Contacts of the helix formed by residues 68 - 97 (chain D) in PDB entry 2ZUQ
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 68 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LYS* 4.6 5.8 - - + +
67D THR* 1.3 97.5 - - + +
69D LEU* 1.3 63.1 + - + +
70D ARG 2.9 10.7 + - - -
71D TYR* 3.2 28.0 + - + +
72D VAL* 4.2 2.1 + - - +
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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
----------------------------------------------------------
60D ILE* 3.1 42.0 - - + +
61D GLY* 4.4 0.2 - - - -
63D ILE 3.2 18.2 - - - +
64D ALA* 3.5 19.3 - - + +
65D PRO 3.8 5.5 - - - +
66D LYS 4.7 0.4 - - - +
67D THR 4.6 0.2 - - - +
68D PRO* 1.3 80.3 - - + +
70D ARG* 1.3 61.4 + - - +
71D TYR 3.3 0.7 - - - -
72D VAL* 4.1 19.7 - - + +
73D ALA* 3.4 19.4 + - - +
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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
----------------------------------------------------------
10D GLN* 3.8 27.1 + - - -
11D GLY* 4.8 0.6 - - - -
15D TRP* 4.1 22.1 - - + +
65D PRO* 2.8 51.7 + - - +
66D LYS* 2.5 35.3 + - - +
67D THR* 3.5 25.8 + - - +
68D PRO 2.9 0.2 - - - -
69D LEU* 1.3 78.0 - - - +
71D TYR* 1.3 68.3 + - + +
73D ALA* 3.4 7.2 - - - +
74D MET* 3.2 33.0 + - + +
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Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D THR 4.6 10.1 - - - -
68D PRO* 3.5 17.5 - - + +
70D ARG* 1.3 79.9 - - + +
72D VAL* 1.3 60.8 + - + +
74D MET* 2.7 47.2 + - + +
75D VAL* 3.2 14.5 + - - +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ILE* 3.9 26.5 - - + -
68D PRO 5.2 1.3 - - - +
69D LEU* 4.0 25.3 + - + +
71D TYR* 1.3 78.9 - - + +
73D ALA* 1.3 61.5 + - - +
75D VAL* 3.2 21.7 - - + +
76D ILE* 3.3 15.9 - - + +
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 3.7 8.2 - - + -
57D ALA* 3.2 17.6 - - - +
60D ILE* 4.0 4.9 - - + +
61D GLY* 3.1 42.0 - - - +
69D LEU 3.4 7.8 + - - +
70D ARG 3.4 10.5 - - - +
72D VAL* 1.3 79.7 - - - +
74D MET* 1.3 57.8 + - - +
76D ILE* 4.5 1.1 - - - -
77D TRP* 3.0 25.5 + - - +
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Residues in contact with MET 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 3.8 9.2 - - + -
70D ARG* 3.2 14.6 - - + +
71D TYR* 2.7 50.9 + - + +
73D ALA* 1.3 73.1 - - - +
75D VAL* 1.3 54.5 + - - +
77D TRP* 3.2 10.0 - - + +
78D LEU* 2.8 38.4 + - + +
157D ALA* 6.5 0.2 - - - -
161D VAL* 3.4 40.2 - - + +
162D ILE* 3.5 34.1 - - + -
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D TYR 3.3 10.8 - - - +
72D VAL* 3.2 26.2 - - + +
74D MET* 1.3 75.0 - - - +
76D ILE* 1.3 54.9 + - + +
77D TRP 2.5 16.7 + - - -
78D LEU* 2.9 16.0 + - + +
79D TYR* 2.7 26.9 + - + +
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLY* 3.2 11.6 - - - +
56D GLY* 4.8 0.7 - - - -
57D ALA* 3.0 33.4 - - - +
60D ILE* 4.6 15.5 - - + -
72D VAL* 3.3 20.2 - - + +
73D ALA* 4.1 1.6 - - - +
75D VAL* 1.3 79.6 - - + +
77D TRP* 1.3 54.8 + - - +
79D TYR* 4.2 16.8 - - + -
80D SER* 3.5 11.4 + - - +
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Residues in contact with TRP 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 4.2 12.6 - + - -
18D MET* 3.1 29.6 - - + -
54D VAL* 3.6 25.9 - - + +
57D ALA* 3.3 7.4 - - + -
58D ALA* 3.0 44.6 - - + -
73D ALA 3.0 20.2 + - - +
74D MET* 3.2 10.8 - - + +
75D VAL 2.5 5.1 + - - -
76D ILE* 1.3 72.7 - - - +
78D LEU* 1.3 72.5 + - - +
79D TYR 3.0 0.6 + - - -
80D SER* 3.4 2.7 + - - +
81D ALA* 3.0 25.8 + - - +
