Contacts of the helix formed by residues 75 - 99 (chain A) in PDB entry 5JNQ
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 LYS 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR 3.3 1.6 - - - -
74A PRO* 1.4 79.4 - - + +
76A ILE* 1.3 60.6 + - - +
77A ILE 3.5 0.2 - - - -
78A PRO* 3.4 21.0 - - - +
79A VAL* 3.8 1.6 - - - +
125A TYR* 5.3 2.0 - - - +
131A GLU* 4.1 35.3 + - + +
132A VAL* 5.5 3.9 - - + +
200A ASP 5.2 2.0 + - - -
201A MET* 4.7 12.5 - - + +
202A GLY* 4.0 34.0 - - - +
203A ILE* 3.4 19.6 - - + +
247A MET* 3.7 29.5 + - + +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 4.0 14.4 - - - +
69A TYR* 3.8 24.9 - - + -
70A ILE* 4.1 14.1 - - + -
73A TYR* 3.5 32.5 - - + +
74A PRO 2.9 0.4 + - - -
75A LYS* 1.3 76.2 - - - +
77A ILE* 1.4 55.4 + - - +
79A VAL* 2.9 7.1 + - - +
80A LEU* 2.8 34.9 + - + -
202A GLY 3.8 11.4 - - - +
203A ILE* 4.4 1.8 - - - -
205A PRO* 3.9 16.2 - - + -
206A ILE* 3.8 43.1 - - + +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 4.0 35.7 - - + -
74A PRO* 3.2 26.6 + - + +
76A ILE* 1.4 74.6 - - - +
78A PRO* 1.4 63.8 - - + +
80A LEU* 3.7 7.9 - - - +
81A PHE* 2.9 34.1 + - + +
125A TYR* 6.3 1.3 - - + -
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Residues in contact with PRO 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO 4.0 2.0 - - - +
75A LYS 3.4 22.2 - - - +
77A ILE* 1.4 94.7 - - + +
79A VAL* 1.4 59.1 + - - +
81A PHE* 3.5 9.5 + - + +
82A VAL* 3.1 31.1 + - - +
122A PHE* 4.6 8.5 - - + -
125A TYR* 3.5 53.8 - - + +
247A MET* 3.7 15.5 - - + -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS 3.8 4.5 - - - +
76A ILE 2.9 6.9 + - - +
78A PRO* 1.4 73.5 - - - +
80A LEU* 1.4 62.0 + - - +
82A VAL* 3.4 4.0 + - - +
83A THR* 3.0 33.0 + - + +
203A ILE* 3.8 21.3 - - + -
206A ILE* 4.0 20.9 - - + -
240A PHE* 4.1 13.9 - - + -
243A ALA* 4.3 19.7 - - + +
244A SER* 3.9 19.5 - - - +
247A MET* 3.6 29.8 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.2 8.1 - - + -
63A ILE* 4.0 33.0 - - + +
66A SER* 3.6 26.5 - - - +
67A VAL* 5.8 1.1 - - + -
70A ILE* 3.8 25.4 - - + -
76A ILE* 2.8 20.4 + - + +
77A ILE* 3.7 6.1 - - - +
79A VAL* 1.4 72.9 - - - +
81A PHE* 1.4 55.8 + - - +
83A THR* 3.4 4.2 + - - +
84A VAL* 3.0 42.3 + - + +
206A ILE* 3.8 18.5 - - + +
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 2.9 20.4 + - + +
78A PRO* 3.8 11.4 - - + +
80A LEU* 1.4 75.2 - - - +
82A VAL* 1.3 65.6 + - + +
84A VAL* 3.8 4.9 - - + +
85A GLY* 2.8 30.4 + - - -
118A ILE* 4.8 14.1 - - + -
121A ILE* 3.7 47.8 - - + -
122A PHE* 4.7 8.3 - + + -
125A TYR* 6.4 1.8 - - + -
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO 3.1 21.0 + - - +
79A VAL 3.8 4.0 - - - +
80A LEU 3.3 0.2 - - - -
