Contacts of the helix formed by residues 66 - 95 (chain D) in PDB entry 4DAJ
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 GLN 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TRP* 1.3 80.7 - - - +
67D VAL* 1.3 57.4 + - - +
69D PHE* 3.4 10.9 - - + +
70D ILE* 2.9 31.7 + - - +
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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
----------------------------------------------------------
65D TRP 3.0 6.8 - - - +
66D GLN* 1.3 77.3 - - - +
68D VAL* 1.3 62.7 + - + +
70D ILE* 4.1 3.6 - - - +
71D ALA* 2.9 32.2 + - - +
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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
----------------------------------------------------------
65D TRP* 3.2 34.4 + - + +
67D VAL* 1.3 77.1 - - + +
69D PHE* 1.3 63.6 + - - +
71D ALA* 3.3 6.5 + - + +
72D PHE* 2.9 25.8 + - + +
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TRP* 3.1 12.5 + - + +
66D GLN* 3.4 15.9 - - + +
68D VAL* 1.3 82.6 - - - +
70D ILE* 1.3 79.0 + - + +
72D PHE* 3.1 5.6 + - - +
73D LEU* 3.0 25.1 + - + +
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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
----------------------------------------------------------
66D GLN 2.9 16.0 + - - +
67D VAL* 4.1 3.8 - - - +
69D PHE* 1.3 84.8 - - + +
71D ALA* 1.3 58.1 + - - +
73D LEU* 2.9 13.6 - - + +
74D THR* 2.9 32.9 + - + +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL 2.9 19.8 + - - +
68D VAL* 3.3 8.7 - - - +
69D PHE 3.1 0.2 - - - -
70D ILE* 1.3 73.3 - - - +
72D PHE* 1.3 66.9 + - - +
74D THR* 2.6 31.5 + - - -
75D GLY* 3.0 4.0 + - - -
125D THR* 4.4 14.7 - - + +
129D ILE* 5.8 7.2 - - + -
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Residues in contact with PHE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D VAL* 2.9 15.2 + - + +
69D PHE* 3.5 9.0 - - + +
71D ALA* 1.3 73.8 - - - +
73D LEU* 1.3 63.3 + - - +
75D GLY* 3.0 5.4 + - - +
76D PHE* 2.9 20.6 + - - +
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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
----------------------------------------------------------
69D PHE* 3.0 16.0 + - + +
70D ILE* 2.9 21.8 - - - +
71D ALA 3.0 0.2 - - - -
72D PHE* 1.3 76.4 - - - +
74D THR* 1.3 60.8 + - + +
76D PHE* 3.0 19.6 + - + +
77D LEU* 3.0 18.9 + - - +
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Residues in contact with THR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 2.9 19.0 + - + +
71D ALA* 2.6 20.5 + - - +
73D LEU* 1.3 68.5 - - + +
75D GLY* 1.3 64.9 + - - +
77D LEU* 3.2 12.3 + - + +
78D ALA* 2.9 23.6 + - - +
125D THR* 3.0 33.0 + - + +
530D TRP* 3.9 29.0 - - + +
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA 3.0 6.9 + - - -
72D PHE* 3.0 6.5 + - - -
74D THR* 1.3 82.6 + - - +
76D PHE* 1.3 62.8 + - - +
78D ALA* 3.0 8.8 + - - +
79D LEU* 2.9 24.3 + - - +
122D ASN* 5.6 1.1 - - - -
125D THR* 5.9 1.1 - - - -
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Residues in contact with PHE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE 2.9 11.1 + - - +
73D LEU* 3.1 17.9 - - + +
75D GLY* 1.3 74.4 - - - +
77D LEU* 1.3 73.5 + - + +
79D LEU* 3.3 12.9 + - + +
80D VAL* 3.0 45.3 + - + +
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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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73D LEU 3.0 11.5 + - - +
