Contacts of the helix formed by residues 87 - 115 (chain C) in PDB entry 1JVM
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 TRP 87 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ALA* 4.2 16.6 - - + +
85C THR* 2.8 7.8 + - - +
86C LEU* 1.3 83.1 - - + +
88C GLY* 1.3 57.1 + - - +
89C ARG 2.9 1.8 - - - -
90C CYS* 2.6 45.0 + - + +
91C VAL* 3.1 12.5 + - + +
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA* 5.0 3.5 - - - +
50C ALA* 4.2 8.0 - - - +
51C GLU* 4.0 7.0 - - - -
68C TRP* 4.3 3.6 - - - -
83C PRO* 3.5 18.1 - - - +
85C THR* 2.7 25.2 + - - -
87C TRP* 1.3 72.7 - - - +
89C ARG* 1.3 56.6 + - - +
91C VAL* 3.3 15.1 + - - +
92C ALA* 3.0 22.3 + - - +
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PRO 5.0 3.0 + - - -
64B ARG* 5.1 4.9 + - - +
67B TRP* 2.8 68.9 - - + +
80B ASP* 4.4 8.5 + - - -
81B LEU* 5.0 2.2 - - - +
82C TYR* 4.9 1.6 - - - -
83C PRO* 3.0 41.3 + - + -
84C VAL* 3.5 25.1 + - - +
85C THR 3.0 17.0 - - - +
86C LEU* 4.0 9.2 - - - +
87C TRP 2.9 0.8 - - - -
88C GLY* 1.3 76.4 - - - +
90C CYS* 1.3 60.6 + - - +
92C ALA* 3.2 9.5 - - - +
93C VAL* 3.0 23.7 - - - +
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Residues in contact with CYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU 3.0 22.4 - - - -
87C TRP* 2.6 34.7 + - + +
89C ARG* 1.3 70.3 - - - +
91C VAL* 1.3 63.8 + - + +
92C ALA 2.8 5.8 + - - -
93C VAL* 3.1 8.7 + - - +
94C VAL* 3.1 29.6 + - + +
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY* 3.4 27.1 - - - +
46C LEU* 4.0 26.5 - - + -
47C ALA* 3.4 35.7 - - + +
50C ALA* 4.7 4.5 - - + -
68C TRP* 4.3 4.7 - - + -
87C TRP* 3.6 16.8 - - + +
88C GLY* 3.5 11.2 - - - +
90C CYS* 1.3 77.3 - - + +
92C ALA* 1.3 60.6 + - - +
94C VAL* 3.6 7.9 + - - +
95C VAL* 2.9 29.9 + - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 4.0 17.0 - - + -
78B TYR* 4.9 1.6 - - - +
68C TRP* 3.8 25.6 - - + -
83C PRO* 4.4 0.9 - - + -
88C GLY 3.0 12.6 + - - +
89C ARG* 3.2 16.8 - - - +
90C CYS 2.8 0.6 - - - -
91C VAL* 1.3 74.1 - - - +
93C VAL* 1.3 59.0 + - - +
95C VAL* 2.6 28.6 + - - +
96C MET* 2.8 22.6 + - + -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 4.8 2.2 - - + -
70B VAL* 3.8 26.0 - - + -
89C ARG 3.0 18.8 - - - +
90C CYS* 3.1 9.8 + - - +
92C ALA* 1.3 73.9 - - + +
94C VAL* 1.3 64.7 + - + +
96C MET* 3.2 14.7 - - + +
97C VAL* 2.9 42.7 + - + +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 4.1 18.2 - - + -
90C CYS* 3.1 15.2 + - + +
91C VAL* 3.7 9.9 - - - +
92C ALA 2.8 3.4 + - - -
93C VAL* 1.3 77.9 - - + +
95C VAL* 1.3 63.9 + - + +
97C VAL* 3.8 3.9 - - - +
98C ALA* 2.9 26.1 + - + +
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 6.1 0.2 - - + -
39C VAL* 4.1 18.4 - - + +
40C LEU* 4.3 7.2 - - + -
43C GLY* 4.4 20.6 - - - -
68C TRP* 4.5 8.5 - - + -
69C SER* 3.6 31.6 - - - +
72C THR* 3.9 9.4 - - + -
73C ALA* 3.8 17.6 - - + +
91C VAL* 2.9 24.9 - - + +
92C ALA* 2.6 13.5 + - - +
94C VAL* 1.3 72.3 - - + +
96C MET* 1.3 66.5 + - - +
98C ALA* 3.1 4.2 - - - +
99C GLY 3.0 15.6 + - - -
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Residues in contact with MET 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 5.3 3.6 - - + -
70B VAL* 3.4 28.9 - - + +
71B GLU* 5.3 3.4 - - - -
74B THR* 3.6 23.3 - - + +
76B VAL* 3.4 28.7 - - + -
78B TYR* 5.2 4.3 - - - -
72C THR* 3.3 35.0 - - + +
73C ALA* 4.5 1.1 - - - +
92C ALA* 2.8 14.8 + - + +
93C VAL* 3.2 30.1 - - + +
