Contacts of the helix formed by residues 74 - 100 (chain A) in PDB entry 1BAD
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 GLU 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 5.7 1.5 - - - +
75A GLN* 1.3 77.7 + - + +
76A ASN* 3.3 20.2 - - - +
77A PRO* 3.2 18.7 - - - +
78A ILE* 4.3 8.0 - - - +
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Residues in contact with GLN 75 (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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74A GLU* 1.3 90.4 + - + +
76A ASN* 1.3 77.7 + - - +
77A PRO* 3.2 4.2 - - - +
78A ILE* 3.7 15.5 + - + +
79A TYR* 3.1 34.7 - - + +
82A ARG* 6.1 0.2 - - - -
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Residues in contact with ASN 76 (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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74A GLU 3.4 22.2 - - - +
75A GLN* 1.3 89.7 + - - +
77A PRO* 1.4 67.4 - - + +
78A ILE 3.0 6.5 + - - -
79A TYR* 3.1 31.3 + - - +
80A TRP* 4.6 6.4 - - + -
126A ALA* 5.4 0.3 - - - +
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Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.2 16.8 - - - +
75A GLN 3.2 5.2 - - - -
76A ASN* 1.4 98.7 - - + +
78A ILE* 1.3 67.1 + - + +
79A TYR 3.2 0.4 - - - -
80A TRP* 2.9 55.8 + - + -
81A ALA* 4.3 1.7 - - - +
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Residues in contact with ILE 78 (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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9A GLU* 4.6 10.5 - - - +
56A MET* 4.3 7.4 - - + -
60A MET* 4.1 49.8 - - + +
74A GLU 4.3 16.4 - - - +
75A GLN* 4.2 12.8 - - - +
76A ASN 3.0 0.6 + - - -
77A PRO* 1.3 85.4 - - + +
79A TYR* 1.3 67.1 + - + +
80A TRP 3.3 0.2 - - - -
81A ALA* 3.0 8.6 + - + +
82A ARG* 2.9 52.2 + - + +
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Residues in contact with TYR 79 (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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75A GLN* 3.1 43.6 - - + +
76A ASN* 3.1 15.5 + - - +
78A ILE* 1.3 81.4 - - + +
80A TRP* 1.3 62.7 + - + +
82A ARG* 3.3 27.0 + - - +
83A TYR* 3.0 47.8 - - - +
126A ALA* 3.7 25.8 - - + -
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Residues in contact with TRP 80 (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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76A ASN* 4.6 6.7 - - + -
77A PRO* 2.9 46.4 + - + -
79A TYR* 1.3 77.4 - - - +
81A ALA* 1.3 83.8 + - + +
83A TYR* 3.4 12.0 + - + +
84A ALA* 2.9 30.2 + - + +
119A ILE* 5.6 0.3 - - - +
123A LEU* 3.9 27.9 - - + +
126A ALA* 4.2 26.9 - - + -
127A LEU* 3.6 33.9 - - + -
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Residues in contact with ALA 81 (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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56A MET* 3.8 21.4 - - + +
59A SER* 5.6 6.3 - - - +
77A PRO 4.3 1.6 - - - +
78A ILE* 3.0 18.1 + - + +
80A TRP* 1.3 91.6 - - + +
82A ARG* 1.3 59.5 + - - +
84A ALA* 3.5 6.2 + - - +
85A ASP* 2.9 30.1 + - - +
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Residues in contact with ARG 82 (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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216 RET 6.3 2.5 - - + -
56A MET* 4.0 12.6 - - + -
60A MET* 4.0 22.4 - - - +
78A ILE* 2.9 37.1 + - + +
79A TYR* 3.4 27.2 - - - +
80A TRP 3.2 0.2 - - - -
81A ALA* 1.3 77.1 - - - +
83A TYR* 1.3 63.0 + - + +
85A ASP* 3.0 3.5 + - - +
86A TRP* 2.8 50.5 + - + +
189A TRP* 4.3 21.2 + - - +
204A GLU* 4.2 18.6 + - - +
208A PHE* 3.5 42.5 - - + -
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Residues in contact with TYR 83 (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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79A TYR* 3.0 50.6 + - + +
80A TRP* 3.7 9.6 - - - +
82A ARG* 1.3 79.5 - - + +
84A ALA* 1.3 62.0 + - - +
86A TRP* 3.6 44.3 + + + +
87A LEU* 3.5 14.2 + - - +
115A ASP 5.4 0.3 - - - +
118A MET* 4.8 2.4 - - - +
119A ILE* 3.6 34.6 - - + +
