Contacts of the helix formed by residues 68 - 92 (chain D) in PDB entry 2QW4
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 ASP 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D LYS 3.6 4.4 + - - -
67D GLU* 1.3 75.9 - - - +
69D ALA* 1.3 56.7 + - - +
70D GLY* 2.7 30.4 + - - -
71D ASP* 2.9 26.3 + - - +
72D VAL* 3.4 5.2 + - - -
146D ARG* 4.5 4.4 + - - +
250D LEU* 4.9 2.7 - - - -
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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
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68D ASP* 1.3 73.0 + - - +
70D GLY* 1.3 55.8 - - - +
72D VAL* 3.4 5.4 + - - +
73D GLN* 2.8 31.4 + - - +
250D LEU* 3.7 35.5 - - + +
251D VAL* 3.7 22.7 - - + +
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Residues in contact with GLY 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASP* 2.7 24.3 + - - -
69D ALA* 1.3 71.4 - - - +
71D ASP* 1.3 54.6 + - - -
73D GLN* 3.0 7.6 + - - +
74D GLN* 2.8 28.2 + - - +
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Residues in contact with ASP 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 3.3 14.1 - - + -
68D ASP* 2.9 30.5 + - - +
70D GLY* 1.3 67.7 - - - -
72D VAL* 1.3 67.3 + - - +
74D GLN* 3.3 8.4 + - - +
75D PHE* 3.0 22.9 + - - +
143D GLN 5.5 0.2 - - - +
146D ARG* 3.0 59.5 + - + +
147D GLY* 4.3 6.5 - - - +
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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
----------------------------------------------------------
67D GLU* 4.0 16.4 - - + +
68D ASP 3.8 8.1 - - - +
69D ALA* 3.4 4.9 + - - +
70D GLY 3.3 0.6 - - - -
71D ASP* 1.3 75.2 - - - +
73D GLN* 1.3 57.4 + - - +
75D PHE* 3.4 7.6 - - - +
76D TYR* 3.1 50.3 + - + +
147D GLY* 5.6 1.6 - - - -
245D LEU* 4.4 26.0 - - + +
248D GLU* 6.3 0.2 - - + -
250D LEU* 3.8 30.3 - - + -
251D VAL* 3.2 28.0 - - + +
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Residues in contact with GLN 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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69D ALA 2.8 18.8 + - - +
70D GLY* 3.0 6.7 + - - +
72D VAL* 1.3 74.0 - - - +
74D GLN* 1.3 59.3 + - - +
75D PHE 3.1 1.8 - - - -
76D TYR* 3.2 11.9 + - - +
77D ASP* 2.9 63.1 + - - +
251D VAL* 3.5 29.3 - - + +
252D PRO* 5.4 3.1 + - - +
254D PRO* 6.2 0.6 - - - +
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Residues in contact with GLN 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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55D LYS* 4.0 25.1 - - - +
70D GLY 2.8 15.5 + - - +
71D ASP* 3.7 11.0 - - - +
73D GLN* 1.3 72.7 - - - +
75D PHE* 1.3 62.0 + - - +
77D ASP* 3.9 8.5 + - - +
78D LEU* 3.1 35.0 + - + +
137D LEU* 4.7 10.3 - - + +
139D LEU* 3.2 29.5 - - - +
143D GLN* 5.1 5.7 - - - +
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Residues in contact with PHE 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 ASP 3.0 12.6 + - - +
72D VAL* 3.4 11.0 - - - +
73D GLN 3.1 0.2 - - - -
74D GLN* 1.3 76.1 - - - +
76D TYR* 1.3 71.8 + + - +
78D LEU* 2.9 25.8 + - - +
79D LEU* 2.9 40.2 + - + +
147D GLY* 3.8 22.4 - - - +
148D PHE* 3.7 45.1 - + - -
151D TRP* 3.9 17.3 - + - -
241D ARG* 4.5 7.4 - - + -
242D ILE* 4.3 21.8 - - + -
245D LEU* 3.6 26.7 - - + -
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Residues in contact with TYR 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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72D VAL* 3.1 41.8 + - + +
73D GLN* 3.2 12.5 + - - +
75D PHE* 1.3 95.3 - + - +
77D ASP* 1.3 62.8 - - - +
79D LEU* 3.4 6.5 + - + +
80D SER* 3.1 25.9 + - - -
242D ILE* 4.4 10.8 + - + +
245D LEU* 3.5 26.5 - - + +
