Contacts of the helix formed by residues 56 - 85 (chain D) in PDB entry 5MEP
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 GLY 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLN 3.5 3.6 + - - -
55D GLU* 1.3 79.3 - - - +
57D PRO* 1.3 70.1 - - - +
58D GLU* 3.2 5.6 - - - -
59D TYR* 2.9 28.1 + - - +
60D TRP* 3.4 6.3 + - - -
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Residues in contact with PRO 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 6.0 0.2 - - - +
56D GLY* 1.3 83.8 - - - +
58D GLU* 1.3 59.4 + - + +
60D TRP* 3.3 9.9 + - + +
61D ASP* 2.9 41.0 + - - +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLY* 3.2 3.3 + - - -
57D PRO* 1.3 82.0 - - + +
59D TYR* 1.3 58.5 + - - +
61D ASP* 3.4 7.3 + - - +
62D GLY* 2.8 27.0 + - - -
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Residues in contact with TYR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 4.7 0.7 + - - -
33D PHE* 4.1 7.4 - - - -
34D VAL* 5.1 3.7 - - + +
52D ILE* 3.7 16.4 - - + +
55D GLU* 3.5 29.6 - - + -
56D GLY 2.9 16.1 + - - +
58D GLU* 1.3 79.0 - - - +
60D TRP* 1.3 93.4 + + - -
62D GLY* 3.2 1.9 + - - -
63D GLU* 2.8 63.1 + - + +
167D TRP* 3.9 24.0 - + - -
171D TYR* 2.7 28.9 + - - -
1F ILE* 4.3 6.2 + - + -
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Residues in contact with TRP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D VAL* 3.7 22.7 - - + -
44D ARG* 3.4 19.1 - - - +
45D MET* 3.4 30.1 - - + +
47D PRO* 3.6 44.9 - - + -
52D ILE* 3.5 36.5 + - + -
53D GLU* 4.6 5.1 + - - +
55D GLU 3.2 20.6 + - - -
56D GLY 3.4 16.8 + - - -
57D PRO* 3.3 8.5 + - + +
59D TYR* 1.3 86.4 - + - +
61D ASP* 1.3 64.8 + - - +
63D GLU* 4.0 1.0 - - + +
64D THR* 2.9 31.7 + - - -
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Residues in contact with ASP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 2.9 25.5 + - - +
57D PRO* 2.9 25.5 + - - +
58D GLU* 3.6 7.6 - - - +
60D TRP* 1.3 76.9 - - - +
62D GLY* 1.3 63.2 + - - +
64D THR* 3.8 0.6 - - - -
65D ARG* 3.0 50.4 + - - +
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Residues in contact with GLY 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLU 2.8 19.1 + - - -
59D TYR* 3.6 2.7 - - - -
61D ASP* 1.3 72.4 - - - +
63D GLU* 1.3 63.3 + - - +
65D ARG* 3.1 8.9 + - - +
66D LYS* 3.1 35.3 + - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 4.3 2.4 + - - -
34D VAL* 6.1 0.4 - - + -
45D MET* 3.9 24.8 - - + +
59D TYR* 2.8 47.6 + - + +
60D TRP* 4.0 3.6 - - - +
62D GLY* 1.3 77.0 - - - +
64D THR* 1.3 58.1 + - - +
66D LYS* 2.7 33.4 + - - +
67D VAL* 2.8 32.7 + - - +
1F ILE* 3.4 20.1 - - - +
2F LEU* 3.0 37.6 + - - +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D PHE* 5.2 0.4 - - + -
43D GLN 3.8 23.3 - - - +
44D ARG* 3.8 18.0 - - - +
45D MET* 3.0 22.2 + - - +
60D TRP 2.9 21.5 + - - -
61D ASP 3.8 3.4 - - - -
63D GLU* 1.3 73.2 - - - +
65D ARG* 1.3 86.3 + - - +
67D VAL* 3.5 9.5 - - + +
68D LYS* 3.2 34.5 + - + +
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASP* 4.2 23.7 + - - +
225A THR* 5.6 8.8 - - - +
44D ARG* 4.1 9.7 - - - +
61D ASP* 3.0 50.9 + - - +
62D GLY* 3.1 11.9 + - - +
64D THR* 1.3 101.4 - - - +
66D LYS* 1.3 62.3 + - + +
68D LYS* 3.5 8.4 + - - +
69D ALA* 3.1 24.8 + - - +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLY* 3.1 18.9 + - - +
63D GLU* 2.7 36.4 + - - +
65D ARG* 1.3 80.8 - - + +
67D VAL* 1.3 66.5 + - - +
69D ALA* 3.1 7.4 + - + +
70D HIS* 2.9 30.4 + - + -
1F ILE* 3.8 10.5 - - - +
