Contacts of the helix formed by residues 61 - 90 (chain D) in PDB entry 2FBW
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 GLY 61 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D HIS* 1.3 75.3 - - - +
62D ASP* 1.3 68.5 + - - -
63D THR 3.3 2.7 - - - -
64D PRO* 3.6 9.0 - - - -
65D ILE* 3.0 31.8 + - - +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLY* 1.3 72.5 - - - +
63D THR* 1.3 65.5 + - - +
64D PRO* 4.3 0.2 - - - +
65D ILE* 3.4 7.3 + - - +
66D LYS* 3.1 37.3 + - - +
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Residues in contact with THR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASP* 1.3 76.4 - - - +
64D PRO* 1.3 76.4 - - + +
65D ILE 3.2 0.2 + - - -
66D LYS* 3.2 17.4 + - + +
67D VAL* 2.9 39.2 + - + +
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Residues in contact with PRO 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL* 3.6 12.1 - - + +
60D HIS 3.6 22.0 - - - +
61D GLY* 3.6 9.4 - - - +
63D THR* 1.3 96.9 - - + +
65D ILE* 1.3 56.6 + - - +
67D VAL* 3.4 6.3 + - + +
68D ALA* 2.9 30.5 + - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS* 6.2 2.5 - - - +
210B PHE* 5.6 10.1 - - + -
55D ILE* 5.1 5.4 - - + +
56D THR* 6.1 3.6 - - - +
59D VAL* 3.5 37.0 - - + +
60D HIS* 4.1 1.8 - - + -
61D GLY 3.0 32.2 + - - +
62D ASP* 3.7 7.9 - - - +
64D PRO* 1.3 72.2 - - - +
66D LYS* 1.3 69.6 + - + +
68D ALA* 3.2 2.8 + - - +
69D ASN* 3.0 43.5 + - - +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASP* 3.1 34.1 + - - +
63D THR* 3.2 14.7 + - - +
65D ILE* 1.3 77.5 - - + +
67D VAL* 1.3 64.9 + - + +
69D ASN* 3.9 4.0 - - - +
70D THR* 2.9 30.3 + - - +
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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
----------------------------------------------------------
63D THR* 2.9 34.7 + - + +
64D PRO* 3.8 6.3 - - + +
66D LYS* 1.3 76.7 - - + +
68D ALA* 1.3 66.3 + - - +
70D THR* 3.2 6.5 + - - -
71D GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE* 3.8 31.7 - - + +
59D VAL* 4.3 12.1 - - + -
64D PRO 2.9 18.1 + - - +
65D ILE 3.7 3.4 - - - +
67D VAL* 1.3 79.4 - - - +
69D ASN* 1.3 57.3 + - - +
71D GLY* 3.3 1.8 + - - -
72D LEU* 3.0 27.2 + - - +
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Residues in contact with ASN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 5.3 0.4 - - - -
52D GLY* 4.8 6.5 + - - -
55D ILE* 3.9 25.3 - - - +
56D THR* 5.7 1.4 + - - -
65D ILE* 3.0 37.6 + - - +
66D LYS* 4.1 4.7 - - - +
68D ALA* 1.3 73.6 - - - +
70D THR* 1.3 64.8 + - - +
72D LEU* 3.4 13.0 + - - +
73D TYR* 3.1 36.5 + - + -
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LYS* 2.9 20.6 + - - +
67D VAL* 3.2 7.1 + - - -
69D ASN* 1.3 77.5 - - - +
71D GLY* 1.3 62.1 + - - +
73D TYR* 3.3 12.1 + - + +
74D VAL* 3.2 28.2 + - + +
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Residues in contact with GLY 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL 3.0 14.0 + - - -
68D ALA* 3.8 3.1 - - - -
70D THR* 1.3 76.9 - - - +
72D LEU* 1.3 62.4 + - - +
74D VAL* 3.1 11.7 + - - +
75D LEU* 3.0 22.0 + - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 3.4 40.2 - - + +
51D LEU* 3.7 31.0 - - + -
52D GLY* 3.6 22.0 - - - +
55D ILE* 3.8 16.2 - - + -