74D THR* 3.3 12.3 - - + +
76D PHE* 1.3 86.9 - - + +
78D ALA* 1.3 63.9 + - - +
80D VAL* 3.0 9.8 + - + +
81D THR* 2.9 23.0 + - - -
121D MET* 3.6 20.4 - - + -
530D TRP* 4.0 16.2 - - + -
534D ILE* 3.6 29.2 - - + -
537D THR* 3.8 26.9 - - + +
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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
----------------------------------------------------------
74D THR 2.9 15.2 + - - +
75D GLY* 3.6 9.2 - - - +
77D LEU* 1.3 72.5 - - - +
79D LEU* 1.3 64.0 + - - +
81D THR* 3.2 3.3 + - - -
82D ILE* 3.0 29.8 + - + +
117D GLY 4.1 2.9 - - - +
121D MET* 3.5 29.1 - - + +
122D ASN* 3.0 29.4 - - - +
125D THR* 6.2 0.2 - - - +
530D TRP* 5.6 0.2 - - + -
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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
----------------------------------------------------------
75D GLY 2.9 12.7 + - - +
76D PHE* 3.4 16.2 - - + +
78D ALA* 1.3 75.4 - - - +
80D VAL* 1.3 66.6 + - + +
82D ILE* 2.9 22.2 - - + +
83D ILE* 2.9 47.2 + - + +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 3.0 46.9 + - + +
77D LEU* 3.5 11.0 - - + +
79D LEU* 1.3 77.5 - - + +
81D THR* 1.3 58.3 + - - +
83D ILE* 3.0 17.5 - - + +
84D GLY* 2.9 28.1 + - - -
537D THR* 4.5 15.2 - - + +
541D VAL* 5.8 6.7 - - + -
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Residues in contact with THR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU 2.9 11.5 + - - -
78D ALA 3.4 8.1 - - - -
79D LEU 3.1 0.2 - - - -
80D VAL* 1.3 76.4 - - - +
82D ILE* 1.3 64.9 + - - +
84D GLY* 3.3 1.1 + - - -
85D ASN* 2.9 46.7 + - - +
113D ASP 3.8 10.8 - - - +
117D GLY* 4.0 3.4 - - - +
121D MET* 3.5 21.1 - - - -
536D SER* 3.7 18.6 - - - +
537D THR* 2.6 35.5 + - - +
540D PRO* 5.3 0.5 - - - +
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Residues in contact with ILE 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 ALA 3.0 15.7 + - - +
79D LEU* 2.9 44.9 - - + +
81D THR* 1.3 76.4 - - - +
83D ILE* 1.3 64.0 + - + +
85D ASN* 3.3 7.1 + - - +
86D ILE* 2.9 32.1 + - - +
114D LEU* 4.3 13.4 - - + +
117D GLY* 3.6 5.8 - - - +
118D VAL* 3.3 46.2 - - + +
122D ASN* 5.8 2.0 - - - +
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 2.9 40.4 + - + +
80D VAL* 3.0 35.7 - - + +
82D ILE* 1.3 74.5 - - + +
84D GLY* 1.3 68.3 + - - +
86D ILE* 2.7 28.5 - - + +
87D LEU* 2.9 17.6 + - + +
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Residues in contact with GLY 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 VAL 2.9 17.2 + - - -
81D THR* 3.7 0.7 - - - -
83D ILE* 1.3 79.0 - - - +
85D ASN* 1.3 61.8 + - - +
87D LEU* 3.0 16.8 + - - +
88D VAL* 2.9 27.0 + - - +
540D PRO* 4.3 10.5 - - - -
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Residues in contact with ASN 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D THR* 2.9 37.1 + - - +
82D ILE 3.8 3.6 - - - +
84D GLY* 1.3 73.8 - - - +
86D ILE* 1.3 58.1 + - - +
88D VAL* 3.1 9.5 + - - +
89D ILE* 3.0 34.1 + - - +
110D ALA* 3.5 18.7 - - - +
113D ASP* 3.1 46.1 + - - +
114D LEU* 3.3 11.7 - - + +
536D SER 3.9 0.6 + - - -
540D PRO* 2.9 27.3 - - - +
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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 ILE 2.9 18.2 + - - +
83D ILE* 2.7 35.0 - - + +
85D ASN* 1.3 72.6 - - - +
87D LEU* 1.3 67.6 + - + +
