Contacts of the helix formed by residues 66 - 88 (chain D) in PDB entry 3DOY
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 PRO 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MET* 3.9 16.2 - - + -
72C GLU* 5.4 1.3 - - - +
54D VAL* 3.7 26.5 - - + -
58D HIS* 3.6 34.8 - - + +
64D ILE 3.3 6.7 - - - +
65D PHE* 1.3 94.5 - - + +
67D GLY* 1.3 67.2 - - - +
68D VAL* 4.3 4.7 - - + -
69D LEU* 2.9 33.1 + - + +
70D ILE* 3.2 10.6 + - - +
1004D CL 4.1 0.4 - - + -
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLU* 5.8 0.2 + - - -
65D PHE 3.4 2.0 + - - -
66D PRO* 1.3 71.1 - - - +
68D VAL* 1.3 61.4 + - - +
70D ILE* 3.0 25.7 + - - +
71D VAL* 3.2 8.8 + - - +
109D PHE* 3.3 37.0 - - - -
1004D CL 3.3 20.1 - - - +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET* 4.9 0.2 - - + -
68C VAL* 3.5 45.1 - - + +
69C LEU* 4.4 10.1 - - + -
71C VAL* 4.7 4.3 - - + -
72C GLU* 3.7 38.1 - - + +
75C ALA* 6.2 1.1 - - + -
104C ILE* 4.5 20.4 - - + -
66D PRO* 4.3 11.4 - - + -
67D GLY* 1.3 76.5 - - - +
69D LEU* 1.3 66.5 + - + +
71D VAL* 3.4 7.8 + - - +
72D GLU 3.0 20.6 + - - -
109D PHE* 4.1 1.7 - - + -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET* 5.0 4.0 - - - -
68C VAL* 4.5 14.1 - - + -
69C LEU* 4.6 9.2 - - + -
27D MET* 4.5 17.0 - - + -
29D LEU* 3.8 26.2 - - + +
54D VAL* 4.0 29.4 - - + -
65D PHE* 3.9 26.7 - - + -
66D PRO* 2.9 25.1 + - + +
68D VAL* 1.3 86.3 - - + +
70D ILE* 1.3 61.3 + - - +
72D GLU* 3.3 4.9 + - + +
73D GLY* 2.9 24.3 + - - -
121D TYR* 4.7 0.5 + - - -
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PHE* 3.6 25.6 - - + +
66D PRO 3.2 10.2 + - - +
67D GLY* 3.0 22.3 + - - +
69D LEU* 1.3 78.0 - - - +
71D VAL* 1.3 61.2 + - + +
73D GLY* 3.2 3.5 + - - -
74D MET* 3.1 24.0 + - - +
109D PHE* 4.9 10.3 - - + -
111D ILE 5.4 2.7 - - - +
113D VAL* 3.8 26.9 - - + +
119D LEU* 3.9 13.5 - - + -
121D TYR* 3.7 2.8 - - + -
139D ALA* 3.6 30.3 - - + -
146D VAL* 4.9 5.2 - - + +
147D ALA* 4.3 10.1 - - + -
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 4.6 1.8 - - + -
104C ILE* 5.8 2.2 - - + -
67D GLY 3.2 11.5 + - - +
68D VAL* 3.6 10.1 - - - +
69D LEU 3.2 0.2 - - - -
70D ILE* 1.3 75.4 - - + +
72D GLU* 1.3 60.0 + - - +
74D MET* 3.0 12.9 + - - +
75D ALA* 2.8 26.5 + - - +
101D PHE* 4.0 19.3 - - + -
104D ILE* 4.1 22.7 - - + -
107D VAL* 4.6 8.5 - - + -
109D PHE* 4.3 18.4 - - + -
148D GLU 5.4 0.7 - - - +
149D ALA* 4.4 18.8 - - + -
151D LEU* 4.0 11.6 - - + +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS* 4.3 7.9 + - - -
66C PRO* 5.2 1.2 - - - +
67C GLY 5.5 0.7 + - - -
68C VAL* 3.6 20.3 + - + +
23D HIS* 3.8 17.0 + - - -
27D MET* 4.1 20.5 - - + +
29D LEU* 3.9 13.2 - - + -
68D VAL 3.0 13.7 + - - +
69D LEU* 3.4 12.3 - - - +
71D VAL* 1.3 75.3 - - - +
73D GLY* 1.3 57.2 + - - +
75D ALA* 3.1 8.7 + - - +
76D GLN* 2.9 52.0 + - - +
101D PHE* 3.4 22.6 - - - -
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Residues in contact with GLY 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 4.1 12.3 - - - +
30D VAL* 3.8 2.9 - - - +