68D ALA 3.0 16.7 + - - +
69D ASN* 3.7 12.3 - - - +
70D THR 3.3 0.2 - - - -
71D GLY* 1.3 75.9 - - - +
73D TYR* 1.3 56.3 + - - +
75D LEU* 3.1 15.0 + - + +
76D SER* 2.8 39.9 + - - +
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Residues in contact with TYR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D HIS* 4.0 27.1 + + - -
69D ASN* 3.1 31.1 + - + -
70D THR* 3.3 12.1 + - + +
72D LEU* 1.3 76.2 - - - +
74D VAL* 1.3 64.7 + - + +
76D SER* 3.8 2.5 - - - -
77D ALA* 2.9 26.7 + - - +
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 3.3 24.0 - - + +
71D GLY* 3.1 10.4 + - - +
73D TYR* 1.3 76.8 - - + +
75D LEU* 1.3 64.1 + - - +
77D ALA* 3.3 4.9 + - - +
78D ILE* 2.9 49.6 + - + +
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C SER 6.4 0.2 - - - -
51C LEU* 4.9 13.7 - - + -
54C SER* 3.4 35.7 - - - +
51D LEU* 4.5 21.5 - - + -
71D GLY 3.0 12.8 + - - +
72D LEU* 3.6 14.4 - - + +
74D VAL* 1.3 77.4 - - - +
76D SER* 1.3 58.4 + - - +
78D ILE* 3.4 9.4 + - + -
79D THR* 2.8 34.8 + - - +
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Residues in contact with SER 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D THR* 3.7 14.1 + - - +
48D HIS* 2.7 45.8 + - - +
72D LEU* 2.8 20.3 + - - +
73D TYR* 3.8 5.2 - - - -
75D LEU* 1.3 73.8 - - - +
77D ALA* 1.3 58.3 + - - +
79D THR* 3.1 6.7 + - - -
80D PHE* 2.8 32.2 + - - +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TYR 2.9 18.3 + - - +
74D VAL* 3.8 4.9 - - - +
76D SER* 1.3 75.7 - - - +
78D ILE* 1.3 60.2 + - + +
80D PHE* 4.0 4.5 - - - +
81D THR* 2.7 34.9 + - - +
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Residues in contact with ILE 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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54C SER 6.1 0.2 - - - +
57C SER* 3.3 3.9 + - - +
58C LEU* 4.4 20.2 - - + +
61C LEU* 4.1 19.0 - - + +
74D VAL* 2.9 42.1 + - + +
75D LEU* 3.8 9.6 - - + +
77D ALA* 1.3 75.8 - - + +
79D THR* 1.3 63.7 + - - +
81D THR* 3.3 6.7 + - - -
82D GLY* 3.0 19.1 + - - -
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Residues in contact with THR 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL* 3.7 29.8 - - + -
54C SER* 2.7 36.0 + - - +
57C SER* 2.8 23.3 + - - -
44D THR* 4.2 13.0 - - + +
75D LEU* 2.8 25.6 + - - +
76D SER* 3.5 7.4 - - - -
78D ILE* 1.3 78.0 - - - +
80D PHE* 1.3 62.7 + - - +
83D LEU* 3.1 14.0 + - + +
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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
----------------------------------------------------------
37D TYR 4.9 1.3 - - - -
40D ALA* 3.6 20.0 - - + -
41D ALA* 3.9 30.1 - - + -
44D THR* 3.5 20.6 + - + +
76D SER 2.8 17.6 + - - +
77D ALA* 4.2 4.3 - - - +
79D THR* 1.3 74.6 - - - +
81D THR* 1.3 68.0 + - - +
83D LEU* 3.6 2.9 + - - +
84D CYS* 3.2 50.2 + - - -
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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
----------------------------------------------------------
61C LEU* 4.7 13.5 - - + -
77D ALA* 2.7 23.4 + - - +
78D ILE* 3.6 7.0 - - - -
79D THR 3.2 0.2 - - - -
80D PHE* 1.3 83.2 - - - +
82D GLY* 1.3 57.6 + - - +
84D CYS* 3.9 4.2 - - - +
85D TYR* 2.9 28.8 + - + +
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER* 3.1 22.0 - - - -
