Contacts of the helix formed by residues 74 - 110 (chain A) in PDB entry 5LLU
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 SER 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PRO* 3.0 8.5 + - - -
73A LEU* 1.4 74.8 - - - +
75A PRO* 1.4 69.3 - - - +
76A ARG* 3.6 12.8 + - - +
77A GLU* 3.1 37.4 + - - +
78A VAL* 2.9 26.3 + - - +
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Residues in contact with PRO 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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73A LEU 3.4 5.8 - - - +
74A SER* 1.4 85.7 - - - +
76A ARG* 1.4 60.9 + - + +
78A VAL* 3.5 7.7 + - + +
79A LYS* 3.2 35.5 + - - +
283A GLU* 5.9 1.6 - - - +
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Residues in contact with ARG 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 SER* 3.3 7.9 + - - +
75A PRO* 1.4 80.2 - - + +
77A GLU* 1.4 57.7 + - + +
79A LYS* 3.5 26.6 - - - +
80A TYR* 3.2 76.5 + - + +
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Residues in contact with GLU 77 (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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72A PRO* 3.4 27.7 - - - +
74A SER* 3.1 31.7 + - - +
76A ARG* 1.4 77.3 - - + +
78A VAL* 1.4 59.5 + - + +
80A TYR* 3.4 14.4 + - + +
81A PHE* 3.0 28.9 + - - +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.7 21.1 - - + +
74A SER 2.9 20.0 + - - +
75A PRO* 3.8 7.4 - - + +
77A GLU* 1.4 73.9 - - + +
79A LYS* 1.4 59.8 + - + +
81A PHE* 3.3 7.8 + - + +
82A ALA* 2.9 31.4 + - + +
279A GLY* 4.2 12.3 - - - +
282A VAL* 3.9 22.9 - - + -
283A GLU* 3.5 39.0 - - + +
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Residues in contact with LYS 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 PRO* 3.2 25.1 + - - +
76A ARG* 3.5 36.0 - - - +
77A GLU 3.3 0.2 - - - -
78A VAL* 1.4 78.1 - - + +
80A TYR* 1.4 60.0 + - + +
82A ALA* 3.7 4.3 + - - +
83A PHE* 3.1 26.0 + - - +
86A GLU* 4.2 11.5 - - - +
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Residues in contact with TYR 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 ARG* 3.2 63.3 + - + +
77A GLU* 3.6 14.4 - - + +
79A LYS* 1.4 79.9 - - + +
81A PHE* 1.3 64.8 + - - +
83A PHE* 3.3 20.4 - - + +
84A PRO* 4.3 2.4 - - - +
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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
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64A LEU* 3.8 25.1 - - + -
65A GLY* 5.1 0.7 - - - -
68A LEU* 3.7 35.4 - - + -
77A GLU 3.0 16.7 + - - +
78A VAL* 3.6 7.2 - - - +
80A TYR* 1.3 77.0 - - - +
82A ALA* 1.3 61.1 + - - +
84A PRO* 3.3 5.2 - - - +
275A PHE* 3.2 40.1 - + - -
278A ALA* 3.7 24.2 - - + -
279A GLY* 3.6 33.0 - - - -
282A VAL* 4.6 11.9 - - + -
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Residues in contact with ALA 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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78A VAL* 2.9 19.9 + - + +
79A LYS* 3.9 5.2 - - - +
80A TYR 3.4 0.2 - - - -
81A PHE* 1.3 75.8 - - - +
83A PHE* 1.4 51.5 + - - +
84A PRO* 3.4 1.6 - - - -
85A GLY* 2.8 29.5 + - - -
86A GLU* 3.2 8.9 + - - +
275A PHE* 3.8 19.7 - - - +
276A LEU* 4.9 6.3 - - + +
279A GLY* 4.2 14.4 - - - -
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Residues in contact with PHE 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 LYS 3.1 12.6 + - - +
80A TYR* 3.3 19.3 - - - +
81A PHE 3.3 0.4 - - - -
82A ALA* 1.4 73.5 - - - +
84A PRO* 1.4 63.8 - - + +
86A GLU* 2.8 50.9 + - + +
87A LEU* 2.9 51.0 + - + -
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Residues in contact with PRO 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 TYR 4.3 2.0 - - - +