95C VAL* 1.3 71.4 - - - +
97C VAL* 1.3 66.5 + - + +
99C GLY* 2.8 5.5 + - - -
100C ILE* 2.8 30.4 + - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 5.4 2.2 - - + -
103B PHE* 3.9 24.0 - - + -
93C VAL* 2.9 32.2 + - + +
94C VAL* 4.0 3.8 - - - +
96C MET* 1.3 77.2 - - + +
98C ALA* 1.3 55.0 + - - +
100C ILE* 4.1 9.6 - - + +
101C THR* 2.4 48.5 + - - +
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.5 17.3 - - + -
39C VAL* 3.9 22.7 - - + -
94C VAL* 2.9 16.5 + - + +
95C VAL 3.1 11.7 - - - +
96C MET 2.8 0.4 + - - -
97C VAL* 1.3 76.9 - - - +
99C GLY* 1.3 53.0 + - - +
101C THR* 3.3 4.4 - - - -
102C SER* 2.7 38.6 + - - +
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Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.3 22.8 - - - +
73C ALA* 3.5 17.5 - - - -
95C VAL 3.0 4.7 + - - -
96C MET 2.8 10.9 + - - -
98C ALA* 1.3 73.6 - - - +
100C ILE* 1.3 65.5 + - - -
102C SER 3.1 0.7 + - - -
103C PHE* 2.9 33.7 + - - -
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TBA 5.2 13.9 - - + -
74B THR* 4.0 27.8 - - + +
103B PHE* 3.1 59.9 - - + -
107B THR* 5.1 1.0 + - - +
73C ALA 4.0 2.3 + - - -
75C THR* 4.1 18.6 - - + -
96C MET* 2.8 31.4 + - + +
97C VAL 3.8 3.1 - - - +
99C GLY* 1.3 70.7 - - - +
101C THR* 1.3 52.5 + - - +
103C PHE* 4.0 3.8 - - - +
104C GLY* 2.8 32.1 + - - -
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 5.0 4.3 - - - -
106B VAL* 5.7 8.6 - - + +
110B LEU* 4.2 14.1 - - + +
97C VAL* 2.4 39.7 + - - +
98C ALA* 3.3 5.2 - - - -
100C ILE* 1.3 73.9 - - - +
102C SER* 1.3 57.5 + - - +
104C GLY* 3.1 3.1 + - - -
105C LEU* 2.8 34.7 + - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 3.9 26.9 + - - +
33C THR 5.2 0.4 - - - -
35C LEU* 5.5 1.0 - - - +
36C LEU* 3.5 39.3 + - - +
98C ALA* 2.7 26.4 + - - -
99C GLY 3.6 0.7 - - - -
101C THR* 1.3 73.6 - - - +
103C PHE* 1.3 58.9 + - - +
105C LEU* 2.9 25.1 - - - +
106C VAL* 3.0 13.9 + - - +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TBA 6.3 0.7 - - + -
36C LEU* 4.2 19.5 - - + -
73C ALA* 3.9 17.0 - - + -
74C THR* 4.5 10.3 - - + -
99C GLY* 2.9 32.1 + - - +
100C ILE* 4.0 3.4 - - - +
102C SER* 1.3 69.4 - - - +
104C GLY* 1.3 67.6 + - - +
105C LEU 2.9 2.8 + - - -
106C VAL* 2.9 12.0 + - + +
107C THR* 2.8 27.1 + - - +
97D VAL* 4.1 27.1 - - + -
100D ILE* 3.1 56.1 - - + -
101D THR* 5.2 4.0 - - - -
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B THR* 2.8 47.4 - - - +
110B LEU* 4.4 3.1 - - - -
100C ILE 2.8 16.9 + - - -
101C THR* 3.5 4.9 - - - -
103C PHE* 1.3 76.8 - - - +
105C LEU* 1.3 61.4 + - - +
107C THR* 3.4 5.0 + - - -
108C ALA* 3.2 9.9 + - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.5 35.7 - - + -
113B TRP* 5.4 1.3 - - + -
114B PHE* 4.0 24.2 - - + -
28C ALA* 3.5 21.3 - - + +
29C ALA* 3.7 13.9 - - - -
32C ALA* 3.4 29.8 - - + -
101C THR* 2.8 12.2 + - + +
102C SER* 2.9 13.7 - - - +
104C GLY* 1.3 73.7 - - - +
106C VAL* 1.3 56.0 + - + +
107C THR 3.0 1.6 - - - -
108C ALA* 2.6 31.5 + - - +
109C ALA* 3.0 6.0 + - + +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA* 4.8 17.9 - - + +
32C ALA* 5.2 2.2 - - + -
33C THR* 5.6 4.5 - - - +
102C SER* 3.5 14.4 - - - +
103C PHE* 2.9 14.5 + - + +
105C LEU* 1.3 85.0 - - + +
107C THR* 1.3 60.9 + - - +
109C ALA* 3.8 8.5 - - + +
110C LEU* 3.1 33.6 + - + +
101D THR* 5.9 7.9 - - + +
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Residues in contact with THR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 5.9 0.2 - - + -