81A PHE* 1.3 83.2 - - + +
83A THR* 1.4 59.0 + - - +
85A GLY* 3.2 1.0 + - - -
86A PHE* 2.8 46.4 + - + -
118A ILE* 4.1 8.0 - - + +
122A PHE* 3.8 38.1 - - + -
164A MET* 3.6 17.7 - - + -
239A GLY 3.5 25.1 - - - +
243A ALA* 3.8 7.0 - - + -
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.5 17.1 - - - +
62A ILE* 5.1 9.8 - - + +
79A VAL* 3.0 25.0 + - + +
80A LEU* 4.0 9.3 + - - +
82A VAL* 1.4 74.7 - - - +
84A VAL* 1.4 58.9 + - - +
86A PHE 3.5 0.2 + - - -
87A GLY* 2.8 23.2 + - - -
206A ILE* 5.5 3.8 - - + -
210A VAL* 6.0 1.3 - - + -
236A ALA* 3.3 34.3 - - - +
240A PHE* 3.6 33.0 - - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.3 11.7 - - + -
63A ILE* 3.8 36.6 - - + -
80A LEU* 3.0 31.7 + - + +
81A PHE* 4.1 4.9 - - + +
83A THR* 1.4 72.7 - - - +
85A GLY* 1.3 57.2 + - - +
87A GLY* 3.1 2.6 + - - -
88A ILE* 2.9 45.4 + - + +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 2.8 23.3 + - - -
82A VAL 3.5 1.6 - - - -
84A VAL* 1.3 76.9 - - - +
86A PHE* 1.3 58.3 + - - +
88A ILE* 3.4 21.7 + - - +
89A ILE* 3.6 13.0 - - - +
118A ILE* 3.7 27.7 - - - +
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 2.8 44.2 + - + +
83A THR* 4.0 3.1 - - - +
85A GLY* 1.3 70.5 - - - +
87A GLY* 1.3 61.8 + - - +
88A ILE 3.3 0.2 - - - -
89A ILE* 3.7 17.1 + - + +
90A GLY 3.4 15.6 + - - -
115A GLN* 3.7 26.0 - - + -
118A ILE* 3.9 13.5 - - + -
119A THR* 3.9 20.0 - - - -
164A MET* 3.8 21.8 - - + -
168A ASP* 3.3 34.1 - - + -
235A LEU* 3.3 34.8 - - + +
236A ALA* 4.0 3.6 - - - -
239A GLY* 3.6 14.6 - - - -
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.0 14.3 - - - +
83A THR 2.8 15.2 + - - -
84A VAL 3.1 6.3 + - - -
86A PHE* 1.3 77.0 - - - +
88A ILE* 1.4 53.7 + - - +
89A ILE 3.5 0.2 - - - -
90A GLY* 3.5 1.0 + - - -
91A PHE* 2.8 34.0 + - - +
232A THR* 3.8 24.1 - - - +
236A ALA* 4.1 0.7 - - - -
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 2.9 32.0 + - + +
85A GLY* 3.4 12.8 - - - +
86A PHE 3.3 0.2 - - - -
87A GLY* 1.4 73.7 - - - +
89A ILE* 1.4 61.8 + - + +
91A PHE* 3.1 13.9 + - + +
92A LEU* 2.9 47.5 + - + +
118A ILE* 5.9 1.6 - - + -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY 3.6 17.0 + - - +
86A PHE* 3.7 23.5 + - + +
87A GLY 3.5 0.2 - - - -
88A ILE* 1.4 76.4 - - + +
90A GLY* 1.3 52.5 + - - +
92A LEU* 3.4 10.4 + - + +
93A ASP* 2.8 37.4 + - - +
107A LYS* 5.6 3.2 + - - +
110A GLN 5.3 0.9 - - - +
111A LYS* 4.5 19.5 - - + +
114A GLY* 3.4 42.8 - - - +
115A GLN* 3.9 4.0 - - + +
118A ILE* 3.7 13.9 - - + -
235A LEU* 4.4 11.2 - - + -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE 3.4 8.4 + - - -
87A GLY 3.5 1.3 + - - -
88A ILE 3.3 0.4 - - - -
89A ILE* 1.3 75.8 - - - +
91A PHE* 1.4 57.3 + - - +
93A ASP* 3.5 4.6 - - - +
94A ASP* 2.9 29.5 + - - +
