Contacts of the helix formed by residues 76 - 110 (chain C) in PDB entry 6XWQ
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 76 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 1.3 76.0 - - - +
77C PRO* 1.3 65.5 - - - +
78C ALA* 3.1 12.6 + - - +
79C ARG* 3.2 14.5 + - - +
80C LEU* 2.7 32.6 + - - +
168C THR* 4.6 2.0 - - - -
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Residues in contact with PRO 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE 4.1 3.4 - - - +
76C SER* 1.3 90.5 - - - +
78C ALA* 1.3 56.2 + - - +
80C LEU* 3.7 10.1 - - + +
81C GLY* 2.9 24.3 + - - -
165C ILE* 5.5 7.4 - - + +
168C THR* 3.8 25.1 - - + +
169C TYR* 3.5 42.8 - - + +
172C ASN* 5.5 4.0 - - - +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C SER* 3.1 9.5 + - - +
77C PRO* 1.3 74.8 - - - +
79C ARG* 1.3 62.0 + - - +
81C GLY* 3.2 1.9 + - - -
82C ARG* 3.0 34.9 + - - +
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER 5.2 5.3 + - - -
75C ILE* 3.7 18.3 - - + +
76C SER* 3.2 16.0 + - - +
78C ALA* 1.3 77.4 - - - +
80C LEU* 1.3 57.7 + - - +
82C ARG* 3.3 27.3 - - - +
83C VAL* 2.9 38.4 + - + +
298C ASP* 6.0 3.2 - - - +
300C GLY* 3.8 28.9 + - - +
301C ILE* 5.2 0.4 - - - +
420C GLU* 3.0 29.6 + - - +
422C GLU* 4.0 17.0 + - - -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA* 3.2 35.9 - - + +
75C ILE* 3.4 24.3 - - + +
76C SER 2.7 21.9 + - - +
77C PRO* 3.7 7.2 - - + +
79C ARG* 1.3 72.9 - - - +
81C GLY* 1.3 57.4 + - - +
83C VAL* 4.9 0.7 - - - -
84C GLY* 2.8 26.0 + - - -
161C ILE* 5.1 3.6 - - + -
165C ILE* 3.6 31.0 - - + -
168C THR* 5.4 0.4 - - + -
304C PHE* 3.6 39.0 - - + -
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PRO 2.9 16.9 + - - -
78C ALA 3.2 1.3 + - - -
80C LEU* 1.3 75.2 - - - +
82C ARG* 1.3 65.2 + - - +
84C GLY* 3.2 1.2 + - - -
85C VAL* 2.9 32.8 + - - +
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA* 3.0 16.7 + - - +
79C ARG* 3.3 44.5 + - - +
81C GLY* 1.3 76.3 - - - +
83C VAL* 1.3 58.9 + - + +
85C VAL* 3.4 3.3 + - - +
86C LYS* 3.0 55.1 + - + +
420C GLU* 4.3 18.3 + - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 5.8 1.1 - - + -
79C ARG* 2.9 25.3 + - + +
80C LEU* 4.1 4.0 - - - +
82C ARG* 1.3 80.9 - - + +
84C GLY* 1.3 56.6 + - - +
86C LYS* 3.7 7.6 - - - +
87C ILE* 2.9 28.8 + - - +
300C GLY 5.0 9.0 - - - +
301C ILE* 4.9 4.7 - - + -
304C PHE* 4.2 12.3 - - + -
305C THR* 3.6 29.6 - - + -
416C VAL* 3.9 16.7 - - + +
420C GLU* 3.3 29.4 - - + +
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 2.8 18.9 + - - -
81C GLY* 3.2 2.4 + - - -
83C VAL* 1.3 78.1 - - - +
85C VAL* 1.3 56.9 + - - +
87C ILE* 3.1 10.6 - - - +
88C VAL* 2.9 36.4 + - - +
304C PHE* 4.1 12.3 - - - -
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY* 2.9 19.8 + - - +
82C ARG* 3.9 4.0 - - - +
84C GLY* 1.3 74.7 - - - +
86C LYS* 1.3 64.3 + - + +
87C ILE 3.0 0.2 - - - -
