Contacts of the helix formed by residues 79 - 103 (chain B) in PDB entry 5FN2
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 ALA 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLY* 1.3 71.3 - - - -
80B LYS* 1.3 57.0 + - - +
81B HIS 3.1 2.5 - - - -
82B VAL* 2.7 33.2 + - - +
83B ILE* 2.9 10.9 + - - -
29C PRO* 3.8 7.0 - - + +
30C LEU* 3.8 34.8 - - + +
33C ILE* 3.7 21.5 - - + -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY* 3.6 0.9 - - - -
79B ALA* 1.3 76.6 - - - +
81B HIS* 1.3 61.6 + - + +
83B ILE* 3.2 7.2 + - + +
84B MET* 2.9 49.3 + - + +
27C GLY 5.8 2.4 + - - -
29C PRO* 3.8 21.2 - - + +
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Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY* 3.5 35.9 + - - +
80B LYS* 1.3 80.8 + - + +
82B VAL* 1.3 62.9 + - - +
84B MET* 3.4 4.1 + - - +
85B LEU* 3.0 23.8 + - - +
378B GLY* 5.0 21.1 + - - -
379B VAL* 3.9 21.9 - - + +
422B LEU* 4.8 10.5 - - + -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY 3.9 14.1 - - - +
79B ALA* 2.7 21.1 + - - +
81B HIS* 1.3 73.1 - - - +
83B ILE* 1.3 57.4 + - - +
85B LEU* 3.2 4.2 + - - +
86B PHE* 2.9 52.7 + - + -
418B LEU* 4.4 1.9 - - + +
419B CYS* 4.6 7.6 - - + +
422B LEU* 3.4 44.6 - - + -
423B LEU* 4.6 13.7 - - + -
33C ILE* 3.9 16.2 - - + -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 2.9 6.9 + - - -
80B LYS* 3.2 15.4 + - + +
82B VAL* 1.3 76.8 - - - +
84B MET* 1.3 74.2 + - + +
86B PHE* 3.2 15.6 + - + +
87B VAL* 3.0 43.6 + - + +
26C ALA 4.5 10.8 - - - +
27C GLY 4.7 3.1 - - - +
29C PRO* 3.5 39.9 - - + +
32C VAL* 4.2 28.9 - - + -
33C ILE* 5.3 1.3 - - + -
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LYS* 2.9 37.7 + - + +
81B HIS* 4.0 4.7 - - - +
83B ILE* 1.3 84.1 - - + +
85B LEU* 1.3 52.0 + - - +
87B VAL* 4.8 4.5 - - + -
88B PRO* 2.5 38.5 - - - +
220B ARG* 5.0 18.6 - - - +
223B GLN* 5.5 4.0 - - - +
287B ILE 5.4 3.6 - - - +
288B TYR* 4.3 39.5 - - + -
379B VAL* 6.0 1.6 - - + -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B HIS 3.0 13.7 + - - +
82B VAL 3.2 8.5 + - - +
84B MET* 1.3 77.1 - - - +
86B PHE* 1.3 62.1 + - - +
88B PRO* 3.4 7.9 - - - +
89B VAL* 3.5 11.4 - - + +
286B LEU* 5.0 4.9 - - + +
287B ILE 5.8 3.1 - - - -
379B VAL* 3.9 27.7 - - + +
380B LYS 4.8 2.7 - - - +
381B LEU* 3.9 39.3 - - + -
418B LEU* 3.8 25.6 - - + -
422B LEU* 3.3 28.5 - - + -
425B LEU* 6.0 1.6 - - + -
432B LEU* 6.0 2.7 - - + -
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 2.9 36.9 + - + -
83B ILE* 3.2 20.4 - - + +
85B LEU* 1.3 78.4 - - - +
87B VAL* 1.3 68.0 + - + +
89B VAL* 2.9 9.2 + - + +
90B THR* 2.8 27.1 + - - +
415B LEU* 3.1 58.8 - - + -
418B LEU* 3.6 21.5 - - + +
419B CYS* 3.9 16.4 - - + -
32C VAL* 5.5 5.2 - - + -
33C ILE* 4.1 17.9 - - + -
36C VAL* 4.6 11.4 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.0 38.3 + - + +