122A GLY* 3.4 44.0 - - - -
123A LEU* 3.9 1.1 - - - +
126A ALA* 4.2 1.8 - - + -
189A TRP* 3.8 28.5 + + - -
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Residues in contact with ALA 84 (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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80A TRP* 2.9 18.2 + - + +
81A ALA* 3.7 7.4 - - - +
83A TYR* 1.3 75.6 - - - +
85A ASP* 1.3 64.9 + - - +
87A LEU* 3.0 12.8 + - - +
88A PHE* 3.0 37.6 + - + -
119A ILE* 3.9 15.2 - - + +
123A LEU* 6.6 0.2 - - + -
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Residues in contact with ASP 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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216 RET 3.3 34.0 - - - +
52A ILE* 3.2 32.6 - - - +
53A ALA* 4.6 1.0 - - - -
56A MET* 3.4 25.7 - - - +
81A ALA 2.9 19.4 + - - +
82A ARG* 3.0 7.2 + - - +
84A ALA* 1.3 73.3 - - - +
86A TRP* 1.3 67.9 + - - +
88A PHE* 3.0 10.6 + - - +
89A THR* 2.8 34.1 + - - +
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Residues in contact with TRP 86 (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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216 RET 3.5 55.0 - - + +
82A ARG* 2.8 46.5 + - + +
83A TYR* 3.6 29.6 - + - +
84A ALA 3.2 0.2 - - - -
85A ASP* 1.3 82.7 - - - +
87A LEU* 1.3 62.9 + - - +
89A THR* 4.0 5.8 - - - -
90A THR* 2.7 33.8 + - - +
115A ASP* 3.6 12.1 - - - +
118A MET* 4.4 34.3 - - + -
189A TRP* 3.7 54.1 - + + -
208A PHE* 6.1 2.6 - + - -
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Residues in contact with LEU 87 (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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83A TYR 3.5 8.8 + - - +
84A ALA 3.0 10.1 + - - +
86A TRP* 1.3 79.9 - - - +
88A PHE* 1.3 77.4 + - + +
91A PRO* 3.2 25.2 - - + +
112A VAL* 4.6 20.9 - - + +
115A ASP* 3.7 33.1 - - + +
116A GLY* 4.8 2.5 - - - +
119A ILE* 4.0 23.8 - - + -
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Residues in contact with PHE 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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52A ILE* 3.7 37.6 - - + +
84A ALA* 3.0 41.5 - - + -
85A ASP* 3.0 7.8 + - - +
87A LEU* 1.3 102.8 - - + +
89A THR* 1.3 60.5 + - - +
91A PRO* 3.4 7.7 - - - +
92A LEU* 3.7 12.5 - - - +
119A ILE* 5.7 1.1 - - + -
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Residues in contact with THR 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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216 RET 3.8 36.7 - - + +
49A VAL* 5.3 1.4 - - - +
52A ILE* 3.9 19.7 - - - +
53A ALA* 5.3 1.2 - - - +
85A ASP* 2.8 33.5 + - - +
86A TRP* 3.7 7.2 - - - +
88A PHE* 1.3 77.0 - - - +
90A THR* 1.3 79.9 + - - +
91A PRO* 3.3 1.2 - - - -
92A LEU* 3.9 4.6 + - - +
93A LEU* 3.2 23.2 - - - +
216A LYS* 4.0 7.1 + - - -
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Residues in contact with THR 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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216 RET 3.6 38.1 - - + +
86A TRP* 2.7 23.3 + - - -
89A THR* 1.3 87.5 - - - +
91A PRO* 1.4 65.8 - - + +
92A LEU 3.1 5.6 + - - -
93A LEU* 3.1 15.2 + - - +
94A LEU* 3.1 23.4 + - + +
111A LEU* 5.2 6.1 - - + -
115A ASP* 3.5 26.8 + - - +
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Residues in contact with PRO 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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87A LEU* 3.2 24.7 - - + +
88A PHE* 3.4 5.8 - - - +
89A THR 3.3 5.2 - - - -
90A THR* 1.4 94.7 - - + +
92A LEU* 1.3 71.8 + - + +
93A LEU 3.4 0.2 - - - -
94A LEU* 3.7 9.5 - - + +
95A LEU* 2.8 31.4 + - - +
108A ILE* 5.1 8.9 - - + +
111A LEU* 5.7 4.0 - - + -
112A VAL* 4.2 25.8 - - + -
115A ASP* 5.3 2.2 - - - +
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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
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45A ILE* 3.4 23.2 - - + +
48A LEU* 3.8 36.3 - - + -
49A VAL* 3.8 31.6 - - + +
52A ILE* 4.7 10.8 - - + -