153D TYR* 3.5 20.4 + + + -
156D VAL* 2.9 41.4 + - + -
157D ALA* 3.3 28.5 - - + +
161D VAL* 4.5 7.3 - - + +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D MET* 2.8 27.1 + - + +
75D VAL* 3.2 14.8 - - + +
77D TRP* 1.3 76.5 - - - +
79D TYR* 1.3 56.6 + - - +
81D ALA* 4.5 0.2 - - - -
82D PHE* 2.9 26.0 + - + +
154D LEU* 3.1 25.5 - - + +
157D ALA* 4.0 11.2 - - + -
158D VAL* 3.5 25.1 - - + -
162D ILE* 3.6 27.1 - - + -
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Residues in contact with TYR 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D VAL* 2.7 22.7 + - + +
76D ILE* 4.3 15.5 - - + -
78D LEU* 1.3 69.7 - - - +
80D SER* 1.3 86.3 + - - +
81D ALA 2.9 1.1 - - - -
82D PHE* 2.7 23.4 + + - -
83D ARG* 2.7 49.1 + - + +
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL 5.3 0.2 + - - -
50D ALA* 3.3 22.7 - - - +
53D GLY* 3.0 45.6 + - - -
54D VAL* 3.7 10.3 - - - -
76D ILE* 3.5 11.2 + - - +
77D TRP 3.4 3.3 + - - -
79D TYR* 1.3 88.7 - - - +
81D ALA* 1.3 55.1 - - - +
83D ARG* 3.8 3.9 - - - -
84D GLY* 2.8 22.3 + - - -
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 4.4 5.8 - - + +
77D TRP* 3.0 18.3 + - + +
78D LEU 3.6 4.5 - - - +
79D TYR 2.7 3.2 + - - -
80D SER* 1.3 72.5 - - - +
82D PHE* 1.3 58.8 + - - +
84D GLY* 2.9 3.6 + - - -
85D VAL* 2.8 30.3 + - - +
150D PHE* 3.6 17.2 - - - +
153D TYR* 3.8 11.9 - - + +
154D LEU* 3.8 32.8 - - + +
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU 2.9 19.3 + - - +
79D TYR* 2.7 15.4 + + - +
81D ALA* 1.3 72.6 - - - +
83D ARG* 1.3 70.3 + - + +
85D VAL* 3.6 2.6 + - - +
86D GLN* 2.9 55.3 + - - +
154D LEU* 3.6 26.8 - - + +
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D TYR* 5.4 6.7 - - - -
50D ALA* 4.5 9.2 - - + -
79D TYR* 2.7 64.4 + - + +
80D SER* 3.9 6.5 - - - +
82D PHE* 1.3 78.5 - - + +
84D GLY* 1.3 63.3 + - - +
86D GLN* 2.8 41.7 + - - +
87D LEU* 3.2 70.9 + - + +
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLU* 5.8 0.9 - - - -
50D ALA* 4.2 7.2 - - - +
80D SER 2.8 11.6 + - - -
81D ALA 2.9 5.6 + - - -
83D ARG* 1.3 77.4 - - - +
85D VAL* 1.3 54.3 + - - -
87D LEU* 3.9 1.7 - - - +
88D THR* 2.4 38.6 + - - +
150D PHE* 3.4 30.7 - - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ALA 2.8 12.9 + - - +
82D PHE 3.8 8.3 - - - +
84D GLY* 1.3 69.1 - - - +
86D GLN* 1.3 58.2 + - + +
88D THR* 2.6 9.1 + - - -
89D TYR* 2.6 39.4 + - + +
147D LEU* 3.4 13.3 - - + +
150D PHE* 3.5 39.1 - - + +
151D ILE* 3.6 18.8 - - + +
154D LEU* 4.2 14.8 - - + -
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PHE* 2.9 46.2 + - - +
83D ARG* 2.8 40.3 + - - +
85D VAL* 1.3 78.7 - - + +
87D LEU* 1.3 69.7 + - + +
89D TYR* 3.4 10.4 - - + +
90D GLU* 3.0 26.9 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 4.5 18.7 - - + +
46D TYR* 3.8 37.7 - - + +
47D GLU* 3.1 27.3 - - + +
50D ALA* 4.5 8.1 - - + -
83D ARG* 3.2 56.4 + - + +
84D GLY 3.9 0.7 - - - +
86D GLN* 1.3 77.2 - - + +
88D THR* 1.3 64.9 + - - +
90D GLU* 3.4 11.4 - - + +
91D HIS* 3.0 20.1 + - - +
----------------------------------------------------------
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Residues in contact with THR 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLU* 2.9 36.8 + - + +
84D GLY 2.4 30.1 + - - +
85D VAL* 2.6 14.7 + - - -
87D LEU* 1.3 73.6 - - - +
89D TYR* 1.3 52.6 + - - +
91D HIS* 3.4 4.2 - - - +
92D THR* 2.6 33.7 + - - -
143D PRO* 3.5 6.2 - - + +
146D LEU* 4.1 11.2 - - + -
147D LEU* 3.4 21.7 - - - -
150D PHE* 3.6 24.0 - - + -
