Contacts of the helix formed by residues 80 - 108 (chain D) in PDB entry 1TU8
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 80 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLY 3.6 0.2 - - - -
79D GLU* 1.3 80.3 - - - +
81D GLU* 1.3 65.2 + - - +
82D MET* 3.2 15.3 - - - +
83D GLU* 3.0 42.3 + - - +
84D THR* 3.0 25.1 + - - -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 5.7 0.4 - - - +
69C HIS* 2.7 40.2 - - + +
72C ARG* 3.0 43.1 + - - +
73C LYS* 5.3 6.5 - - + -
80D ASN* 1.3 74.8 - - - +
82D MET* 1.3 60.6 + - + +
84D THR* 3.3 4.5 + - - -
85D THR* 2.9 43.1 + - - -
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Residues in contact with MET 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASP* 5.4 8.1 - - - +
58C GLN* 3.4 40.9 + - + +
80D ASN* 3.2 11.4 - - - +
81D GLU* 1.3 81.5 - - + +
83D GLU* 1.3 57.3 - - + +
85D THR* 3.5 2.4 + - - -
86D TYR* 2.9 28.6 + - - +
135D ARG* 4.1 13.7 + - - +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLY* 3.9 8.7 - - - -
79D GLU* 2.9 35.9 + - - +
80D ASN* 3.0 33.4 - - - +
82D MET* 1.3 72.6 - - - +
84D THR* 1.3 64.9 + - - +
86D TYR* 3.2 3.3 + - - +
87D ILE* 3.0 31.2 + - - +
135D ARG* 3.6 25.5 + - - +
143D LEU* 3.7 32.7 - - + +
146D LYS* 5.4 2.9 - - - +
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ARG* 3.5 35.0 - - - +
77D ASN* 2.7 48.8 + - - +
78D GLY* 4.2 2.6 + - - -
80D ASN 3.0 15.2 + - - -
81D GLU* 3.5 10.5 - - - -
83D GLU* 1.3 76.6 - - - +
85D THR* 1.3 62.0 + - - +
87D ILE* 3.4 5.9 - - - +
88D ASP* 3.3 24.5 + - + +
149D TYR* 4.7 0.5 + - - -
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Residues in contact with THR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 4.1 11.0 - - - +
60C ILE* 3.6 41.7 - - + -
65C ALA* 4.3 4.2 - - + +
69C HIS* 3.4 15.7 - - + -
72C ARG* 3.1 9.1 + - - +
81D GLU* 2.9 34.9 + - - +
82D MET* 3.8 4.5 - - - -
83D GLU 3.3 0.2 - - - -
84D THR* 1.3 75.9 - - - +
86D TYR* 1.3 58.6 + - - +
88D ASP* 3.4 5.1 + - - +
89D MET* 2.9 29.1 + - + +
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Residues in contact with TYR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 5.5 3.1 - - - +
82D MET 2.9 18.2 + - - +
83D GLU 3.2 4.5 + - - +
85D THR* 1.3 77.4 - - - +
87D ILE* 1.3 59.2 + - - +
89D MET* 3.2 22.0 + - + +
90D PHE* 2.8 40.4 + + - +
131D LEU* 2.9 49.4 + - + +
132D LEU* 4.5 1.0 - - - -
134D THR* 2.9 14.0 + - - -
135D ARG* 3.6 31.4 - - - +
142D ILE* 3.6 33.9 + - + -
143D LEU* 3.9 11.9 - - + -
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ASN* 3.6 33.0 - - - +
78D GLY* 3.8 3.4 - - - +
83D GLU 3.0 21.0 + - - +
84D THR 3.4 6.5 - - - +
86D TYR* 1.3 74.2 - - - +
88D ASP* 1.3 56.7 + - - +