88C VAL* 4.7 3.4 - - - -
89C VAL* 3.0 45.4 + - + +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG* 3.0 47.7 + - + +
83C VAL* 4.0 4.2 - - - +
85C VAL* 1.3 76.9 - - + +
87C ILE* 1.3 58.2 + - - +
89C VAL* 5.0 3.0 - - - +
90C TYR* 3.6 15.5 + - - +
416C VAL* 3.5 35.3 + - + +
419C THR* 3.3 52.8 + - + +
420C GLU* 3.9 6.7 - - - +
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL 2.9 15.9 + - - +
84C GLY* 3.1 17.7 - - - +
86C LYS* 1.3 78.6 - - - +
88C VAL* 1.3 70.2 + - + +
89C VAL 3.4 0.4 - - - -
90C TYR* 3.4 5.4 + - + +
91C TYR* 2.9 76.7 + - + +
304C PHE* 4.7 5.6 - - + -
305C THR* 3.9 19.7 - - + -
308C LEU* 4.5 15.3 - - + -
412C GLY 3.9 15.0 - - - +
416C VAL* 3.5 22.9 - - + -
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY* 2.9 23.1 + - - +
85C VAL* 4.1 3.8 - - - +
87C ILE* 1.3 83.0 - - + +
89C VAL* 1.3 68.5 + - + +
91C TYR* 3.2 8.9 + - + +
92C LEU* 2.9 43.9 + - + +
308C LEU* 4.9 12.1 - - + -
312C ILE* 5.4 5.6 - - + -
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.0 34.2 + - + +
86C LYS* 5.0 3.1 - - - +
88C VAL* 1.3 78.7 - - + +
90C TYR* 1.3 56.7 + - - +
92C LEU* 4.0 4.7 - - - +
93C ALA* 2.9 36.4 + - + +
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS 3.6 16.5 + - - +
87C ILE* 3.4 9.9 + - + +
88C VAL 3.2 0.4 - - - -
89C VAL* 1.3 79.8 - - - +
91C TYR* 1.3 86.3 + + - +
93C ALA* 3.3 4.2 + - - -
94C THR* 2.9 57.7 + - + +
249C TYR* 3.7 15.8 - - - -
252C LEU* 3.5 20.4 - - + +
253C LEU* 6.2 0.2 - - + -
313C ASN* 4.6 2.0 - - - -
315C ASP* 5.4 0.2 - - - -
408C GLY 3.3 20.4 + - - -
411C ALA* 3.7 11.5 - - - +
412C GLY* 3.4 33.2 + - - -
415C ILE* 5.2 15.3 - - + -
416C VAL* 5.3 1.6 - - + -
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 2.9 54.7 + - + +
88C VAL* 3.2 7.4 + - - +
90C TYR* 1.3 90.4 - + - +
92C LEU* 1.3 60.3 + - + +
94C THR* 3.2 4.3 + - - -
95C SER* 2.4 39.8 + - - -
305C THR* 3.1 14.8 + - - -
306C LEU* 5.1 0.3 - - - -
308C LEU* 4.4 7.4 - - + -
309C GLY* 3.1 34.6 - - - -
312C ILE* 3.9 24.9 - - + -
313C ASN* 3.4 37.9 - - + -
353C ILE* 6.1 1.6 - - + -
409C ASP* 4.3 7.1 + - - -
412C GLY* 5.0 2.5 - - - -
413C THR 5.3 0.3 + - - -
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 2.9 36.8 + - + +
89C VAL* 4.0 4.7 - - - +
91C TYR* 1.3 81.5 - - + +
93C ALA* 1.3 63.9 + - - +
95C SER* 3.3 3.9 + - - -
96C ALA* 3.0 25.7 + - - +
312C ILE* 6.4 0.9 - - + -
349C VAL* 4.5 10.4 - - + +
350C LEU* 6.3 0.4 - - + -
353C ILE* 3.7 29.4 - - + -
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 2.9 23.3 + - + +
90C TYR* 3.8 4.3 - - - +
92C LEU* 1.3 76.9 - - - +
94C THR* 1.3 60.3 + - + +
96C ALA* 3.4 5.0 + - - +
97C MET* 2.9 36.5 + - + +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 2.9 54.3 + - + +
91C TYR* 3.2 6.2 + - - -
93C ALA* 1.3 75.9 - - + +
95C SER* 1.3 62.6 + - - +
97C MET* 3.7 7.6 - - - +
98C ALA* 2.8 26.9 + - - +
