Contacts of the helix formed by residues 60 - 83 (chain D) in PDB entry 3LOC
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 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 4.8 4.3 - - - -
54D LEU* 5.6 0.2 - - - +
55D LEU* 4.3 4.7 - - - -
58D PHE 2.9 7.5 + - - +
59D PRO* 1.3 83.4 - - - +
61D LYS* 1.3 59.3 + - - +
62D GLU* 3.5 11.5 + - - +
63D ALA* 3.0 22.2 + - - +
64D LEU* 3.0 25.8 + - - +
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Residues in contact with LYS 61 (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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30D PHE* 3.9 16.7 - - + -
35D PHE* 2.7 58.6 + - + +
36D HIS* 3.9 11.9 + - - +
38D THR* 3.3 22.6 + - + +
39D ARG* 5.4 1.1 - - - +
40D LEU* 3.5 39.1 - - + +
60D SER* 1.3 70.7 - - - +
62D GLU* 1.3 66.8 + - - +
64D LEU* 3.2 2.8 + - - +
65D TYR* 2.9 26.9 + - - +
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Residues in contact with GLU 62 (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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35D PHE* 3.8 15.7 - - + -
60D SER* 3.3 9.3 + - - +
61D LYS* 1.3 79.4 - - - +
63D ALA* 1.3 61.6 + - - +
65D TYR* 3.7 1.7 - - - +
66D ILE* 3.0 45.3 + - + +
124D LEU* 3.8 28.7 - - + +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PHE* 4.4 4.7 - - + -
59D PRO* 3.8 26.7 - - + -
60D SER* 3.0 22.9 + - - +
62D GLU* 1.3 78.1 - - - +
64D LEU* 1.3 57.1 + - - +
66D ILE* 3.3 10.6 + - - +
67D ALA* 2.8 30.2 + - - +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 4.1 6.3 - - + -
23D LEU* 3.7 20.2 - - + -
26D ALA* 3.7 28.5 - - + -
30D PHE* 4.3 3.6 - - + -
40D LEU* 4.5 3.4 - - + -
43D ILE* 4.0 11.9 - - + -
54D LEU* 4.0 37.2 - - + -
58D PHE* 3.6 36.9 - - + +
60D SER 3.0 12.3 + - - +
61D LYS* 3.2 6.0 + - - +
63D ALA* 1.3 75.5 - - - +
65D TYR* 1.3 57.5 + - - +
67D ALA* 3.1 5.4 + - - +
68D VAL* 2.9 30.6 + - - +
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Residues in contact with TYR 65 (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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30D PHE* 3.6 39.6 - + + -
35D PHE* 3.7 36.5 - + + +
61D LYS 2.9 17.1 + - - +
62D GLU 3.7 2.2 - - - +
64D LEU* 1.3 77.4 - - - +
66D ILE* 1.3 65.3 + - + +
68D VAL* 3.2 4.0 + - - +
69D LEU* 3.0 40.7 + - + +
113D LEU* 4.3 27.6 + - + +
116D MSE 5.8 0.7 - - - +
117D GLU* 2.6 47.6 + - - +
124D LEU* 4.2 21.8 - - + -
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLU* 3.0 43.2 + - + +
63D ALA* 3.6 8.3 - - - +
65D TYR* 1.3 73.7 - - + +
67D ALA* 1.3 69.8 + - - +
69D LEU* 3.2 2.5 + - - +
70D ARG* 2.8 25.4 + - + +
124D LEU* 3.7 33.4 - - + +
125D LEU* 4.5 13.8 - - + +
128D GLU* 4.5 22.2 - - + +
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Residues in contact with ALA 67 (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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23D LEU* 3.7 19.8 - - + +
58D PHE* 3.7 20.2 - - + -
63D ALA 2.8 14.2 + - - +
64D LEU 3.1 9.4 + - - +
66D ILE* 1.3 78.8 - - - +
68D VAL* 1.3 63.4 + - - +
70D ARG* 3.3 6.9 + - - +
71D GLN* 3.1 25.1 + - - +
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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
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23D LEU* 3.8 20.0 - - + +
26D ALA* 3.6 30.3 - - + -
27D LEU* 4.1 25.1 - - + +
30D PHE* 4.4 4.3 - - + -
64D LEU 2.9 19.1 + - - +
65D TYR* 3.6 9.0 - - - +
66D ILE 3.2 0.4 - - - -
67D ALA* 1.3 78.1 - - - +
69D LEU* 1.3 63.6 + - - +
71D GLN* 3.3 22.1 + - - +
72D ILE* 3.5 11.4 + - + +
113D LEU* 3.8 26.7 - - + -