2F LEU* 2.9 33.4 + - + +
3F GLY 3.8 19.5 - - - +
4F LYS* 4.1 26.0 - - + +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 4.7 6.3 - - + -
22D PHE* 3.7 10.0 - - + -
24D ALA* 4.0 27.1 - - + -
36D PHE* 4.1 32.1 - - + -
45D MET* 3.6 28.5 - - + -
63D GLU 2.8 25.7 + - - +
64D THR* 3.5 14.8 - - - +
66D LYS* 1.3 71.4 - - - +
68D LYS* 1.3 65.1 + - - +
70D HIS* 3.2 7.9 + - - +
71D SER 3.0 17.8 + - - -
2F LEU* 3.8 9.6 - - + +
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLN* 5.5 0.6 + - - -
223A ASP* 2.2 35.6 + - + +
36D PHE* 4.3 15.9 - - + -
43D GLN* 3.4 45.4 + - - +
64D THR* 3.2 28.2 + - + +
65D ARG* 3.6 7.8 - - - +
66D LYS 3.2 0.6 - - - -
67D VAL* 1.3 80.2 - - - +
69D ALA* 1.3 61.6 + - - +
71D SER* 2.7 25.5 + - - +
72D GLN* 3.0 14.2 + - + +
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG 3.1 14.4 + - - +
66D LYS* 3.1 13.5 + - + +
68D LYS* 1.3 75.9 - - - +
70D HIS* 1.3 65.5 + - + +
72D GLN* 3.0 19.0 + - - +
73D THR* 3.0 19.5 + - + +
5F PHE 5.0 6.3 - - - +
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Residues in contact with HIS 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.3 25.4 - + + -
22D PHE* 4.2 12.1 - - + -
66D LYS* 2.9 29.2 + - - -
67D VAL* 3.3 11.0 - - - +
69D ALA* 1.3 77.8 - - + +
71D SER* 1.3 61.2 + - - +
73D THR* 2.8 24.2 + - - -
74D HIS* 3.1 15.1 + - + -
97D ARG* 4.3 17.8 + - - +
99D TYR* 2.8 37.9 - + - -
2F LEU* 4.4 6.2 - - + +
3F GLY 3.4 20.8 + - - -
5F PHE* 4.2 20.7 + + + +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 4.7 1.2 + - - -
19D GLU* 5.6 2.3 + - - -
22D PHE* 3.3 49.4 - - - -
36D PHE* 5.4 3.1 - - - -
38D SER* 6.1 0.7 - - - -
67D VAL 3.0 6.7 + - - -
68D LYS* 2.7 22.5 + - - +
70D HIS* 1.3 76.5 - - - +
72D GLN* 1.3 66.9 + - - +
74D HIS* 3.3 4.2 + - - +
75D ARG* 2.8 27.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 6.0 1.6 - - - -
19D GLU* 4.0 17.3 - - - +
68D LYS* 3.0 17.1 + - + +
69D ALA* 3.0 10.7 + - - +
71D SER* 1.3 87.0 + - - +
73D THR* 1.3 65.0 + - + +
75D ARG* 3.2 36.5 + - - +
76D VAL* 3.2 26.4 + - + +
8F TRP* 5.5 0.2 - - - -
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ALA* 3.0 12.6 + - + +
70D HIS* 2.8 19.1 + - - -
72D GLN* 1.3 75.9 - - + +
74D HIS* 1.3 50.0 + - - +
76D VAL* 3.0 5.2 + - - +
77D ASP* 2.7 39.7 + - - +
97D ARG* 2.9 21.2 + - - +
5F PHE 4.5 9.4 - - - +
6F LEU* 4.6 3.1 - - - -
7F HIS 3.4 37.5 - - - +
8F TRP* 4.2 22.8 - - + +
----------------------------------------------------------
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Residues in contact with HIS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.9 10.5 - - + +
11D SER* 3.2 36.8 - - - +
22D PHE* 4.1 13.5 - + - -
70D HIS* 3.1 10.6 + - + +
71D SER* 3.5 7.0 - - - +
73D THR* 1.3 79.8 + - - +
75D ARG* 1.3 66.6 + - - +
77D ASP* 3.6 12.7 + - - +
78D LEU* 3.0 28.9 + - - +
95D VAL* 4.1 20.5 - - + +
97D ARG* 3.2 52.1 + - + +
116D TYR* 3.7 16.6 - + - -
----------------------------------------------------------
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Residues in contact with ARG 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 4.8 0.4 + - - -
18D GLY* 3.4 27.4 + - - +
19D GLU* 3.3 27.8 + - - +
20D PRO* 3.9 27.4 - - + -
71D SER 2.8 17.9 + - - +
72D GLN* 3.2 36.4 + - - +
74D HIS* 1.3 73.9 - - - +
76D VAL* 1.3 65.5 + - + +
78D LEU* 3.3 4.6 + - - +
79D GLY* 3.6 2.1 + - - -
302D EDO 3.2 24.1 + - - +
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLN* 3.2 12.3 + - - +
73D THR 3.0 8.1 + - - +