244C GLN* 4.6 1.7 + - - +
248C THR* 4.6 12.3 - - + -
249C TYR* 4.9 0.7 - - - -
252C LEU* 4.1 13.0 - - + -
313C ASN* 3.9 5.4 + - - -
315C ASP* 3.2 27.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 2.4 29.5 + - - +
92C LEU* 3.7 4.4 - - - -
94C THR* 1.3 76.6 + - - +
96C ALA* 1.3 57.4 + - - +
98C ALA* 3.3 4.2 + - - +
99C VAL* 3.0 32.7 + - - +
313C ASN* 4.4 5.4 + - - -
314C MET 4.8 12.2 + - - -
315C ASP* 3.3 12.5 + - - -
318C ALA* 4.3 5.7 - - - +
349C VAL* 4.1 25.4 - - - +
352C SER* 5.3 2.2 - - - -
353C ILE* 5.2 6.4 - - - +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU 3.0 17.1 + - - +
93C ALA* 3.8 5.2 - - - +
95C SER* 1.3 76.9 - - - +
97C MET* 1.3 58.7 + - + +
99C VAL* 3.3 2.1 + - - +
100C PHE* 2.9 30.0 + - - +
345C VAL* 3.8 22.3 - - + +
349C VAL* 4.1 11.6 - - + +
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Residues in contact with MET 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA* 2.9 25.9 + - + +
94C THR* 3.8 7.2 - - - +
95C SER 3.3 0.4 - - - -
96C ALA* 1.3 76.1 - - + +
98C ALA* 1.3 58.7 + - - +
100C PHE* 3.3 12.3 + - - +
101C PHE* 2.9 47.4 + - + -
244C GLN* 4.3 0.4 - - - +
248C THR* 4.4 17.7 - - + +
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C THR 2.8 17.8 + - - +
95C SER* 3.3 4.7 + - - +
97C MET* 1.3 73.9 - - - +
99C VAL* 1.3 60.6 + - - +
101C PHE* 3.3 1.5 + - - -
102C GLY 2.9 23.9 + - - -
244C GLN* 3.2 28.0 + - - +
315C ASP* 3.6 30.5 - - + +
318C ALA* 4.8 0.7 - - + -
319C LEU* 3.3 17.0 - - + +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C SER 3.0 22.7 + - - +
96C ALA 3.8 3.8 - - - +
98C ALA* 1.3 74.4 - - - +
100C PHE* 1.3 58.8 + - - +
102C GLY* 3.3 1.6 + - - -
103C LEU* 2.9 33.3 + - + +
318C ALA* 3.6 32.8 - - + +
319C LEU* 4.7 1.6 - - - +
322C GLY* 4.5 12.5 - - - -
344C VAL* 4.3 2.5 - - + +
345C VAL* 3.7 33.0 - - + +
348C ALA* 3.8 20.6 - - + -
349C VAL* 4.6 8.1 - - + -
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA 2.9 17.0 + - - +
97C MET* 3.7 13.9 - - - +
99C VAL* 1.3 78.4 - - - +
101C PHE* 1.3 73.9 + + - +
103C LEU* 3.2 9.1 + - + +
104C ILE* 2.9 60.2 + - + +
341C GLN* 3.8 28.3 - - + -
345C VAL* 4.7 6.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C MET* 2.9 38.9 + - + +
98C ALA* 3.7 5.8 - - - +
100C PHE* 1.3 89.8 - + - +
102C GLY* 1.3 58.0 + - - +
104C ILE* 3.3 10.8 + - + +
105C VAL* 2.9 35.1 + - + +
240C GLY 5.1 1.3 - - - +
243C LEU* 4.0 38.6 - - + -
244C GLN* 4.6 9.9 - - - +
247C ILE* 3.6 32.3 - - + -
248C THR* 4.1 16.4 - - - -
319C LEU* 4.3 10.3 - - + -
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Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ALA 2.9 11.1 + - - -
99C VAL 3.6 3.4 - - - -
101C PHE* 1.3 77.2 - - - +
103C LEU* 1.3 57.3 + - - +
105C VAL* 3.1 7.2 - - - +
106C GLY* 2.9 24.8 + - - -
319C LEU* 3.6 17.1 - - - +
322C GLY 5.2 0.2 - - - -
