Contacts of the helix formed by residues 74 - 99 (chain B) in PDB entry 1L8A
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 ASN 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY* 1.3 68.0 - - - -
75B LEU* 1.3 53.1 + - - +
76B GLU* 2.9 31.9 - - - +
77B LEU* 3.2 28.1 + - + +
78B GLU* 2.8 37.5 + - - +
446B GLU* 4.5 6.7 + - - -
450B TYR* 3.0 29.3 + - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.6 34.8 - - + -
73B GLY 3.2 3.4 + - - +
74B ASN* 1.3 72.3 - - - +
76B GLU* 1.3 76.7 + - - +
78B GLU* 3.4 7.0 + - - +
79B ARG* 3.0 26.0 + - - +
82B ARG* 4.9 1.6 + - - -
366B PRO* 3.8 28.7 - - + -
367B LYS* 3.7 31.6 - - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 5.0 0.2 - - - +
74B ASN* 2.9 25.2 - - - +
75B LEU* 1.3 90.7 + - - +
77B LEU* 1.3 60.2 + - + +
79B ARG* 3.1 24.8 + - - +
80B ARG* 3.4 20.5 + - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 3.1 30.3 + - + +
76B GLU* 1.3 79.0 - - - +
78B GLU* 1.3 63.1 + - - +
80B ARG* 3.2 30.4 + - - +
81B ILE* 3.2 28.1 + - + +
446B GLU* 3.7 24.9 - - + +
447B GLU* 3.4 39.9 - - + +
450B TYR* 3.6 37.9 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 2.5 33.7 + - - -
73B GLY* 3.5 1.4 - - - -
74B ASN 2.8 19.7 + - - +
75B LEU* 3.7 8.1 - - - +
77B LEU* 1.3 78.2 - - - +
79B ARG* 1.3 56.2 + - - +
81B ILE* 3.4 8.5 + - - +
82B ARG* 2.8 37.1 + - - +
118B ASP* 3.6 8.1 - - - +
119B VAL* 5.4 0.3 - - - +
122B ASN* 3.6 19.7 + - - +
123B HIS* 2.8 22.1 + - - -
366B PRO* 5.1 1.0 - - - +
450B TYR* 2.5 39.6 + - + -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 3.0 14.5 + - - +
76B GLU* 3.1 24.1 + - - +
78B GLU* 1.3 73.9 - - - +
80B ARG* 1.3 85.8 + - - +
82B ARG* 3.3 28.9 + - - +
83B SER* 2.8 49.0 + - - +
424B PHE* 3.2 25.2 + - - +
425B ASN* 3.4 26.1 + - - +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 3.8 16.2 + - - +
77B LEU* 3.2 32.9 + - - +
79B ARG* 1.3 109.5 - - - +
81B ILE* 1.3 64.3 + - - +
83B SER* 3.3 3.1 + - - -
84B ALA* 3.0 22.7 + - - +
441B PHE* 3.9 5.3 - - + -
446B GLU* 3.8 21.8 + - - +
447B GLU* 2.6 46.6 + - + +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.2 14.9 + - + +
78B GLU* 3.7 8.7 - - - +
80B ARG* 1.3 74.7 - - - +
82B ARG* 1.3 65.9 + - - +
84B ALA* 3.1 4.5 + - - +
85B ILE* 3.1 38.4 + - + +
118B ASP* 5.0 4.5 - - - +
122B ASN* 5.7 4.9 - - - +
150B ARG* 5.3 1.3 - - - +
153B LEU* 4.2 7.9 - - + -
441B PHE* 4.0 9.6 - - + -
447B GLU* 3.5 45.1 - - + +
450B TYR* 3.9 25.8 - - + -
451B LEU* 4.1 24.5 - - + +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 4.9 1.8 + - - -
78B GLU* 2.8 31.2 + - - +
79B ARG* 3.3 29.4 - - - +
81B ILE* 1.3 76.6 - - - +
83B SER* 1.3 58.3 + - - +
85B ILE* 3.2 13.7 + - + +
86B ARG* 2.9 63.4 + - + +
114B ALA* 4.8 4.7 - - + +
115B THR* 3.8 32.1 + - - +
118B ASP* 2.7 53.8 + - + +
119B VAL* 5.7 1.6 - - - +
364B HIS 5.8 0.4 + - - -
366B PRO* 4.3 19.0 - - - +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 2.8 38.8 + - - +
80B ARG 3.6 5.2 - - - -
82B ARG* 1.3 74.7 - - - +
84B ALA* 1.3 55.3 + - - +