89D ILE* 3.2 9.8 + - + +
90D VAL* 2.9 48.6 + - + +
114D LEU* 3.9 18.0 - - + +
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Residues in contact with LEU 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 ILE* 2.9 19.1 + - + +
84D GLY* 3.0 17.3 - - - +
86D ILE* 1.3 76.9 - - + +
88D VAL* 1.3 64.3 + - - +
90D VAL* 3.8 4.6 - - + +
91D ALA* 2.9 29.4 + - + +
554D PHE* 3.4 43.5 - - + +
557D LEU* 5.7 5.8 - - + -
558D LEU* 5.0 17.0 - - + +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLY 2.9 19.1 + - - +
85D ASN 3.2 7.6 - - - +
87D LEU* 1.3 75.7 - - - +
89D ILE* 1.3 65.9 + - - +
91D ALA* 3.8 1.4 - - - +
92D PHE* 3.0 25.4 + - + +
106D LEU* 4.3 4.7 - - + +
107D LEU* 4.9 4.3 - - - -
110D ALA* 3.5 21.1 - - + -
540D PRO* 3.4 31.6 - - + -
543D TYR* 4.1 20.9 - - + -
550D PHE* 4.7 11.3 - - + -
554D PHE* 3.9 19.1 - - + -
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Residues in contact with ILE 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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85D ASN 3.0 11.3 + - - +
86D ILE* 3.8 11.9 - - + +
88D VAL* 1.3 77.0 - - - +
90D VAL* 1.3 64.0 + - + +
92D PHE* 3.3 5.5 + - - +
93D LYS* 3.0 26.7 + - + +
107D LEU* 4.5 24.4 - - + +
110D ALA* 4.1 20.2 - - + +
111D CYS* 4.6 14.4 - - - -
114D LEU* 3.5 33.2 - - + -
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ILE* 2.9 47.1 + - + +
87D LEU* 3.8 5.8 - - + +
89D ILE* 1.3 72.1 - - + +
91D ALA* 1.3 67.8 + - - +
93D LYS* 3.0 6.5 + - - +
94D VAL* 2.9 36.9 + - + +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 2.9 22.5 + - + +
88D VAL 3.8 1.6 - - - +
90D VAL* 1.3 73.9 - - - +
92D PHE* 1.3 64.7 + - - +
94D VAL* 3.6 8.6 - - - +
95D ASN* 3.2 15.6 + - - +
98D LEU* 3.0 20.1 - - + +
550D PHE* 5.6 0.7 - - + -
553D THR* 3.4 25.1 - - + +
554D PHE* 3.7 21.1 - - + -
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Residues in contact with PHE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 3.0 16.6 + - + +
89D ILE* 3.5 7.9 - - - +
91D ALA* 1.3 75.4 - - - +
93D LYS* 1.3 72.6 + - + +
94D VAL 3.1 0.3 + - - -
95D ASN 2.9 22.3 + - - +
98D LEU* 3.1 38.3 - - + +
99D LYS* 3.4 37.8 - - + -
100D THR 4.3 1.1 - - - -
103D ASN* 3.5 33.7 - - + -
104D TYR* 3.8 23.1 - + - -
107D LEU* 3.4 30.1 - - + -
181D THR* 6.0 0.2 - - + -
550D PHE* 5.7 6.2 - + + -
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Residues in contact with LYS 93 (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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89D ILE* 3.0 21.3 + - + +
90D VAL* 3.9 4.3 - - - +
92D PHE* 1.3 85.8 - - + +
94D VAL* 1.3 60.7 + - + +
99D LYS* 3.2 25.3 + - - +
107D LEU* 5.8 1.6 - - + -
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D VAL* 2.9 29.8 + - + +
91D ALA* 3.6 12.6 - - - +
93D LYS* 1.3 77.5 - - + +
95D ASN* 1.3 64.6 + - + +
96D LYS 4.2 0.2 - - - -
553D THR* 5.3 3.4 - - + -
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Residues in contact with ASN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ALA 3.2 14.9 + - - +
92D PHE 2.9 19.4 + - - +
93D LYS 3.4 1.5 - - - -
94D VAL* 1.3 84.2 - - + +
96D LYS* 1.3 63.9 + - - +
97D GLN* 2.9 40.1 + - - +
98D LEU* 3.1 18.9 + - + +
99D LYS* 3.7 3.5 + - - +
553D THR* 3.7 23.8 + - + +
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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