69D LEU 2.9 11.6 + - - -
70D ILE 3.2 1.3 + - - -
71D VAL 3.1 0.4 - - - -
72D GLU* 1.3 77.6 - - - +
74D MET* 1.3 61.0 + - - +
76D GLN* 3.2 6.7 + - - +
77D SER* 3.1 25.1 + - - -
121D TYR* 3.4 31.2 - - - -
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Residues in contact with MET 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 3.1 18.1 + - - +
71D VAL* 3.0 13.5 + - - +
73D GLY* 1.3 75.8 - - - +
75D ALA* 1.3 63.3 + - - +
77D SER 3.2 0.5 + - - -
78D GLY* 2.9 9.0 + - - -
121D TYR* 3.7 19.7 - - + -
123D LEU* 2.8 47.2 - - + +
135D VAL* 5.0 0.3 - - - +
137D GLY 3.5 11.9 - - - +
138D THR* 3.3 41.5 - - - +
139D ALA* 4.2 14.8 - - + -
147D ALA* 5.2 2.2 - - - +
148D GLU 4.9 2.5 - - - -
149D ALA* 4.2 23.8 - - + +
151D LEU* 4.4 7.4 - - + +
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL 2.8 6.2 + - - +
72D GLU* 3.2 11.0 - - - +
74D MET* 1.3 78.2 - - - +
76D GLN* 1.3 57.4 + - + +
78D GLY* 3.2 1.9 + - - -
79D GLY* 2.8 26.2 + - - -
99D VAL* 5.8 2.1 - - - +
101D PHE* 3.2 42.4 - - + -
151D LEU* 3.9 19.3 - - + +
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.9 13.2 - - + +
23D HIS* 3.1 32.8 - - + +
27D MET 2.5 25.7 - - - +
28D LEU* 3.6 11.1 - - - +
29D LEU* 2.7 31.9 + - - +
30D VAL* 3.3 25.2 - - + +
72D GLU* 2.9 29.8 + - - +
73D GLY 3.2 2.4 + - - +
75D ALA* 1.3 72.8 - - + +
77D SER* 1.3 60.6 + - - +
79D GLY* 3.2 2.5 + - - +
80D PHE* 2.9 27.5 + - - +
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Residues in contact with SER 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 4.0 7.4 - - - +
33D ILE* 5.6 0.2 - - - -
42D ILE* 3.6 21.8 - - - +
44D ALA* 3.7 13.4 - - - +
73D GLY 3.1 5.6 + - - -
74D MET 3.5 0.7 - - - -
76D GLN* 1.3 75.1 - - - +
78D GLY* 1.3 64.8 + - - +
80D PHE* 3.1 9.2 + - - +
81D LEU* 3.0 18.5 + - - +
121D TYR* 3.2 33.9 - - - +
123D LEU* 3.5 21.8 - - - -
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Residues in contact with GLY 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 4.9 1.6 - - - -
74D MET 2.9 14.0 + - - -
75D ALA 3.6 3.4 - - - -
77D SER* 1.3 77.4 - - - +
79D GLY* 1.3 56.3 + - - +
81D LEU* 3.0 9.7 + - - +
82D ALA* 2.8 30.4 + - - +
123D LEU* 3.8 8.0 - - - +
133D TRP* 5.6 1.0 - - - -
135D VAL* 4.5 24.2 - - - +
151D LEU* 5.8 0.4 - - - -
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Residues in contact with GLY 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.3 8.9 - - - +
75D ALA 2.8 14.9 + - - -
76D GLN* 3.2 4.2 + - - -
77D SER 3.2 0.2 - - - -
78D GLY* 1.3 75.0 - - - +
80D PHE* 1.3 61.7 + - - +
82D ALA* 3.6 7.1 - - - +
83D PHE* 3.0 26.5 + - - +
99D VAL* 4.9 21.1 - - - +
153D ALA* 6.0 2.0 - - - -
155D ILE* 4.8 2.9 - - - +
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Residues in contact with PHE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.7 39.3 - + + -
16D HIS 4.4 0.7 - - - -
17D ILE* 4.0 25.6 - - + -
20D ILE* 3.7 38.8 - - + -
21D LEU* 3.9 19.2 - - + +
30D VAL* 6.5 0.2 - - + -
33D ILE* 4.1 10.3 - - + -
36D LEU* 3.7 26.9 - - + -