86B ARG* 3.4 13.8 + - - +
87B TRP* 3.0 27.4 + - - +
424B PHE* 3.2 41.2 + - - +
425B ASN 5.0 0.9 - - - -
426B VAL* 4.0 11.4 - - - +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG 3.0 7.3 + - - +
81B ILE 3.1 5.1 + - - +
83B SER* 1.3 73.5 - - - +
85B ILE* 1.3 60.9 + - - +
87B TRP* 3.5 6.3 - - - +
88B ASN* 3.0 35.5 + - - -
153B LEU* 4.2 3.8 - - + -
427B PRO* 6.2 1.3 - - + -
439B ILE* 3.7 23.9 - - + +
441B PHE* 3.4 38.1 - - + -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 3.1 27.2 + - + +
82B ARG* 3.2 11.9 + - + +
84B ALA* 1.3 75.2 - - - +
86B ARG* 1.3 64.7 + - + +
88B ASN* 3.3 2.0 + - - +
89B ALA* 2.9 22.0 + - - +
110B PHE* 4.2 16.8 - - + -
118B ASP* 4.4 0.2 - - - +
146B GLY 3.7 23.1 - - - +
149B ALA* 3.3 13.6 - - + +
150B ARG* 3.5 50.3 - - + +
153B LEU* 3.5 17.9 - - + -
451B LEU* 5.3 0.4 - - + -
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 2.9 47.8 + - + +
83B SER* 3.6 12.3 + - - +
85B ILE* 1.3 77.1 - - - +
87B TRP* 1.3 62.8 + - - +
89B ALA* 3.4 4.4 + - - +
90B ILE* 3.1 32.4 + - + +
110B PHE* 4.7 3.6 - - + -
111B GLN* 3.8 33.7 + - - +
114B ALA* 3.7 25.6 - - + +
115B THR* 3.1 24.5 + - - +
364B HIS* 4.7 0.2 - - - -
394B TYR* 3.7 22.4 - - - -
420B ILE* 6.4 0.2 - - + -
424B PHE* 3.5 45.6 - - + -
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Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B SER 3.0 17.7 + - - +
84B ALA 3.5 5.4 - - - +
86B ARG* 1.3 76.4 - - - +
88B ASN* 1.3 63.8 + - - +
90B ILE* 3.1 9.4 + - + +
91B MET* 2.8 65.5 + - + +
417B VAL* 3.8 24.7 - - + -
420B ILE* 5.1 3.6 - - + -
421B ARG* 3.2 27.1 - - + -
426B VAL* 3.5 30.5 - - + +
428B VAL* 3.6 27.0 - - + +
433B ILE* 4.1 8.5 - - + -
436B LEU* 5.2 0.4 - - - -
437B PRO* 2.6 33.4 + - + +
439B ILE* 3.5 24.0 - - + +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA 3.0 13.2 + - - +
85B ILE* 3.8 3.8 - - - +
87B TRP* 1.3 83.2 - - - +
89B ALA* 1.3 53.4 + - - +
91B MET* 3.7 5.8 - - - +
92B THR* 2.7 39.0 + - - -
149B ALA* 3.9 16.2 + - + -
152B PHE* 3.5 18.0 - - + -
153B LEU* 3.2 18.2 - - - +
162B LEU* 5.0 1.1 - - + -
438B TYR* 3.3 13.3 - - + -
439B ILE* 2.7 49.8 + - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE 2.9 17.6 + - - +
86B ARG 3.6 6.1 - - - +
88B ASN* 1.3 78.3 - - - +
90B ILE* 1.3 64.3 + - + +
92B THR* 3.4 4.6 + - - -
93B VAL* 3.2 27.4 + - - +
107B MET* 5.5 1.1 - - - -
110B PHE* 4.2 11.7 - - + -
111B GLN* 5.4 0.2 - - - +
145B PRO* 3.7 29.7 - - + +
146B GLY* 3.9 7.6 - - - +
149B ALA* 3.6 6.7 - - + +
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.1 21.6 + - + +
87B TRP* 3.1 9.9 + - + +
89B ALA* 1.3 76.8 - - + +
91B MET* 1.3 81.0 + - + +
93B VAL* 3.3 1.2 + - - +
94B LEU* 2.8 43.5 + - + +
107B MET* 3.7 28.5 - - + -
111B GLN* 3.7 32.3 - - + +
396B MET* 4.4 10.5 - - + -
417B VAL* 5.1 10.1 - - + -
420B ILE* 4.5 18.4 - - + -
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Residues in contact with MET 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 2.8 68.3 + - + +
88B ASN* 3.7 2.2 - - - +