75D ARG* 1.3 79.0 - - + +
77D ASP* 1.3 67.8 + - - +
79D GLY* 3.1 4.9 + - - +
80D THR* 2.9 31.0 + - - +
8F TRP* 3.6 30.7 - - + +
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Residues in contact with ASP 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 2.7 26.6 + - - +
74D HIS* 3.1 23.7 + - - +
76D VAL* 1.3 78.8 - - - +
78D LEU* 1.3 57.2 + - - +
80D THR* 3.1 7.7 + - - -
81D LEU* 2.9 35.1 + - - +
95D VAL* 4.6 8.7 - - + -
116D TYR* 3.9 12.5 + - - -
7F HIS 4.3 2.9 - - - +
8F TRP* 3.5 12.0 - - - +
9F LEU* 3.2 49.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 4.1 13.0 - - - -
13D SER* 4.2 10.8 - - - +
20D PRO* 3.8 33.9 - - + -
74D HIS 3.0 19.8 + - - +
75D ARG 3.6 0.9 - - - +
76D VAL 3.2 0.2 - - - -
77D ASP* 1.3 76.1 - - - +
79D GLY* 1.3 63.4 + - - +
81D LEU* 4.0 3.4 - - - +
82D ARG* 3.1 26.6 + - - +
93D HIS* 3.9 34.1 - - + +
94D THR 4.3 0.4 - - - +
95D VAL* 3.3 26.9 - - + +
118D TYR* 4.5 4.8 + - + -
302D EDO 3.4 23.3 - - - +
----------------------------------------------------------
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Residues in contact with GLY 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG 3.6 5.1 + - - -
76D VAL* 3.1 7.2 + - - -
78D LEU* 1.3 77.7 - - - +
80D THR* 1.3 63.8 + - - +
82D ARG* 3.2 21.6 + - - +
83D GLY* 3.2 17.7 + - - -
302D EDO 4.0 3.6 + - - -
----------------------------------------------------------
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 2.9 27.6 + - - +
77D ASP* 3.1 11.5 + - - -
79D GLY* 1.3 75.1 - - - +
81D LEU* 1.3 60.6 + - + +
83D GLY* 3.2 5.6 + - - -
84D TYR* 3.0 58.6 + - + +
8F TRP* 5.8 0.5 - - - +
9F LEU* 3.6 22.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ASP 2.9 18.2 + - - +
78D LEU 4.0 1.3 - - - +
80D THR* 1.3 74.3 - - - +
82D ARG* 1.3 66.0 + - - +
83D GLY 3.1 1.6 - - - -
84D TYR* 3.5 27.4 - - + +
85D TYR* 3.0 32.8 + - + +
87D GLN* 4.0 0.2 - - - +
95D VAL* 4.6 7.0 - - + -
118D TYR* 3.2 56.8 - - + -
123D TYR* 3.6 26.2 - - + +
9F LEU* 4.0 24.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.1 13.0 + - - +
79D GLY* 3.7 23.4 - - - +
81D LEU* 1.3 74.3 - - - +
83D GLY* 1.3 57.2 + - - +
86D ASN* 2.9 8.8 + - - -
87D GLN* 2.9 53.8 + - + +
88D SER 3.8 24.8 + - - +
89D GLU* 3.3 36.8 + - - +
91D GLY 5.4 2.0 - - - -
93D HIS* 4.3 14.4 - - + -
118D TYR* 4.1 4.4 + - - +
302D EDO 2.7 41.9 + - - -
----------------------------------------------------------
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Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLY 3.2 8.8 + - - -
80D THR* 3.2 8.1 + - - -
81D LEU 3.1 0.6 - - - -
82D ARG* 1.3 74.5 - - - +
84D TYR* 1.3 65.9 + - - +
86D ASN* 3.0 16.0 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D THR* 3.0 35.1 + - + +
81D LEU* 3.2 27.1 + - + +
83D GLY* 1.3 75.2 - - - +
85D TYR* 1.3 63.3 + - + +
86D ASN* 3.5 1.6 + - - +
123D TYR* 3.5 17.7 - - - -
139D ALA* 3.8 26.9 - - + +
142D THR* 3.8 22.5 - - + +
143D THR* 3.8 1.8 - - - -
146D LYS* 3.6 13.3 - - - -
9F LEU 2.7 30.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 3.0 24.3 + - + +
84D TYR* 1.3 80.2 - - + +
86D ASN* 1.3 71.6 + - - +
87D GLN* 3.4 22.8 + - - +
118D TYR* 3.7 33.0 - + - +
121D LYS* 5.5 2.8 + - - -
123D TYR* 3.5 22.4 - + - -
136D ALA* 5.8 0.3 - - - +
137D ASP* 2.8 35.6 + - - -
139D ALA* 3.7 19.1 - - + -
----------------------------------------------------------
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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