246D LYS* 4.2 13.5 + - - +
251D VAL* 3.4 28.7 + - + -
252D PRO 4.4 5.2 - - - +
253D PRO* 3.9 25.3 - - + +
254D PRO* 3.6 27.1 - - + +
257D ILE* 5.0 9.9 - - + -
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Residues in contact with ASP 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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73D GLN* 2.9 58.4 + - - +
74D GLN* 3.9 7.3 + - - +
76D TYR* 1.3 71.3 - - - +
78D LEU* 1.3 57.2 + - + +
80D SER* 3.7 5.2 - - - -
81D GLY* 2.6 34.7 + - - -
135D SER* 5.9 0.2 - - - -
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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
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74D GLN* 3.1 24.3 + - + +
75D PHE 2.9 5.7 + - - +
77D ASP* 1.3 78.5 - - + +
79D LEU* 1.3 64.6 + - - +
81D GLY* 4.1 1.2 - - - -
82D SER* 2.8 29.6 + - - -
116D PHE* 4.0 4.7 - - + -
133D PHE* 3.5 50.9 - - + -
135D SER* 4.1 18.7 + - - +
137D LEU* 3.7 25.4 - - + -
139D LEU* 4.1 10.8 - - + -
148D PHE* 4.0 17.9 - - + -
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Residues in contact with LEU 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 PHE* 2.9 66.2 + - + +
76D TYR* 3.5 10.3 - - + +
78D LEU* 1.3 76.6 - - + +
80D SER* 1.3 55.1 + - - +
82D SER* 2.8 25.5 + - - -
83D LEU 3.0 8.5 + - - -
112D PHE* 3.6 33.2 - - + -
113D LEU* 4.6 9.4 - - + -
116D PHE* 4.2 28.9 - - + -
151D TRP* 5.5 1.6 - - + -
242D ILE* 5.9 2.9 - - + -
257D ILE* 4.0 23.6 - - + -
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Residues in contact with SER 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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76D TYR 3.1 14.3 + - - -
77D ASP* 3.7 6.1 - - - -
79D LEU* 1.3 76.4 - - - +
81D GLY* 1.3 60.9 + - - +
83D LEU* 2.8 25.1 + - - +
84D GLU* 3.1 24.6 + - - +
254D PRO* 3.5 15.8 - - - +
256D ILE* 3.4 28.6 - - - +
257D ILE* 4.0 4.6 - - - +
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Residues in contact with GLY 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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77D ASP 2.6 22.5 + - - -
78D LEU 4.1 0.9 - - - -
80D SER* 1.3 74.2 - - - +
82D SER* 1.3 60.5 + - - +
84D GLU* 4.0 12.6 + - - +
85D VAL* 3.4 27.9 + - - +
135D SER* 4.5 18.1 - - - -
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Residues in contact with SER 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 LEU 2.8 20.4 + - - -
79D LEU 2.8 6.3 + - - -
81D GLY* 1.3 79.8 - - - +
83D LEU* 1.3 54.7 + - - +
85D VAL* 4.1 1.1 - - - +
86D ILE* 2.7 39.6 + - - +
112D PHE* 4.2 2.0 - - - -
116D PHE* 3.6 29.5 - - - -
133D PHE* 4.7 2.4 - - - +
134D CYS* 3.2 36.7 + - - +
135D SER* 4.3 2.3 + - - -
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Residues in contact with LEU 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 LEU 3.0 6.1 + - - +
80D SER* 2.8 10.4 + - - +
82D SER* 1.3 76.9 - - - +
84D GLU* 1.3 55.5 + - + +
86D ILE* 3.2 4.7 + - + +
87D ARG* 2.8 54.2 + - - +
108D LEU* 3.8 27.1 - - + -
112D PHE* 3.7 30.7 - - + -
256D ILE* 3.9 34.1 - - + -
257D ILE* 4.1 13.7 - - + -
260D ILE* 4.8 12.3 - - + -
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Residues in contact with GLU 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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80D SER* 3.1 28.9 + - - +
81D GLY* 4.0 9.7 - - - +
83D LEU* 1.3 77.6 - - + +
85D VAL* 1.3 67.1 + - + +
87D ARG* 3.2 8.3 + - - +
88D LYS* 3.1 43.5 + - - +
256D ILE* 6.2 3.1 - - + -
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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
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44D SER* 3.9 21.3 - - - +