90D PHE* 3.6 7.3 - - - +
91D CYS* 2.8 36.0 + - - +
142D ILE* 4.1 9.4 - - + -
143D LEU* 3.5 30.7 - - + -
148D SER* 3.6 18.2 - - - +
149D TYR* 3.5 31.0 - - + -
150D ALA* 3.6 12.1 - - + +
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA* 3.5 18.1 - - + +
68C ARG* 2.8 51.9 + - - +
72C ARG* 4.7 5.8 + - - +
68D ARG* 3.9 10.5 + - - -
84D THR* 3.3 16.6 + - + +
85D THR* 3.4 7.2 - - - +
87D ILE* 1.3 78.9 - - - +
89D MET* 1.3 59.9 + - - +
91D CYS* 3.2 3.4 + - - +
92D GLU* 2.8 31.2 + - - +
149D TYR* 3.3 16.1 + - - +
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Residues in contact with MET 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLN* 3.6 31.6 - - + +
47C PHE* 3.4 11.9 - - + -
59C GLN 4.3 1.8 - - - +
60C ILE* 4.2 9.9 - - + -
61C VAL* 3.3 52.7 - - + +
62C GLN* 3.6 6.9 - - + +
65C ALA* 3.7 11.3 - - + +
85D THR* 2.9 18.1 + - - +
86D TYR* 3.5 32.5 - - + +
88D ASP* 1.3 74.3 - - - +
90D PHE* 1.3 62.5 + - - +
92D GLU 3.4 0.5 + - - -
93D GLY 3.1 17.2 + - - -
131D LEU* 4.2 13.7 - - + -
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.2 7.4 - - - -
86D TYR* 2.8 43.5 + + - +
87D ILE* 3.6 8.7 - - - +
89D MET* 1.3 72.1 - - - +
91D CYS* 1.3 63.6 + - - +
93D GLY* 3.0 12.1 + - - -
94D VAL* 3.1 14.6 + - + +
128D PHE* 3.4 43.5 - + + -
131D LEU* 3.6 24.7 - - + -
132D LEU* 4.0 14.1 - - + -
142D ILE* 3.8 33.0 - - + -
150D ALA* 4.8 0.4 - - + -
154D LEU* 3.9 30.3 - - + -
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Residues in contact with CYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 4.3 7.2 - - - -
68D ARG* 6.0 3.8 - - - +
87D ILE 2.8 21.4 + - - +
88D ASP* 3.7 4.0 - - - +
90D PHE* 1.3 74.7 - - - +
92D GLU* 1.3 63.4 + - - +
94D VAL* 3.2 10.6 + - - +
95D ARG* 3.1 35.3 + - - +
149D TYR* 3.9 29.4 - - + -
150D ALA* 4.0 9.0 - - + -
153D ALA* 3.7 27.6 - - - -
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLN* 3.5 39.5 + - + +
64C GLY* 4.7 2.1 - - - -
65C ALA 4.5 3.8 - - - +
68C ARG* 3.6 21.6 + - - +
92C GLU* 5.1 4.5 - - - +
95C ARG* 4.2 21.5 + - - -
2004C GTX 5.3 0.5 + - - -
68D ARG* 3.8 12.3 + - - -
88D ASP* 2.8 29.6 + - - +
91D CYS* 1.3 75.3 - - - +
93D GLY* 1.3 65.8 + - - +
95D ARG* 3.2 32.7 + - - +
96D ASP* 3.1 21.1 + - - +
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 3.6 22.6 - - - -
62C GLN* 3.4 13.4 + - - -
89D MET 3.1 7.1 + - - -
90D PHE 3.0 8.8 + - - -
92D GLU* 1.3 73.7 - - - +
94D VAL* 1.3 64.4 + - - +
96D ASP* 3.2 8.5 + - - +
97D LEU 3.2 16.3 + - - -
128D PHE* 3.4 13.8 - - - -
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 3.1 23.3 + - + +
91D CYS* 3.4 12.6 - - - +
93D GLY* 1.3 75.7 - - - +
95D ARG* 1.3 59.1 + - + +
97D LEU* 3.1 5.3 + - - +
98D HIS* 3.0 24.5 + - + +