60C ALA* 4.5 1.4 - - - +
61C LEU* 3.8 25.7 - - - +
78D ILE 3.0 11.9 + - - -
79D THR 3.3 0.2 + - - -
81D THR* 1.3 76.8 - - - +
83D LEU* 1.3 51.1 + - - +
85D TYR* 3.2 2.4 + - - +
86D PHE* 2.6 37.7 + - - +
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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
----------------------------------------------------------
53C VAL* 3.9 25.6 - - + -
56C PHE* 3.9 31.9 - - + -
57C SER* 3.6 10.5 + - - -
40D ALA* 3.9 38.8 - - + +
43D LEU* 4.7 7.6 - - + -
44D THR* 4.2 7.0 - - - +
79D THR* 3.1 17.0 + - + +
80D PHE 4.0 2.5 - - - +
82D GLY* 1.3 74.9 - - - +
84D CYS* 1.3 57.8 + - - +
86D PHE* 3.2 5.2 + - - +
87D ASN* 2.8 34.8 + - - -
93D ILE* 4.3 18.3 - - + +
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Residues in contact with CYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D TYR* 4.1 28.7 - - + -
40D ALA* 4.4 3.4 - - - -
80D PHE* 3.2 58.0 + - - +
81D THR* 3.9 4.3 - - - +
83D LEU* 1.3 76.9 - - - +
85D TYR* 1.3 57.4 + - - +
87D ASN* 3.1 3.4 + - - +
88D TYR* 2.9 31.9 + - - +
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Residues in contact with TYR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 3.4 28.5 + - + -
61C LEU* 3.8 32.0 + - + -
66C GLN* 6.1 1.3 - - - -
81D THR* 2.9 21.2 + - + +
82D GLY 3.4 4.3 - - - +
84D CYS* 1.3 76.1 - - - +
86D PHE* 1.3 61.8 + - - +
88D TYR* 4.7 3.4 - - - -
89D TYR* 2.9 68.7 + + + +
90D ASP* 6.5 0.9 - - + -
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.6 32.8 - + + -
60C ALA* 4.0 23.8 - - + -
67C PHE* 3.8 15.0 - + + -
82D GLY 2.6 20.9 + - - +
83D LEU* 3.6 6.3 - - - +
85D TYR* 1.3 76.9 - - - +
87D ASN* 1.3 64.6 + - - +
90D ASP* 3.0 59.6 + - + +
91D VAL* 4.0 12.3 - - + -
92D GLY* 3.4 32.1 - - - -
93D ILE* 3.9 7.2 - - + -
96D ALA* 3.6 20.9 - - + -
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Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASP* 2.9 41.8 + - + +
37D TYR* 3.5 36.6 + - + +
40D ALA* 4.0 7.7 - - - +
83D LEU 2.8 24.2 + - - +
84D CYS 3.1 2.2 + - - +
86D PHE* 1.3 73.7 - - - +
88D TYR* 1.3 62.5 + - - +
90D ASP 3.5 10.2 - - - +
91D VAL 4.9 0.3 - - - -
92D GLY* 3.4 8.9 - - - -
93D ILE* 3.1 33.9 + - - +
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D TYR* 3.4 16.2 - + + +
84D CYS 2.9 16.7 + - - +
85D TYR* 4.0 2.9 - - - +
87D ASN* 1.3 79.1 - - - +
89D TYR* 1.3 101.0 + + + +
90D ASP 3.6 2.4 + - - +
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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
----------------------------------------------------------
66C GLN* 2.8 27.1 + - - +
85D TYR* 2.9 54.1 + + + +
88D TYR* 1.3 108.1 - + + +
90D ASP* 1.3 58.1 + - - +
----------------------------------------------------------
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Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLN* 3.1 22.3 + - - +
67C PHE 3.0 22.3 + - - -
68C PRO* 3.7 10.2 - - - +
85D TYR* 6.5 0.4 - - + -
86D PHE* 3.0 45.0 + - + +
87D ASN 3.5 10.9 - - - +
88D TYR 4.3 2.3 - - - +
89D TYR* 1.3 78.1 - - + +
91D VAL* 1.3 92.9 + - - +
92D GLY 3.3 2.7 + - - -
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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