42D ILE* 3.9 9.6 - - + -
76D GLN 2.9 13.2 + - - +
77D SER* 3.1 9.6 + - - +
79D GLY* 1.3 76.7 - - - +
81D LEU* 1.3 61.3 + - - +
83D PHE* 4.2 0.5 - - - +
84D THR* 2.9 43.9 + - + +
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 4.0 18.6 - - + -
37D GLN 3.5 24.0 - - - +
38D ALA* 4.5 0.4 - - - -
39D ASN 4.1 1.1 - - - +
41D LYS* 3.5 32.1 - - - +
42D ILE* 4.0 13.5 - - + -
77D SER 3.0 12.7 + - - +
78D GLY* 3.3 11.9 - - - +
80D PHE* 1.3 75.0 - - - +
82D ALA* 1.3 57.6 + - - +
84D THR* 3.3 5.7 + - - -
85D SER* 2.6 47.7 + - - +
123D LEU* 4.7 2.7 - - + +
125D VAL* 3.7 29.8 - - + +
133D TRP* 4.9 0.9 - - + -
135D VAL* 5.2 4.9 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLY 2.8 14.9 + - - +
79D GLY* 3.6 9.2 - - - +
81D LEU* 1.3 77.4 - - - +
83D PHE* 1.3 63.5 + - - +
85D SER* 3.2 15.2 + - - -
86D LEU* 3.2 9.9 + - - +
133D TRP* 3.5 54.6 - - + -
155D ILE* 3.9 12.8 - - + -
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ILE* 3.6 26.9 - - + -
21D LEU* 6.2 0.4 - - + -
79D GLY 3.0 14.1 + - - +
80D PHE 4.2 2.9 - - - +
82D ALA* 1.3 79.5 - - - +
84D THR* 1.3 61.0 + - - +
86D LEU* 3.0 4.2 + - - -
87D TRP* 2.8 69.0 + + + -
88D GLY 3.7 17.5 - - - -
90D ASP 3.5 15.3 - - - -
93D ILE* 3.8 13.0 - - + -
94D ALA* 3.3 41.3 - - + -
97D LYS* 4.1 9.0 - - + -
155D ILE* 3.9 15.0 - - + +
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 5.2 7.4 - - + -
20D ILE* 4.5 6.3 - - + -
36D LEU* 3.6 23.4 - - - +
38D ALA* 5.5 1.0 - - - +
80D PHE* 2.9 44.7 + - + +
81D LEU 3.3 4.0 + - - -
83D PHE* 1.3 84.7 - - + +
85D SER* 1.3 62.0 + - - +
86D LEU 3.3 0.2 - - - -
88D GLY* 2.8 47.5 + - - +
89D PHE* 4.6 4.0 - - + +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 3.8 12.3 - - - +
39D ASN* 3.0 36.7 + - - +
81D LEU* 2.6 30.5 + - - +
82D ALA 3.2 7.0 - - - -
83D PHE 3.0 0.2 - - - -
84D THR* 1.3 80.8 + - - +
86D LEU* 1.3 63.5 + - - +
88D GLY 5.0 0.2 + - - -
133D TRP* 3.4 21.4 - - - -
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASN* 4.1 9.4 - - - +
82D ALA 3.2 5.6 + - - +
83D PHE 3.0 3.8 + - - +
85D SER* 1.3 85.7 - - - +
87D TRP* 1.3 81.2 + - + +
128D HIS* 5.0 5.2 - - + -
130D GLY* 3.3 27.1 - - - +
131D MET* 3.9 20.0 - - + -
133D TRP* 3.6 30.3 - - + +
155D ILE* 5.4 1.3 - - + -
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Residues in contact with TRP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 2.8 67.8 + + + +
86D LEU* 1.3 89.1 + - + +
88D GLY* 1.3 64.2 + - - +
89D PHE 4.5 0.3 - - - -
90D ASP* 3.7 17.3 - - + +
93D ILE* 3.4 33.7 - - + +
97D LYS* 3.2 32.5 - - + -
131D MET* 3.5 30.1 - - + -
155D ILE* 4.3 15.5 - - + -
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Residues in contact with GLY 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.7 8.1 - - - -
84D THR* 2.8 41.9 + - - +
85D SER 4.7 0.2 - - - -
86D LEU 3.9 0.2 - - - -
87D TRP* 1.3 81.7 - - - +
89D PHE* 1.3 57.6 + - - -
90D ASP 2.9 8.3 + - - -
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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