128D PHE* 3.8 20.6 - - + -
150D ALA 5.4 0.9 - - - +
153D ALA* 3.6 31.4 - - + +
154D LEU* 4.1 22.4 - - + +
157D GLU* 3.7 22.5 - - + +
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Residues in contact with ARG 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 3.9 18.1 + - - -
13D LEU* 5.5 5.5 - - - +
63D SER* 2.8 21.4 + - - -
64D GLY* 3.3 21.2 - - - +
68D ARG* 5.6 0.9 - - - +
91D CYS* 3.1 24.2 + - - +
92D GLU* 3.5 34.5 + - - +
93D GLY 3.2 0.4 - - - -
94D VAL* 1.3 75.9 - - + +
96D ASP* 1.3 59.6 + - - +
98D HIS* 3.2 8.4 + - + +
99D VAL* 2.9 35.0 + - + +
2003D GTX 3.1 28.5 + - - -
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 5.6 2.6 - - + +
49C GLN* 4.3 8.5 + - - -
62C GLN* 2.9 16.3 - - - +
2004C GTX 2.9 39.6 + - - +
92D GLU 3.1 12.8 + - - +
93D GLY* 3.2 10.1 + - - +
95D ARG* 1.3 77.5 - - - +
97D LEU* 1.3 61.8 + - - +
99D VAL* 3.3 12.1 + - - +
100D LYS* 3.2 38.7 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLY 3.2 9.7 + - - +
94D VAL 3.1 9.7 + - - +
96D ASP* 1.3 75.7 - - - +
98D HIS* 1.3 58.6 + - - +
100D LYS* 3.1 10.0 + - + +
101D TYR* 2.9 25.3 + - - +
116D TYR* 3.4 20.2 - - + +
121D LEU* 4.2 5.6 - - + -
124D GLU* 3.9 31.0 - - + +
125D LEU* 4.3 20.0 - - + -
128D PHE* 4.0 25.6 - - + -
157D GLU* 4.0 12.8 - - + +
158D LEU* 6.2 0.7 - - + -
161D HIS* 3.9 22.2 - - + +
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Residues in contact with HIS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLY* 4.1 26.4 - - - -
13D LEU* 4.5 21.5 - - + +
94D VAL* 3.0 9.8 + - + +
95D ARG* 3.2 12.3 + - + +
97D LEU* 1.3 77.8 - - - +
99D VAL* 1.3 55.7 + - + +
101D TYR* 3.5 12.2 - + - +
102D THR* 2.9 55.1 + - + +
156D GLU* 5.7 6.0 - - + +
157D GLU* 2.6 38.8 + - - +
160D VAL* 5.3 6.5 - - + -
202D VAL* 6.1 1.6 - - + -
203D ASN* 5.2 2.3 + - - -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 6.6 0.4 - - + -
95D ARG* 2.9 21.3 + - + +
96D ASP* 3.5 13.9 - - - +
97D LEU 3.2 0.2 - - - -
98D HIS* 1.3 73.6 - - - +
100D LYS* 1.3 61.4 + - + +
102D THR* 3.2 7.4 + - - -
103D ARG* 2.8 67.6 + - + +
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Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN* 5.3 7.9 - - - +
96D ASP* 3.2 28.9 + - - +
97D LEU* 3.1 11.0 + - + +
99D VAL* 1.3 79.4 - - + +
101D TYR* 1.3 62.4 + - - +
103D ARG* 3.5 12.1 + - - +
104D MET* 3.2 22.0 + - - +
116D TYR* 4.0 16.7 - - + +
120D ILE* 4.4 12.1 - - + -
124D GLU* 4.2 36.9 + - + -
127D LYS* 5.9 0.2 - - - +
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU 2.9 16.2 + - - +
98D HIS* 3.5 10.1 - + - +
100D LYS* 1.3 76.2 - - - +
102D THR* 1.3 69.0 + - + +
104D MET* 3.2 8.0 + - + +
105D ILE* 2.9 52.7 + - + +
116D TYR* 3.6 15.8 + - - +