107B THR* 4.1 12.3 - - + -
103C PHE* 2.8 16.6 + - - +
104C GLY* 3.4 12.7 - - - -
105C LEU 3.0 0.2 - - - -
106C VAL* 1.3 75.8 - - - +
108C ALA* 1.3 62.6 + - - +
110C LEU* 3.5 7.2 + - - +
111C ALA* 3.2 22.5 + - + +
100D ILE* 5.2 1.0 + - - +
104D GLY* 3.1 43.0 - - - +
107D THR* 4.2 18.6 - - + -
108D ALA* 4.2 2.5 - - - +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B THR* 4.0 5.8 - - - +
110B LEU* 4.0 8.1 - - + -
111B ALA* 3.3 40.8 - - + +
114B PHE* 4.2 5.6 - - + -
104C GLY 3.2 12.2 + - - +
105C LEU 2.6 20.6 + - - +
107C THR* 1.3 69.9 - - - +
109C ALA* 1.3 58.2 + - - +
111C ALA* 3.1 4.4 + - - +
112C THR* 2.8 31.9 + - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.9 10.7 - - + -
25C HIS* 3.7 21.6 + - + +
26C TRP* 4.5 14.1 - - + -
29C ALA* 5.0 10.5 - - + -
105C LEU* 3.0 9.3 + - + +
106C VAL* 3.9 11.9 - - + +
107C THR 3.4 0.2 - - - -
108C ALA* 1.3 75.8 - - - +
110C LEU* 1.3 64.0 + - - +
112C THR* 3.1 12.2 - - - +
113C TRP* 3.1 26.6 + - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 5.2 9.2 - - + -
106C VAL* 3.1 29.3 + - + +
107C THR* 3.6 7.4 - - - +
108C ALA 3.3 0.2 - - - -
109C ALA* 1.3 76.4 - - - +
111C ALA* 1.3 60.1 + - - +
113C TRP* 3.4 34.0 - - + -
114C PHE* 3.3 20.7 + - + -
101D THR* 4.3 15.7 - - + +
104D GLY 4.3 2.9 - - - -
105D LEU* 3.5 51.4 - - + +
108D ALA* 4.0 8.3 - - + -
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 5.2 5.8 - - + -
107C THR* 3.2 7.5 + - + +
108C ALA* 3.1 8.7 + - - +
109C ALA 3.1 0.4 - - - -
110C LEU* 1.3 77.8 - - - +
112C THR* 1.3 55.6 + - - +
113C TRP 2.9 5.2 - - - -
114C PHE* 2.6 28.4 + - - +
115C VAL* 3.1 14.8 + - + +
108D ALA* 3.6 31.6 - - + +
111D ALA* 5.1 7.9 - - + -
112D THR* 5.4 1.3 - - - +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 4.3 3.9 - - - +
114B PHE* 3.3 26.8 + - + +
115B VAL* 3.0 36.8 + - - +
118B GLU* 4.5 6.4 - - - +
25C HIS* 3.1 42.0 - - + +
108C ALA 2.8 18.6 + - - +
109C ALA* 3.1 11.0 - - - +
111C ALA* 1.3 71.9 - - - +
113C TRP* 1.3 57.6 - - - +
115C VAL* 3.8 7.0 + - - +
116C GLY* 3.5 13.5 + - - -
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C HIS* 4.2 7.4 - + - +
26C TRP* 3.5 37.6 - + + -
109C ALA 3.1 19.4 + - - +
110C LEU* 3.4 35.0 - - + +
112C THR* 1.3 77.3 - - - +
114C PHE* 1.3 82.2 + + - +
115C VAL 3.2 0.2 - - - -
116C GLY* 2.7 27.0 + - - +
117C ARG* 3.4 5.9 + - + +
28D ALA* 5.6 4.5 - - + -
105D LEU* 5.4 1.6 - - + -
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU 3.3 10.3 + - - -
111C ALA 2.6 14.1 + - - +
113C TRP* 1.3 103.0 - + - +
115C VAL* 1.3 55.1 + - - +
116C GLY 3.0 5.2 - - - -
117C ARG* 3.4 7.3 + - + +
118C GLU* 3.2 24.9 + - - +
25D HIS* 3.5 47.2 + - + +
28D ALA* 3.7 15.7 - - + -
105D LEU* 4.0 17.9 - - + -
108D ALA* 4.0 10.5 - - + -
109D ALA* 3.8 23.8 - - + -
112D THR* 3.1 36.3 + - + +
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 6.1 0.4 - - + -
115B VAL* 4.6 24.2 - - + -
119B GLN* 5.0 1.5 - - - +
111C ALA* 3.1 12.8 + - + +
112C THR* 4.0 11.7 - - - +
113C TRP 3.2 0.2 - - - -
114C PHE* 1.3 74.3 - - - +
116C GLY* 1.3 59.3 - - - +
117C ARG 3.4 0.4 - - - -
118C GLU* 3.7 10.1 - - + -
119C GLN* 3.3 35.0 + - + +
112D THR* 3.3 28.3 - - - +
115D VAL* 4.3 29.2 - - + -
----------------------------------------------------------
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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