81A PHE 3.3 15.5 - - - +
82A ALA 3.5 2.5 - - - -
83A PHE* 1.4 95.1 - - + +
85A GLY* 1.3 56.0 + - - +
87A LEU* 4.0 2.2 - - + -
88A LEU 3.7 1.4 + - - -
268A TYR* 2.7 42.7 + - - +
271A LEU* 3.9 10.8 - - + -
272A GLY* 3.4 7.1 - - - -
275A PHE* 3.6 38.4 - - + -
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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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82A ALA 2.8 10.2 + - - -
84A PRO* 1.3 76.3 - - - +
86A GLU* 1.4 58.9 + - - +
87A LEU 3.3 0.4 - - - -
88A LEU* 3.5 5.0 + - - +
89A MET* 3.2 21.3 + - - +
272A GLY* 3.3 23.6 - - - -
275A PHE* 3.8 2.6 - - - +
276A LEU* 3.4 29.4 - - - +
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Residues in contact with GLU 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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79A LYS* 4.2 13.7 - - - +
82A ALA* 3.2 5.0 + - + +
83A PHE* 2.8 39.1 + - + +
85A GLY* 1.4 76.5 - - - +
87A LEU* 1.4 58.6 + - - +
89A MET* 3.3 9.5 + - + +
90A ARG* 3.1 46.2 + - + +
276A LEU* 4.3 2.4 - - - +
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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 PHE* 2.9 47.0 + - + +
84A PRO* 5.3 0.7 - - + -
85A GLY 3.3 0.2 - - - -
86A GLU* 1.4 74.5 - - - +
88A LEU* 1.4 63.2 + - - +
90A ARG* 3.6 15.6 + - + +
91A MET* 3.3 30.3 + - + +
268A TYR* 3.6 28.7 - - + +
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Residues in contact with LEU 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 PRO 3.7 0.6 + - - -
85A GLY 3.5 8.4 + - - +
86A GLU 3.3 0.6 - - - -
87A LEU* 1.4 73.8 - - - +
89A MET* 1.3 65.5 + - - +
91A MET* 3.2 8.2 + - - +
92A LEU* 3.0 44.4 + - + +
265A ILE* 3.7 19.5 - - + +
268A TYR* 3.6 33.7 - - + -
269A ALA* 3.7 31.0 - - + +
272A GLY* 4.0 5.2 - - - -
273A ILE* 3.7 35.9 - - + +
276A LEU* 4.9 5.8 - - + -
338A THR* 5.4 0.9 - - + -
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Residues in contact with MET 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 3.2 13.8 + - - +
86A GLU* 3.3 13.4 + - + +
88A LEU* 1.3 77.2 - - - +
90A ARG* 1.4 56.5 + - + +
92A LEU* 3.5 5.5 + - - +
93A LYS* 2.9 47.1 + - + +
276A LEU* 3.9 20.9 - - + -
342A THR* 3.4 51.1 - - - +
344A SER* 5.3 2.2 - - - -
347A ALA* 4.7 10.5 - - - -
424A PRO* 5.2 9.2 - - + -
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Residues in contact with ARG 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLU* 3.1 30.9 + - + +
87A LEU* 3.8 18.2 - - + +
88A LEU 3.3 0.2 - - - -
89A MET* 1.4 71.7 - - + +
91A MET* 1.4 59.7 + - + +
93A LYS* 3.5 20.2 + - - +
94A MET* 3.0 31.6 + - - +
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Residues in contact with MET 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.3 19.5 + - + +
88A LEU* 3.2 9.3 + - + +
90A ARG* 1.4 75.9 - - + +
92A LEU* 1.3 60.7 + - - +
94A MET* 3.3 33.7 - - + +
95A LEU* 3.7 11.3 + - - +
264A ILE* 4.5 6.7 - - + +
265A ILE* 3.6 43.0 - - + +
268A TYR* 3.8 43.5 - - + -
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Residues in contact with LEU 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.0 39.7 + - + +
89A MET* 3.9 4.3 - - - +
91A MET* 1.3 73.9 - - - +
93A LYS* 1.4 64.2 + - - +
94A MET 3.4 0.3 + - - -
95A LEU* 3.5 7.9 + - - -
96A ILE* 3.2 19.4 + - - +
265A ILE* 3.7 25.4 - - + -
338A THR* 5.5 2.2 - - - -
342A THR* 4.2 22.2 - - + -
347A ALA* 3.4 27.4 - - + +
348A THR* 4.8 4.9 - - + -
350A PRO* 3.6 24.4 - - + +
351A ILE* 3.8 20.4 - - + -
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Residues in contact with LYS 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A MET* 2.9 39.1 + - + +
90A ARG* 3.5 19.9 + - - +