81D GLY 3.4 19.4 + - - +
82D SER 4.1 3.4 - - - +
83D LEU 3.2 0.4 - - - -
84D GLU* 1.3 80.7 - - + +
86D ILE* 1.3 57.0 + - - +
88D LYS* 3.3 12.6 + - - +
89D TRP* 2.9 25.5 + - - +
119D ARG* 3.7 26.7 - - - +
134D CYS* 4.1 25.8 - - + +
135D SER* 4.9 4.3 - - - +
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Residues in contact with ILE 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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82D SER* 2.7 33.1 + - - +
83D LEU* 3.2 9.5 + - + +
85D VAL* 1.3 72.1 - - - +
87D ARG* 1.3 64.3 + - - +
89D TRP* 2.9 15.8 + - + +
90D ALA* 2.8 26.9 + - - +
108D LEU* 3.8 28.5 - - + -
112D PHE* 5.1 7.9 - - + -
115D LEU* 4.2 30.5 - - + -
116D PHE* 4.9 5.6 - - - +
119D ARG* 3.3 34.3 - - - +
134D CYS* 3.4 15.9 - - - -
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Residues in contact with ARG 87 (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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83D LEU* 2.8 46.2 + - - +
84D GLU* 3.8 8.4 - - - +
86D ILE* 1.3 75.5 - - - +
88D LYS* 1.3 64.2 + - + +
90D ALA* 3.1 9.8 + - + +
91D GLU* 3.1 30.7 + - + +
96D PHE* 6.0 1.3 - - + -
104D GLN* 6.5 0.4 - - - -
105D ASP* 3.7 21.8 + - - +
108D LEU* 4.0 31.1 - - + +
109D GLU* 5.6 4.9 - - - +
256D ILE* 5.0 9.3 - - - +
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Residues in contact with LYS 88 (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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44D SER* 5.4 1.6 - - - -
84D GLU* 3.1 33.9 + - - +
85D VAL* 3.7 12.6 - - - +
87D ARG* 1.3 77.5 - - + +
89D TRP* 1.3 59.9 + - - +
91D GLU* 3.7 9.6 + - + +
92D LYS* 3.5 27.9 + - - +
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Residues in contact with TRP 89 (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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37D LEU* 5.3 1.6 + - + +
40D ALA* 3.1 34.4 - - + +
41D HIS* 3.6 21.0 - - - +
44D SER* 3.7 21.3 - - - +
85D VAL 2.9 11.6 + - - +
86D ILE* 2.9 25.1 + - + +
88D LYS* 1.3 72.8 - - - +
90D ALA* 1.3 76.9 + - + +
92D LYS* 3.4 13.7 + - - +
93D ILE* 3.6 29.1 + - + +
115D LEU* 4.0 25.8 - - + -
119D ARG* 3.8 17.2 - - - +
173D ALA 4.7 3.5 + - - -
176D SER* 3.2 49.4 - - - -
177D ALA* 3.8 6.7 - - + -
180D LEU* 4.1 15.5 - - + -
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Residues in contact with ALA 90 (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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86D ILE 2.8 14.6 + - - +
87D ARG 3.4 9.0 - - - +
89D TRP* 1.3 82.5 - - + +
91D GLU* 1.3 61.0 + - - +
93D ILE* 3.3 17.3 + - - +
96D PHE* 3.3 42.7 - - + +
108D LEU* 3.7 16.4 - - + -
180D LEU* 3.9 12.1 - - + -
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Residues in contact with GLU 91 (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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87D ARG* 3.1 20.6 + - + +
88D LYS* 3.9 13.2 - - + +
89D TRP 3.3 0.6 - - - -
90D ALA* 1.3 71.2 - - - +
92D LYS* 1.3 58.8 + - + +
93D ILE 2.9 19.8 + - - +
96D PHE* 3.0 34.9 - - - -
97D ALA* 3.3 34.0 - - - +
104D GLN* 3.5 12.9 + - - +
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Residues in contact with LYS 92 (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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36D SER* 4.9 5.2 + - - +
39D ARG 5.5 0.2 - - - -
40D ALA* 3.6 30.6 - - + +
43D ASP* 4.0 42.6 + - + +
88D LYS* 3.5 17.0 + - - +
89D TRP* 3.4 4.8 + - - +
91D GLU* 1.3 75.0 - - + +
93D ILE* 1.3 58.3 + - - +
94D PRO* 3.6 7.4 - - - +
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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