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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
----------------------------------------------------------
65D TYR* 3.0 47.7 + - + +
68D VAL* 1.3 75.6 - - - +
70D ARG* 1.3 63.0 + - - +
72D ILE* 3.3 25.2 + - + +
73D LEU* 3.1 26.6 + - - +
113D LEU* 4.0 17.3 - - + -
114D PHE* 3.7 30.0 - - + +
117D GLU* 3.8 21.5 - - + -
125D LEU* 3.7 31.0 - - + -
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Residues in contact with ARG 70 (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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66D ILE* 2.8 24.6 + - + +
67D ALA* 3.3 8.5 + - - +
69D LEU* 1.3 69.3 - - - +
71D GLN* 1.3 59.6 + - - +
73D LEU* 3.3 18.7 + - - +
74D ASP* 2.9 61.9 + - - +
77D LEU* 5.9 2.2 - - - +
125D LEU* 4.9 1.0 - - + +
128D GLU* 3.1 31.3 + - + +
132D ASP* 4.6 20.9 + - - +
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Residues in contact with GLN 71 (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 LYS* 5.0 13.1 - - - +
23D LEU* 3.5 48.3 - - + +
24D SER* 5.6 0.4 - - - +
27D LEU* 5.6 5.9 - - - +
67D ALA 3.1 13.1 + - - +
68D VAL* 3.4 15.0 - - - +
69D LEU 3.3 0.2 - - - -
70D ARG* 1.3 76.3 - - - +
72D ILE* 1.3 63.3 + - + +
74D ASP* 3.1 9.5 + - - +
75D ILE* 3.1 35.9 + - + +
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Residues in contact with ILE 72 (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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27D LEU* 5.2 1.6 - - + -
68D VAL* 3.5 24.0 + - + +
69D LEU* 3.3 29.3 + - + +
71D GLN* 1.3 76.7 - - + +
73D LEU* 1.3 58.4 + - - +
75D ILE* 3.3 10.8 + - + +
76D TRP* 2.8 68.8 + - + +
103D VAL* 5.8 2.7 - - + -
107D TYR* 6.2 0.4 - - + -
110D ALA* 3.2 52.5 - - + +
111D SER 4.6 0.2 - - - +
113D LEU* 4.8 1.8 - - + -
114D PHE* 4.6 2.7 - - + -
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Residues in contact with LEU 73 (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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178C GLN* 4.8 1.1 - - - +
69D LEU 3.1 17.5 + - - +
70D ARG* 3.5 28.7 - - - +
72D ILE* 1.3 80.2 - - - +
74D ASP* 1.3 64.2 + - - +
76D TRP* 3.0 5.6 + - + -
77D LEU* 2.9 37.9 + - + +
114D PHE* 3.6 27.6 - - + -
125D LEU* 4.6 12.3 - - + -
128D GLU* 4.8 8.1 - - + +
129D LEU* 4.7 7.9 - - + -
133D LEU* 4.6 15.3 - - + -
212D URA 3.5 32.3 - - + -
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Residues in contact with ASP 74 (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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70D ARG* 2.9 58.6 + - - +
71D GLN* 3.1 9.0 + - - +
73D LEU* 1.3 74.9 - - - +
75D ILE* 1.3 62.1 + - + +
77D LEU* 4.9 2.4 - - - +
78D ALA* 3.1 25.6 + - - +
81D LYS* 3.7 18.0 + - - +
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Residues in contact with ILE 75 (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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71D GLN* 3.1 32.0 + - + +
72D ILE* 3.6 9.6 - - + +
74D ASP* 1.3 79.0 - - + +
76D TRP* 1.3 63.6 + - - +
77D LEU 3.4 0.2 + - - -
78D ALA* 3.7 9.2 + - - +
79D PRO* 3.7 8.8 - - - +
103D VAL* 3.8 35.9 - - + +
107D TYR* 4.6 33.7 - - + +
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Residues in contact with TRP 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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175C PHE* 5.9 0.2 - + - -
72D ILE* 2.8 38.5 + - + +
73D LEU* 3.0 11.2 + - + +
75D ILE* 1.3 72.7 - - - +
77D LEU* 1.3 61.7 + - - +
79D PRO* 3.5 10.2 - - - +
96D TYR* 4.0 9.2 + - - -
100D LYS* 3.2 42.6 + - + +
103D VAL* 3.5 31.0 - - + +
104D SER* 5.6 2.4 + - - +