92A LEU* 1.4 74.8 - - - +
94A MET* 1.3 62.6 + - - +
96A ILE* 3.2 32.9 + - + +
97A LEU* 4.3 0.9 + - - +
347A ALA* 5.0 12.6 - - + +
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Residues in contact with MET 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG 3.0 18.9 + - - +
91A MET* 3.3 28.7 - - + +
93A LYS* 1.3 76.2 - - - +
95A LEU* 1.3 71.5 + - + +
97A LEU* 4.2 3.5 + - - +
98A PRO* 3.3 18.9 - - - +
261A LEU* 5.5 8.1 - - + -
265A ILE* 4.5 11.4 - - + -
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Residues in contact with LEU 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A MET 4.0 8.3 - - - +
92A LEU 3.5 7.9 + - - +
93A LYS 3.4 0.6 - - - -
94A MET* 1.3 88.6 - - + +
96A ILE* 1.4 63.0 + - - +
97A LEU 3.5 0.4 - - - -
98A PRO* 3.3 7.9 - - + +
99A LEU* 3.2 27.6 + - + +
258A THR* 3.6 35.0 - - + +
261A LEU* 3.8 16.8 - - + -
262A VAL* 4.0 27.6 - - + +
265A ILE* 3.7 33.2 - - + -
350A PRO* 4.6 12.1 - - + -
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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 3.2 18.6 - - - +
93A LYS* 3.2 23.3 + - + +
95A LEU* 1.4 75.7 - - - +
97A LEU* 1.3 61.8 + - + +
99A LEU* 3.1 6.2 + - - +
100A ILE* 2.9 44.2 + - + +
221A MET* 3.8 29.4 - - + -
223A ILE* 3.8 25.1 - - + -
346A SER* 3.2 33.0 - - - +
347A ALA* 4.2 2.2 - - - -
349A LEU* 5.7 1.8 - - + -
350A PRO* 4.2 11.2 - - + -
423A ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS 5.5 0.4 - - - +
94A MET 4.2 4.6 + - - +
96A ILE* 1.3 81.0 - - + +
98A PRO* 1.4 70.3 - - + +
99A LEU 3.1 1.0 + - - -
101A VAL* 3.4 38.5 + - + +
192A ALA* 3.8 30.1 - - + +
221A MET* 3.7 19.5 - - - -
226A LEU* 3.7 29.6 - - + -
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Residues in contact with PRO 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MET 3.3 15.0 - - - +
95A LEU* 3.3 22.7 - - + +
97A LEU* 1.4 93.8 - - + +
99A LEU* 1.3 49.6 + - - -
101A VAL* 5.0 2.5 - - + -
102A SER* 2.7 36.0 + - - -
254A LEU* 4.2 16.7 - - + +
258A THR* 3.7 33.2 + - + -
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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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95A LEU* 3.2 21.1 + - + +
96A ILE* 3.1 5.8 + - - +
97A LEU 3.1 0.8 - - - -
98A PRO* 1.3 75.4 - - - +
100A ILE* 1.4 58.4 + - + +
101A VAL 3.2 0.3 + - - -
102A SER* 3.3 3.7 + - - -
103A SER* 2.7 46.2 + - - +
255A ASN* 4.7 3.1 - - - +
258A THR* 3.4 28.5 - - - +
259A MET* 3.8 23.6 - - + -
262A VAL* 5.9 0.4 - - + -
349A LEU* 4.6 3.8 - - + -
350A PRO* 3.7 31.2 - - + -
353A PHE* 3.6 37.9 - - + -
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Residues in contact with ILE 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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96A ILE* 2.9 39.8 + - + +
97A LEU 4.4 1.8 - - - +
99A LEU* 1.4 71.5 - - - +
101A VAL* 1.4 62.6 + - + +
103A SER* 3.9 1.2 - - - -
104A LEU* 3.3 31.5 + - + +
221A MET* 3.8 14.6 - - + -
223A ILE* 3.8 24.9 - - + +
226A LEU* 4.6 11.2 - - + -
227A VAL* 3.7 36.3 - - + +
346A SER* 5.4 2.7 - - - +
349A LEU* 3.9 25.7 - - + +
372A PRO* 4.5 12.3 - - + +
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Residues in contact with VAL 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.4 36.2 + - + +
98A PRO* 5.0 2.5 - - + +
99A LEU 3.3 0.6 - - - -
100A ILE* 1.4 75.8 - - + +
102A SER* 1.3 63.1 + - - +
105A ILE* 3.2 47.6 + - + +
226A LEU* 4.5 20.6 - - + -
229A PHE* 6.5 1.6 - - + -
230A SER* 3.4 16.3 + - - +
251A PHE* 3.8 13.7 - - + -
254A LEU* 5.7 2.5 - - + -
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Residues in contact with SER 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO 2.7 23.2 + - - -