157D GLU* 4.1 7.4 - - - +
160D VAL* 4.0 30.5 + - + +
161D HIS* 3.5 27.1 - + + -
164D LEU* 4.3 20.2 - - + -
202D VAL* 3.4 14.4 - - + +
203D ASN* 3.1 35.4 + - - -
208D GLN* 4.3 7.4 - - - +
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Residues in contact with THR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 6.2 0.2 - - + -
98D HIS* 2.9 51.2 + - + +
99D VAL* 3.2 12.3 + - - -
101D TYR* 1.3 79.0 - - + +
103D ARG* 1.3 66.2 + - - +
105D ILE* 4.2 2.7 - - - -
106D TYR* 2.9 54.2 + - + +
203D ASN* 4.7 2.5 - - - +
2003D GTX 6.2 1.3 - - + -
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 5.9 6.5 - - - +
103C ARG* 4.1 27.3 - - - +
107C MET* 5.7 4.2 - - - +
99D VAL* 2.8 47.7 + - + +
100D LYS* 3.6 12.3 - - - +
102D THR* 1.3 76.9 - - - +
104D MET* 1.3 59.4 + - - +
107D MET* 2.9 45.1 + - + +
108D ALA* 3.7 1.2 + - - +
112D GLU* 5.7 0.7 - - - -
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Residues in contact with MET 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LYS 3.2 9.2 + - - +
101D TYR* 3.2 13.1 + - + +
103D ARG* 1.3 77.7 - - - +
105D ILE* 1.3 75.9 + - + +
108D ALA 3.0 7.9 + - - +
109D TYR* 2.9 43.9 + - - -
112D GLU* 3.9 39.9 - - + +
113D LYS* 3.8 16.2 - - - -
116D TYR* 3.9 24.9 - - + -
164D LEU* 3.7 39.7 - - + -
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TYR* 2.9 56.0 + - + +
102D THR* 3.3 7.4 + - - +
104D MET* 1.3 96.6 - - + +
106D TYR* 1.3 64.3 + - + +
109D TYR* 3.5 34.6 + - + +
164D LEU* 4.4 1.8 - - + -
203D ASN* 3.6 21.8 - - + +
205D ASN* 3.0 36.6 + - - +
207D LYS* 3.8 12.0 + - + +
208D GLN* 4.0 4.0 - - - -
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Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 4.2 0.7 - - - +
12D GLY* 5.9 0.7 - - - -
102D THR* 2.9 49.0 + - + +
105D ILE* 1.3 79.7 - - + +
107D MET* 1.3 81.3 + - + +
203D ASN* 3.5 19.0 + - + +
204D GLY* 2.9 34.4 + - - -
205D ASN* 3.7 26.2 + - + +
207D LYS* 5.6 2.4 + - - -
2003D GTX 3.4 37.0 - - + +
----------------------------------------------------------
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Residues in contact with MET 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ARG* 5.1 14.4 - - - +
103D ARG* 2.9 25.8 + - + +
106D TYR* 1.3 96.3 - - + +
108D ALA* 1.3 61.3 + - + +
109D TYR 4.0 0.2 - - - -
110D GLU* 5.8 0.4 - - - -
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ARG 3.7 2.2 + - - +
104D MET* 3.0 9.1 + - - +
107D MET* 1.3 83.9 - - + +
109D TYR* 1.3 60.8 + - - +
110D GLU* 3.3 5.6 - - - -
111D THR* 3.5 8.4 + - - +
112D GLU* 2.9 63.1 + - + +
113D LYS 4.0 0.2 + - - -
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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