90B ILE* 1.3 100.8 - - + +
92B THR* 1.3 58.3 + - - +
94B LEU* 3.2 3.3 + - + +
95B ARG* 2.6 36.8 + - - +
417B VAL* 4.6 6.5 - - + -
436B LEU* 3.3 50.7 - - + +
437B PRO 3.5 7.0 - - - +
438B TYR* 3.7 19.7 - - + -
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASN 2.7 23.0 + - - -
89B ALA* 3.5 7.5 - - - -
91B MET* 1.3 77.3 - - - +
93B VAL* 1.3 63.5 + - + +
95B ARG* 3.5 3.1 + - - +
96B ALA* 3.3 19.4 + - - +
145B PRO* 5.3 8.0 + - + -
148B TYR* 5.6 1.3 - - + -
149B ALA* 5.5 0.3 - - - +
162B LEU* 3.5 32.4 - - + +
165B PHE* 3.4 39.3 - - + +
438B TYR* 3.6 21.0 - - - -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA 3.2 15.7 + - - +
90B ILE 3.9 0.9 - - - +
92B THR* 1.3 73.6 - - - +
94B LEU* 1.3 65.3 + - + +
96B ALA* 3.2 7.9 + - - +
97B SER* 3.1 23.9 + - - +
104B GLY 4.6 3.7 - - - +
105B GLY* 3.8 28.3 - - - +
106B HIS 3.9 18.4 - - - +
107B MET* 3.9 29.4 - - + -
145B PRO* 3.9 19.1 - - + -
165B PHE* 4.1 11.9 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 2.8 26.7 + - + +
91B MET* 3.7 4.7 - - - +
93B VAL* 1.3 73.7 - - - +
95B ARG* 1.3 60.7 + - - +
97B SER* 2.7 24.4 + - - +
98B LYS* 3.0 25.2 + - + +
107B MET* 3.6 35.4 - - + -
414B MET* 5.2 11.9 - - + +
417B VAL* 4.8 10.1 - - + -
436B LEU* 4.2 29.2 - - + -
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B MET 2.6 28.4 + - - +
92B THR 3.9 4.0 - - - +
94B LEU* 1.3 76.5 - - - +
96B ALA* 1.3 63.2 + - - +
98B LYS* 3.5 14.8 + - - +
99B LYS* 3.5 19.6 + - - +
159B GLN* 3.4 17.8 - - - +
163B ASP* 3.0 42.1 + - - +
435B LYS* 3.1 17.9 + - - +
436B LEU* 2.6 52.6 + - + -
437B PRO* 4.2 5.1 - - - +
438B TYR* 3.6 15.0 + - - +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR 3.3 11.3 + - - +
93B VAL* 3.2 10.0 + - - +
94B LEU 3.2 0.4 - - - -
95B ARG* 1.3 78.2 - - - +
97B SER* 1.3 63.2 + - - +
99B LYS* 3.2 32.1 + - - +
100B ASP 4.1 0.9 + - - -
101B LEU 4.9 0.5 + - - -
103B LEU* 3.9 18.8 + - + +
104B GLY 4.6 8.1 - - - +
165B PHE* 3.9 33.2 - - + +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.1 12.5 + - - -
94B LEU* 2.7 36.2 + - - +
96B ALA* 1.3 73.0 - - - +
98B LYS* 1.3 65.7 + - - +
100B ASP* 2.9 17.5 + - - +
101B LEU 5.9 0.4 - - - +
103B LEU* 5.9 2.7 - - - +
104B GLY 5.5 5.3 + - - +
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Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.0 25.7 + - + +
95B ARG* 3.6 10.1 - - - +
96B ALA 3.2 0.4 - - - -
97B SER* 1.3 77.7 + - - +
99B LYS* 1.3 62.8 + - - +
100B ASP* 3.0 6.8 + - - +
414B MET* 6.0 7.6 - - + -
434B GLU 5.2 5.4 - - - -
436B LEU* 4.2 23.8 - - + -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG 3.5 14.3 - - - +
96B ALA* 3.2 19.4 - - - +
97B SER 3.0 0.4 - - - -
98B LYS* 1.3 76.8 - - + +
100B ASP* 1.3 68.4 + - - +
101B LEU* 3.3 24.9 + - + +
103B LEU* 3.8 9.4 - - + +
163B ASP 2.7 29.5 + - - -
164B ASN* 4.3 7.5 + - - +
165B PHE 4.7 3.0 + - - -
167B GLN* 2.9 33.4 - - - +
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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