99A LEU 3.3 1.0 + - - -
101A VAL* 1.3 75.8 - - - +
103A SER* 1.3 59.7 + - - +
105A ILE 4.2 0.2 - - - -
106A THR* 2.9 32.2 + - - +
251A PHE* 3.4 31.1 - - - +
254A LEU* 3.8 18.8 - - - +
255A ASN* 2.9 27.9 + - - +
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Residues in contact with SER 103 (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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99A LEU* 2.7 31.3 + - - +
100A ILE 3.9 3.6 - - - -
102A SER* 1.3 72.6 + - - +
104A LEU* 1.3 57.9 + - - +
106A THR* 3.4 1.6 + - - -
107A GLY* 2.8 24.1 + - - -
255A ASN* 2.8 20.2 + - - +
353A PHE* 3.6 22.7 - - - -
368A ARG* 3.3 35.9 - - - +
372A PRO* 4.1 3.6 - - - -
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Residues in contact with LEU 104 (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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100A ILE* 3.3 17.3 + - + +
103A SER* 1.3 76.3 - - - +
105A ILE* 1.4 65.0 + - - +
107A GLY* 4.3 0.4 - - - +
108A LEU* 3.0 43.1 + - + +
227A VAL* 3.8 42.6 - - + +
230A SER* 3.7 19.2 - - - +
231A ILE* 3.7 17.7 - - + -
368A ARG 3.6 16.4 - - - +
369A PHE* 3.9 14.8 - - + +
372A PRO* 3.9 15.0 - - + -
373A VAL* 3.9 10.1 - - + -
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Residues in contact with ILE 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 3.2 31.2 + - + +
102A SER 4.5 0.7 - - - +
104A LEU* 1.4 76.9 - - - +
106A THR* 1.4 60.8 + - + +
109A ALA* 3.3 23.6 + - - +
229A PHE* 5.5 4.9 - - + -
230A SER* 3.6 22.9 - - - +
233A PHE* 3.8 24.5 - - + -
234A GLY* 3.4 9.7 - - - -
237A LEU* 3.7 28.9 - - + -
248A VAL* 5.6 0.7 - - - -
251A PHE* 3.8 43.7 - - + -
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Residues in contact with THR 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER 2.9 16.2 + - - +
103A SER 3.4 3.3 + - - -
104A LEU 3.4 0.2 - - - -
105A ILE* 1.4 74.6 - - - +
107A GLY* 1.3 59.7 + - - +
109A ALA* 4.6 3.1 - - - +
110A SER* 2.8 40.8 + - - -
248A VAL* 3.3 32.5 - - + +
251A PHE* 3.5 13.6 + - + -
252A ASN* 3.4 28.0 - - - +
368A ARG* 2.9 28.4 + - - -
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Residues in contact with GLY 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A SER 2.8 20.4 + - - -
104A LEU* 3.4 2.7 + - - -
106A THR* 1.3 78.6 + - - +
108A LEU* 1.4 60.4 + - - +
110A SER* 4.2 0.8 + - - -
111A LEU* 3.4 33.8 - - - +
365A ARG* 4.2 9.4 - - - +
368A ARG* 4.0 19.3 - - - -
369A PHE* 5.6 3.3 - - - +
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Residues in contact with LEU 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.0 39.9 + - + +
107A GLY* 1.4 76.9 - - - +
109A ALA* 1.4 61.9 + - - +
110A SER 3.5 0.4 - - - -
111A LEU* 3.7 7.1 - - + +
116A SER* 3.4 37.3 + - - +
231A ILE* 3.8 22.7 - - + +
234A GLY* 4.1 17.7 - - - +
235A ILE* 3.8 33.3 + - + +
238A GLY* 5.1 2.1 - - - -
369A PHE* 3.7 33.2 - - + -
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Residues in contact with ALA 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE 3.3 19.8 + - - +
106A THR* 3.3 3.0 + - - +
108A LEU* 1.4 73.1 - - - +
110A SER* 1.4 57.3 + - - +
111A LEU 3.2 13.5 + - - +
234A GLY 3.3 17.0 + - - +
237A LEU* 4.1 3.4 - - + -
238A GLY* 4.0 19.5 - - - +
248A VAL* 3.7 29.3 - - + +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR* 2.8 27.4 + - - -
107A GLY* 4.2 1.1 + - - -
108A LEU 3.5 0.2 - - - -
109A ALA* 1.4 74.7 - - - +
111A LEU* 1.3 67.5 + - - +
248A VAL* 3.9 16.4 - - - +
252A ASN* 4.3 6.9 + - - -
365A ARG* 4.6 13.3 - - - -
368A ARG* 5.3 1.8 + - - -
485A GLN* 2.9 28.0 + - - +
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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