231A ASP 3.2 26.9 - - - -
232A THR* 3.2 14.8 + - - -
235A LEU* 3.8 7.0 - - - +
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A MET* 4.0 19.6 - - + +
56A LEU* 3.7 43.7 - - + -
87A GLY 2.8 21.3 + - - +
88A ILE* 3.1 14.1 + - + +
90A GLY* 1.4 71.1 - - - +
92A LEU* 1.3 66.6 + - + +
94A ASP* 4.0 1.4 - - - +
95A TYR* 3.2 43.9 + + + +
232A THR* 3.5 10.7 + - + +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 2.9 36.3 + - + +
89A ILE* 3.6 8.5 - - - +
91A PHE* 1.3 81.3 - - + +
93A ASP* 1.4 62.9 + - - +
95A TYR* 3.2 11.6 + - + +
96A ILE* 3.1 35.3 + - + +
107A LYS* 5.6 0.4 - - - -
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 2.8 19.5 + - - +
90A GLY* 3.3 9.8 + - - +
92A LEU* 1.4 75.1 - - - +
94A ASP* 1.4 57.1 + - - +
96A ILE* 3.2 6.9 + - - +
97A LYS* 3.1 29.3 + - - +
107A LYS* 3.5 36.0 + - - +
111A LYS* 2.8 38.3 + - - +
231A ASP* 3.7 16.9 - - - +
235A LEU* 5.3 1.0 - - + +
401A TUM 4.6 1.0 + - - -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A THR* 4.2 16.7 + - + +
53A MET* 3.9 22.4 - - + -
90A GLY 2.9 15.2 + - - +
91A PHE 4.3 0.7 - - - +
93A ASP* 1.4 69.6 - - - +
95A TYR* 1.3 62.8 + - - +
97A LYS* 3.3 37.8 + - + +
98A ILE* 3.5 18.0 + - - +
230A GLY* 3.5 10.4 + - - +
231A ASP* 3.6 13.5 - - - +
232A THR* 2.8 37.0 + - - +
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.9 7.6 - - + -
53A MET* 4.5 10.5 - - + -
91A PHE* 3.2 37.7 + + + +
92A LEU* 3.2 14.1 + - + +
94A ASP* 1.3 73.6 - - - +
96A ILE* 1.4 67.8 - - + +
98A ILE* 3.5 6.9 + - + +
99A VAL* 3.1 52.0 + - + +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.1 23.8 + - + +
93A ASP 3.4 7.2 - - - +
95A TYR* 1.4 83.8 - - + +
97A LYS* 1.4 61.8 + - - +
98A ILE 3.3 0.9 + - - -
99A VAL* 3.5 23.7 - - + +
107A LYS* 4.4 26.5 - - + +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 5.4 14.5 + - + +
93A ASP* 3.1 17.3 + - - +
94A ASP* 3.3 34.8 - - - +
96A ILE* 1.4 75.4 - - - +
98A ILE* 1.4 60.8 + - + +
99A VAL 5.2 0.2 - - - +
231A ASP* 4.7 3.4 - - - +
401A TUM 3.5 47.7 + - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 6.0 0.2 - - - +
30A LEU* 3.4 45.1 - - + +
31A LYS* 4.7 20.6 - - + +
52A THR* 4.9 12.8 - - + -
53A MET* 4.4 20.0 - - + -
94A ASP 3.5 17.0 + - - +
95A TYR* 3.5 8.3 + - + +
96A ILE 3.2 0.4 - - - -
97A LYS* 1.4 79.8 - - + +
99A VAL* 1.3 70.7 + - + +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.1 47.6 + - + +
96A ILE* 3.5 17.7 - - + +
97A LYS 5.2 0.5 - - - +
98A ILE* 1.3 85.7 - - + +
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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) + - + + + + + -
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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