88A PHE 3.7 17.3 - - - +
89A THR 4.4 4.7 - - - +
90A THR 3.1 0.8 - - - -
91A PRO* 1.3 88.0 - - + +
93A LEU* 1.3 61.3 + - - +
95A LEU* 3.4 5.2 + - + +
96A ASP* 2.9 29.3 + - - +
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Residues in contact with LEU 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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49A VAL* 3.6 28.9 - - + -
89A THR* 3.2 31.0 - - - +
90A THR 3.1 7.0 + - - +
92A LEU* 1.3 78.6 - - - +
94A LEU* 1.3 60.6 + - + +
96A ASP* 3.5 7.4 + - - +
97A LEU* 2.9 28.1 + - - +
215A ALA* 4.8 3.8 - - + +
216A LYS* 3.9 38.8 - - + +
219A PHE* 3.8 35.9 - - + -
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Residues in contact with LEU 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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216 RET 4.6 9.6 - - + -
90A THR* 3.1 31.1 + - + +
91A PRO* 3.9 9.9 - - + +
93A LEU* 1.3 78.9 - - + +
95A LEU* 1.3 59.5 + - - +
97A LEU* 3.3 4.7 + - + +
98A ALA* 2.8 32.1 + - + +
107A THR* 6.0 2.2 - - + -
108A ILE* 5.0 6.7 - - + -
111A LEU* 4.9 15.7 - - + -
148A ILE* 5.3 4.5 - - + -
152A LEU* 4.1 24.2 - - + -
182A TRP* 3.5 44.9 - - + -
219A PHE* 5.5 1.6 - - + -
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Residues in contact with LEU 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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45A ILE* 4.1 24.9 - - + -
91A PRO 2.8 20.2 + - - +
92A LEU* 3.8 5.2 - - + +
93A LEU 3.3 0.2 - - - -
94A LEU* 1.3 74.9 - - - +
96A ASP* 1.3 59.9 + - - +
98A ALA* 3.6 6.2 - - + +
99A LEU* 2.8 41.4 + - + +
108A ILE* 4.1 29.3 - - + +
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Residues in contact with ASP 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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42A PHE* 3.7 17.4 - - - +
45A ILE* 4.2 15.2 - - + +
46A THR* 5.1 1.5 - - - -
92A LEU 2.9 18.4 + - - +
93A LEU* 3.6 9.1 - - - +
95A LEU* 1.3 77.5 - - - +
97A LEU* 1.3 60.4 + - - +
99A LEU* 3.3 6.5 + - - +
100A LEU* 2.8 36.2 + - - +
219A PHE* 4.7 13.5 - - - +
223A LEU* 3.2 43.7 - - - +
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Residues in contact with LEU 97 (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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93A LEU 2.9 18.0 + - - +
94A LEU* 3.6 5.8 - - + +
96A ASP* 1.3 81.1 + - - +
98A ALA* 1.3 63.5 - - - +
100A LEU* 3.1 27.5 + - + -
152A LEU* 4.0 16.6 - - + -
170A THR* 6.6 0.2 - - + -
171A PHE* 5.6 7.7 - - + -
174A LEU* 3.6 31.9 - - + -
178A THR* 4.5 7.6 - - + -
182A TRP* 3.8 34.3 - - + -
219A PHE* 4.0 18.6 - - + -
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Residues in contact with ALA 98 (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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94A LEU* 2.8 20.6 + - + +
95A LEU* 3.2 10.3 + - + +
97A LEU* 1.3 79.1 - - - +
99A LEU* 1.3 62.7 + - - +
100A LEU 4.5 1.9 - - - -
107A THR* 4.8 19.1 - - + -
108A ILE* 5.0 5.8 - - + -
152A LEU* 6.0 5.8 - - + -
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Residues in contact with LEU 99 (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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41A LYS* 3.8 45.3 - - + +
42A PHE* 3.6 31.6 - - + -
45A ILE* 6.0 4.3 - - + -
95A LEU* 2.8 25.6 + - + +
96A ASP* 3.8 5.2 - - - +
98A ALA* 1.3 78.0 - - - +
100A LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 100 (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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42A PHE* 3.9 16.4 - - + -
96A ASP* 2.8 25.4 + - - +
97A LEU* 3.1 22.6 + - + +
98A ALA 4.5 2.5 - - - -
99A LEU* 1.3 83.2 - - - +
166A GLU* 5.8 4.0 - - - +
167A VAL* 5.3 11.1 - - + +
170A THR* 4.1 26.7 - - + -
171A PHE* 3.5 31.4 - - + -
174A LEU* 5.7 1.1 - - + -
219A PHE 5.4 0.2 - - - +
222A ILE* 4.6 10.5 - - + +
223A LEU* 4.2 39.5 - - + +
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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