - - +
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Residues in contact with ASN 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.3 32.4 - - + +
75A ASN* 2.7 33.3 + - - +
15F ILE* 5.7 7.3 - - - +
50L TYR 3.9 0.2 + - - -
51L GLN* 3.2 33.6 + - - +
52L ILE* 4.0 11.1 + - - +
53L ASP 4.5 3.9 + - - +
54L ASN* 1.3 81.4 - - - +
56L SER* 1.3 59.7 + - - +
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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