323C VAL* 3.3 31.1 - - - +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 2.9 23.9 + - + +
100C PHE* 3.6 12.6 - - + +
102C GLY* 1.3 75.9 - - - +
104C ILE* 1.3 59.8 + - + +
106C GLY* 3.4 0.9 + - - -
107C ARG* 2.9 35.4 + - + +
322C GLY* 3.2 26.7 - - - +
323C VAL* 5.8 0.2 - - - +
325C VAL* 6.3 0.4 - - + -
326C LEU* 3.7 25.3 - - + +
336C LEU* 5.7 3.1 - - + -
341C GLN* 3.6 42.6 - - + +
344C VAL* 3.7 27.6 - - + -
345C VAL* 5.3 1.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PHE* 2.9 57.6 + - + +
101C PHE* 3.5 12.6 - - + +
102C GLY 3.2 0.2 - - - -
103C LEU* 1.3 77.6 - - + +
105C VAL* 1.3 64.7 + - + +
107C ARG* 3.0 28.9 + - - +
108C LEU* 2.9 38.0 + - + +
243C LEU* 5.8 2.7 - - + -
341C GLN* 6.0 1.1 - - - +
----------------------------------------------------------
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE 2.9 19.1 + - - +
102C GLY* 3.1 22.0 - - - +
104C ILE* 1.3 76.8 - - + +
106C GLY* 1.3 57.1 + - - +
108C LEU* 3.5 18.2 - - + +
109C PHE* 2.9 37.9 + - + +
236C ALA* 4.2 13.8 - - - +
239C THR* 4.8 6.7 - - + -
240C GLY* 4.0 27.6 - - - +
243C LEU* 3.9 28.5 - - + -
323C VAL* 4.2 8.1 - - + -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLY 2.9 16.7 + - - -
103C LEU 3.7 1.8 - - - -
104C ILE 3.1 0.2 - - - -
105C VAL* 1.3 78.8 - - - +
107C ARG* 1.3 56.3 + - - +
109C PHE* 5.1 0.2 - - - -
110C ASN* 2.9 31.8 + - - -
111C VAL* 3.6 20.2 + - - -
236C ALA* 5.7 0.4 - - - -
323C VAL* 4.5 9.6 - - - -
326C LEU* 4.4 13.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 2.9 21.9 + - + +
104C ILE* 3.6 25.9 - - - +
106C GLY* 1.3 75.5 - - - +
108C LEU* 1.3 59.6 + - - +
110C ASN* 4.2 6.2 + - - +
326C LEU* 4.1 17.9 - - + -
336C LEU 6.0 2.2 - - - -
341C GLN* 4.7 13.7 + - - -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 2.9 31.9 + - + +
105C VAL* 3.5 24.5 - - + +
107C ARG* 1.3 78.2 - - - +
109C PHE* 1.3 93.4 + - + +
110C ASN* 3.4 1.5 - - - +
239C THR* 6.2 1.6 - - + -
243C LEU* 5.6 4.0 - - + -
----------------------------------------------------------
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C VAL* 2.9 19.8 + - + +
106C GLY* 4.5 0.7 - - - +
108C LEU* 1.3 98.9 - - + +
110C ASN* 1.3 71.1 + - - +
111C VAL* 4.7 2.7 - - - +
232C LYS* 3.1 35.2 + - + +
235C GLY 3.3 23.1 - - - -
236C ALA* 3.5 32.3 - - + -
239C THR* 3.7 25.1 - - + -
----------------------------------------------------------
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Residues in contact with ASN 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY 2.9 13.5 + - - -
107C ARG* 4.2 4.7 - - - +
108C LEU 3.4 4.4 - - - +
109C PHE* 1.3 82.2 - - - +
111C VAL* 1.3 63.0 + - - +
112C GLY 3.7 1.0 + - - -
113C ALA* 3.4 32.5 + - - +
232C LYS* 4.3 7.4 + - - +
326C LEU* 6.1 0.4 - - - -
330C ASN* 3.4 24.6 - - - +
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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