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Residues in contact with TYR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D VAL* 2.6 24.0 + - + +
86D GLN* 3.4 12.3 - - + +
87D LEU 3.1 0.4 - - - -
88D THR* 1.3 72.7 - - - +
90D GLU* 1.3 74.0 + - + +
92D THR* 2.7 27.2 + - - -
93D MET* 2.9 52.3 + - + +
147D LEU* 3.5 27.8 - - + -
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.7 24.6 - - - +
86D GLN 3.0 11.3 + - - +
87D LEU* 3.4 16.8 - - - +
89D TYR* 1.3 90.1 - - + +
91D HIS* 1.3 58.6 + - - +
92D THR 3.2 0.2 - - - -
93D MET* 3.2 13.9 - - + +
94D LEU* 2.9 33.0 + - - +
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Residues in contact with HIS 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 3.7 39.3 - - + +
43D LEU* 3.5 24.9 - - + +
44D CYS* 4.0 19.0 + - + -
47D GLU* 3.5 14.2 + - - +
87D LEU 3.0 17.1 + - - +
88D THR* 3.4 8.1 - - - +
90D GLU* 1.3 77.7 - - - +
92D THR* 1.3 60.1 + - - +
94D LEU* 3.3 5.6 + - + +
95D GLN* 2.9 45.2 + - - +
143D PRO* 3.5 31.0 - - + +
177D UQ1 5.1 2.4 + - - -
----------------------------------------------------------
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Residues in contact with THR 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D THR 2.6 21.6 + - - -
89D TYR* 2.7 18.0 + - - -
91D HIS* 1.3 70.1 - - - +
93D MET* 1.3 58.4 + - - -
95D GLN* 2.9 9.8 + - + +
96D LEU* 2.8 39.9 + - + +
141D GLU* 5.6 1.3 - - + -
143D PRO* 3.1 16.2 + - + -
144D GLN* 3.4 41.1 - - + +
147D LEU* 3.8 12.2 - - + +
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Residues in contact with MET 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D TYR* 2.9 55.0 + - + +
90D GLU* 3.2 17.7 - - + +
92D THR* 1.3 75.2 - - - +
94D LEU* 1.3 55.5 + - - +
97D TYR* 2.7 58.3 + - + +
102F ARG* 4.7 24.5 - - + +
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 6.0 9.2 - - + -
43D LEU* 5.0 15.7 - - + -
90D GLU* 2.9 18.8 + - - +
91D HIS* 3.4 12.1 - - - +
92D THR 3.2 0.2 - - - -
93D MET* 1.3 75.0 - - - +
95D GLN* 1.3 70.5 + - - +
97D TYR 4.9 0.4 - - - -
98D PRO* 3.7 26.6 - - + +
99D SER 6.1 0.4 - - - +
102D ALA* 6.1 4.7 - - + -
103D THR 6.0 4.0 - - - +
104D CYS* 6.0 4.0 - - - +
53E ARG* 3.6 8.8 + - - +
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 5.7 5.9 - - - +
91D HIS* 2.9 37.6 + - - +
92D THR* 2.9 13.0 + - + +
94D LEU* 1.3 94.5 - - - +
96D LEU* 1.3 64.0 + - + +
97D TYR 3.6 0.2 - - - -
98D PRO* 4.2 5.1 - - - +
132D GLU* 3.9 8.5 + - - -
141D GLU* 3.4 34.0 + - + +
143D PRO* 4.7 8.5 - - + -
53E ARG* 2.9 60.2 + - - +
54E THR 5.3 0.2 + - - -
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D THR* 2.8 23.9 + - + +
95D GLN* 1.3 82.3 - - + +
97D TYR* 1.3 94.4 + - + +
98D PRO* 3.7 5.5 - - - +
141D GLU* 5.7 7.9 - - + -
144D GLN* 3.4 30.7 - - - +
53E ARG* 6.4 0.7 - - - -
54E THR* 3.8 22.4 - - - +
56E LYS* 5.3 7.3 + - - +
58E TYR* 4.1 5.4 + - - -
76E TRP* 5.2 0.7 - - - -
----------------------------------------------------------
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Residues in contact with TYR 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D MET* 2.7 39.3 + - + +
96D LEU* 1.3 104.5 - - + +
98D PRO* 1.3 70.4 - - - +
99D SER 3.4 1.6 + - - -
56E LYS* 5.4 3.1 - - - -
58E TYR* 4.3 3.8 - - - -
76E TRP* 3.4 34.7 - + - -
102F ARG* 3.1 82.2 + - + +
104F TYR* 3.6 13.1 + - + -
----------------------------------------------------------
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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