84B MET* 4.2 3.6 - - - +
86B PHE* 1.3 76.4 - - + +
88B PRO* 1.3 70.6 - - + +
90B THR* 3.2 10.8 + - + +
91B LEU* 2.9 38.7 + - + +
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Residues in contact with PRO 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET 2.5 30.5 - - - +
85B LEU* 3.4 2.7 - - - +
86B PHE 3.4 2.5 - - - -
87B VAL* 1.3 86.9 - - + +
89B VAL* 1.3 55.8 + - - +
91B LEU* 3.2 8.3 + - + +
92B CYS* 2.9 28.1 + - - +
223B GLN* 4.3 18.6 - - + +
227B ILE* 4.0 15.6 - - + +
286B LEU* 3.2 35.2 - - + -
287B ILE 5.5 2.0 - - - +
386B PHE* 3.8 3.6 - - - -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.5 20.6 - - + +
86B PHE 2.9 8.8 + - - +
88B PRO* 1.3 80.9 - - - +
90B THR* 1.3 57.3 + - - +
92B CYS* 3.2 5.7 + - - +
93B MET* 2.9 45.1 + - + +
286B LEU* 5.4 0.4 - - + -
381B LEU* 5.1 1.3 - - + -
386B PHE* 3.4 33.7 - - + -
389B TYR* 4.2 20.0 - - + -
414B ILE* 4.8 7.0 - - + -
415B LEU* 5.3 6.3 - - + -
418B LEU* 3.8 26.7 - - + -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 2.8 20.5 + - - +
87B VAL* 3.2 13.8 - - + +
89B VAL* 1.3 77.5 - - - +
91B LEU* 1.3 59.5 + - + +
93B MET* 3.2 4.3 + - - +
94B VAL* 2.9 41.2 + - + +
411B PHE* 3.7 30.8 - - + -
415B LEU* 4.3 11.1 - - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL* 2.9 23.0 + - + +
88B PRO* 3.2 10.5 + - + +
90B THR* 1.3 78.2 - - + +
92B CYS* 1.3 57.4 + - - +
94B VAL* 3.2 10.6 + - + +
95B VAL* 2.9 42.2 + - + +
227B ILE* 3.4 26.0 - - + -
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Residues in contact with CYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PRO 2.9 5.8 + - - +
89B VAL* 3.3 9.2 - - - +
91B LEU* 1.3 75.7 - - - +
93B MET* 1.3 63.0 + - - +
95B VAL* 3.2 8.7 + - - +
96B VAL* 2.9 34.0 + - - +
227B ILE* 4.0 16.7 - - + +
230B SER* 5.2 1.8 - - - -
231B ALA* 4.6 2.6 - - + +
386B PHE* 3.2 49.8 - - + -
390B SER* 2.5 36.8 - - - -
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Residues in contact with MET 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 2.9 33.2 + - + +
90B THR 3.3 7.4 - - - +
92B CYS* 1.3 79.3 - - - +
94B VAL* 1.3 55.9 + - - +
96B VAL* 3.2 3.1 + - - +
97B VAL* 2.9 36.7 + - - +
389B TYR* 3.5 35.7 - - - +
390B SER* 3.7 9.2 - - - -
393B VAL* 3.5 28.9 - - + -
411B PHE* 3.3 43.5 - - + -
414B ILE* 3.6 24.9 - - + -
415B LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 2.9 29.2 + - + +
91B LEU* 3.2 12.3 + - + +
93B MET* 1.3 76.9 - - - +
95B VAL* 1.3 59.7 + - + +
97B VAL* 3.6 5.5 - - - +
98B ALA* 2.9 39.5 + - + +
411B PHE* 4.7 7.2 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 2.9 33.0 + - + +
92B CYS* 3.2 10.5 + - - +
94B VAL* 1.3 77.4 - - + +
96B VAL* 1.3 60.9 + - - +
98B ALA* 4.5 2.1 - - - +
99B THR* 3.0 34.1 + - + +
181B TYR* 5.0 10.8 - - + +
227B ILE* 5.0 5.2 - - + -