111D SER* 3.7 27.5 + - - -
114D PHE* 3.3 51.1 - + + -
170D GLN* 3.6 20.0 - - + +
212D URA 3.3 38.8 - + + +
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Residues in contact with LEU 77 (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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70D ARG* 5.9 2.2 - - - +
73D LEU* 2.9 33.3 + - + +
74D ASP* 5.1 2.5 - - - +
76D TRP* 1.3 72.6 - - - +
78D ALA* 1.3 67.3 + - - +
79D PRO* 3.2 4.7 - - - -
80D LEU* 2.6 25.5 + - + -
81D LYS* 2.7 26.1 + - - +
96D TYR* 5.0 0.9 - - - +
133D LEU* 3.9 28.3 - - + -
136D LEU* 3.8 28.5 - - + -
137D ILE* 4.6 3.8 - - + -
166D TRP* 4.3 8.5 - - + -
212D URA 3.7 26.2 - - + +
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Residues in contact with ALA 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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74D ASP 3.1 19.1 + - - +
75D ILE* 4.0 6.1 - - - +
77D LEU* 1.3 73.4 - - - +
79D PRO* 1.3 69.8 - - + +
81D LYS* 3.1 17.5 + - - +
82D ALA* 3.0 22.2 + - - +
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Residues in contact with PRO 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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75D ILE 3.7 7.4 - - - +
76D TRP 3.5 12.8 - - - +
77D LEU 3.2 5.6 - - - -
78D ALA* 1.3 94.9 - - + +
80D LEU* 1.3 60.8 + - - +
82D ALA* 3.1 22.6 + - + +
83D PHE* 3.3 16.0 - - + -
96D TYR* 3.7 23.6 - - + -
99D LEU* 4.3 34.8 - - + -
100D LYS* 5.7 1.6 - - + -
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Residues in contact with LEU 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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77D LEU* 2.6 24.0 + - + +
79D PRO* 1.3 73.7 - - - +
81D LYS* 1.3 64.0 + - - +
82D ALA 3.3 0.3 + - - -
83D PHE* 3.3 43.6 + - + +
96D TYR* 3.6 40.2 - - + +
136D LEU* 5.3 3.4 - - + -
137D ILE* 3.7 29.2 - - + -
140D LYS* 3.6 28.6 - - + -
144D ILE* 5.0 6.5 - - + -
162D ILE* 4.5 14.1 - - + -
166D TRP* 4.9 0.2 - - + -
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Residues in contact with LYS 81 (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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74D ASP* 3.7 24.4 + - - +
77D LEU* 2.7 22.8 + - - +
78D ALA* 3.4 31.1 - - - +
80D LEU* 1.3 73.0 - - - +
82D ALA* 1.3 52.9 + - - +
83D PHE 3.3 0.7 + - - -
84D ARG* 2.7 31.7 + - - -
136D LEU* 3.7 31.8 - - + +
140D LYS* 3.6 12.0 + - - +
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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
----------------------------------------------------------
78D ALA 3.0 12.2 + - - +
79D PRO* 3.2 16.4 - - + +
80D LEU 3.1 0.2 - - - -
81D LYS* 1.3 74.1 - - - +
83D PHE* 1.3 67.3 + - + +
84D ARG* 3.5 17.1 + - - +
87D PHE* 3.3 18.1 - - + -
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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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79D PRO 3.3 17.5 - - - -
80D LEU* 3.5 30.1 - - + +
81D LYS 3.2 1.2 - - - -
82D ALA* 1.3 75.9 - - + +
84D ARG* 1.3 76.6 + - - +
87D PHE* 3.7 8.7 - + - -
92D ALA* 4.0 41.3 - - + -
93D ILE* 4.2 17.0 - - + -
96D TYR* 4.1 25.8 - + + -
140D LYS* 3.2 25.4 + - + -
143D LEU* 4.1 19.5 - - + +
144D ILE* 4.6 18.4 - - + -
147D TRP* 5.0 7.6 - + - -
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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
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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) + - + + + + + -
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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