228B MET* 4.6 17.7 - - + -
231B ALA* 3.9 21.5 - - + -
235B LEU* 5.6 2.5 - - + -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B CYS 2.9 10.5 + - - +
93B MET* 3.5 7.9 - - - +
95B VAL* 1.3 76.9 - - - +
97B VAL* 1.3 62.4 + - - +
99B THR* 3.1 20.3 - - - +
100B ILE* 3.1 35.6 - - + +
231B ALA* 3.9 25.1 - - + +
234B ALA* 4.2 4.9 - - + -
235B LEU* 4.4 5.2 - - + -
238B ILE* 3.8 8.5 - - + -
390B SER* 3.1 52.5 - - - +
393B VAL* 4.5 0.2 - - + -
394B GLY* 3.9 3.8 - - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B MET* 2.9 25.4 + - + +
94B VAL* 3.6 6.7 - - - +
96B VAL* 1.3 76.2 - - - +
98B ALA* 1.3 63.9 + - - +
100B ILE* 3.2 8.4 + - - +
101B LYS* 2.9 33.6 + - + +
393B VAL* 3.6 36.8 - - + +
397B SER* 4.2 5.2 + - - +
404B TRP* 4.2 26.9 - - + -
407B THR* 4.4 13.7 - - + +
411B PHE* 5.6 2.7 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 2.9 24.8 + - + +
95B VAL* 4.5 2.0 - - - +
97B VAL* 1.3 82.5 - - + +
99B THR* 1.3 57.0 + - - +
101B LYS* 3.2 8.9 + - - +
102B SER* 2.9 32.8 + - - -
404B TRP* 5.8 2.9 - - + -
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 3.0 23.6 + - + +
96B VAL 3.1 9.2 - - - +
98B ALA* 1.3 78.3 - - - +
100B ILE* 1.3 60.6 + - - +
102B SER* 3.9 5.8 - - - -
103B VAL* 2.7 52.3 + - - +
106B TYR* 4.4 3.0 - - + -
181B TYR* 3.4 28.2 + - + -
185B VAL* 5.0 0.7 - - - +
235B LEU* 3.3 31.9 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 3.1 31.7 + - + +
97B VAL* 3.2 5.1 + - - +
99B THR* 1.3 82.1 - - - +
101B LYS* 1.3 65.0 + - + +
103B VAL 3.0 16.8 - - - +
106B TYR* 4.8 18.3 - - + +
107B THR* 5.6 8.3 + - - +
235B LEU* 3.6 13.5 - - + -
238B ILE* 3.6 19.5 - - + -
394B GLY* 3.3 39.9 - - - +
397B SER* 4.0 15.5 - - - +
398B ALA* 4.5 13.7 - - + +
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 2.9 18.8 + - + +
98B ALA* 3.4 9.9 - - - +
100B ILE* 1.3 80.5 - - + +
102B SER* 1.3 61.6 + - - +
103B VAL 4.2 1.2 - - - +
397B SER* 3.2 24.8 + - - +
403B ASP* 2.8 30.0 + - - +
404B TRP* 3.5 49.8 - - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA 2.9 17.3 + - - -
99B THR* 3.5 7.4 + - - -
101B LYS* 1.3 78.7 - - - +
103B VAL* 1.3 71.8 + - - +
104B SER 3.6 0.9 + - - -
188B THR* 3.2 18.4 - - - +
189B TYR* 5.1 13.1 - - - -
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 2.7 38.0 + - - +
100B ILE* 3.0 19.4 - - - +
101B LYS 4.2 1.6 - - - +
102B SER* 1.3 79.6 + - - +
104B SER* 1.3 80.3 + - - +
105B PHE* 4.3 3.1 - - + -
106B TYR* 3.5 24.6 - - + +
107B THR* 5.2 2.1 + - - +
184B GLU* 4.1 14.6 - - + +
185B VAL* 4.4 18.6 - - + -
188B THR* 3.3 25.8 - - + +
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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) + - + + + + + -
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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