Contacts of the helix formed by residues 87 - 115 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 4.2 15.9 - - + +
85A THR* 2.8 8.1 + - - +
86A LEU* 1.3 83.3 - - + +
88A GLY* 1.3 57.7 + - - +
89A ARG 2.9 1.8 - - - -
90A CYS* 2.6 45.2 + - + +
91A VAL* 3.2 12.9 + - + +
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 5.1 3.5 - - - +
50A ALA* 4.2 8.6 - - - +
51A GLU* 4.0 6.5 - - - -
68A TRP* 4.3 3.3 - - - -
83A PRO* 3.4 19.2 - - - +
85A THR* 2.6 25.1 + - - -
87A TRP* 1.3 72.9 - - - +
89A ARG* 1.3 55.9 + - - +
91A VAL* 3.3 14.6 + - - +
92A ALA* 3.1 22.0 + - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.9 1.2 - - - -
83A PRO* 3.0 40.6 + - + -
84A VAL* 3.5 24.7 + - - +
85A THR 3.0 16.6 - - - +
86A LEU* 4.0 10.1 - - - +
87A TRP 2.9 0.8 + - - -
88A GLY* 1.3 75.8 - - - +
90A CYS* 1.3 60.5 + - - +
92A ALA* 3.2 9.2 - - - +
93A VAL* 3.0 24.5 - - - +
63D PRO 5.0 3.0 + - - -
64D ARG* 5.0 5.3 + - - +
67D TRP* 2.8 70.8 - - + +
80D ASP* 4.3 8.9 + - - -
81D LEU* 4.9 2.8 - - - +
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Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 3.0 22.9 - - - -
87A TRP* 2.6 33.2 + - + +
89A ARG* 1.3 71.3 - - - +
91A VAL* 1.3 64.5 + - + +
92A ALA 2.8 5.9 + - - -
93A VAL* 3.0 17.3 + - - +
94A VAL* 3.1 20.2 + - + +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 3.4 27.6 - - - +
46A LEU* 4.0 27.4 - - + -
47A ALA* 3.4 35.2 - - + +
50A ALA* 4.7 4.9 - - + -
68A TRP* 4.4 4.3 - - + -
87A TRP* 3.7 16.2 - - + +
88A GLY* 3.5 11.0 - - - +
90A CYS* 1.3 77.7 - - + +
92A ALA* 1.3 60.2 - - - +
94A VAL* 3.6 7.5 + - - +
95A VAL* 2.9 30.1 + - + +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TRP* 3.8 25.5 - - + -
83A PRO* 4.3 0.9 - - + -
88A GLY 3.1 13.1 + - - +
89A ARG 3.2 13.2 - - - +
90A CYS 2.8 0.6 - - - -
91A VAL* 1.3 74.1 - - - +
93A VAL* 1.3 58.6 + - - +
95A VAL* 2.6 28.6 + - - +
96A MET* 2.9 19.7 + - + +
67D TRP* 3.9 20.2 - - + -
78D TYR* 4.8 4.3 - - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG 3.0 18.8 - - - +
90A CYS* 3.5 9.0 - - - +
92A ALA* 1.3 74.1 - - - +
94A VAL* 1.3 63.9 + - + +
96A MET* 3.2 13.4 - - + +
97A VAL* 2.9 43.9 + - + +
67D TRP* 4.7 2.7 - - + -
70D VAL* 3.8 26.5 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.1 17.9 - - + -
90A CYS* 3.1 15.2 + - + +
91A VAL* 3.7 9.6 - - - +
92A ALA 2.8 3.4 + - - -
93A VAL* 1.3 77.9 - - + +
95A VAL* 1.3 64.1 + - + +
97A VAL* 3.5 3.0 + - - +
98A ALA* 2.9 25.6 + - + +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.1 17.9 - - + +
40A LEU* 4.2 8.1 - - + -
43A GLY* 4.4 21.3 - - - -
68A TRP* 4.5 8.5 - - + -
69A SER* 3.6 32.1 - - - +
72A THR* 3.9 9.6 - - + -
73A ALA* 3.8 16.2 - - + +
91A VAL* 2.9 24.7 - - + +
92A ALA* 2.6 12.9 + - - +
94A VAL* 1.3 72.1 - - + +
96A MET* 1.3 65.7 + - - +
98A ALA* 3.1 4.2 - - - +
99A GLY 3.0 15.4 + - - -
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.3 34.8 - - + +
73A ALA* 4.5 1.0 - - - +
92A ALA* 2.9 15.2 + - + +
93A VAL* 3.2 29.4 - - + +
95A VAL* 1.3 70.8 - - - +
97A VAL* 1.3 66.4 + - - +
99A GLY* 2.8 14.2 + - - -
100A ILE* 2.8 21.5 + - + +
67D TRP* 5.2 3.8 - - + -
70D VAL* 3.5 28.0 - - + +
71D GLU* 5.3 3.1 - - - -
74D THR* 3.6 23.8 - - + -
76D VAL* 3.3 30.3 - - + -
78D TYR* 5.1 4.5 - - - -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 2.9 32.6 + - + +
94A VAL* 4.0 4.0 - - - +
96A MET* 1.3 76.3 - - + +
98A ALA* 1.3 54.6 + - - +
100A ILE* 4.1 9.4 - - + -
101A THR* 2.4 49.1 + - - +
74D THR* 5.3 3.6 - - + -
103D PHE* 4.0 24.9 - - + -
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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
----------------------------------------------------------
36A LEU* 3.5 17.7 - - + -
39A VAL* 3.9 22.9 - - + -
94A VAL* 2.9 15.9 + - + +
95A VAL 3.1 12.1 - - - +
96A MET 2.9 0.6 + - - -
97A VAL* 1.3 77.3 - - - +
99A GLY* 1.3 53.2 + - - +
101A THR* 3.3 4.2 - - - -
102A SER* 2.7 38.2 + - - -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.2 22.1 - - - +
73A ALA* 3.5 17.9 - - - -
95A VAL 3.0 4.4 + - - -
96A MET 2.8 10.7 + - - -
98A ALA* 1.3 73.1 - - - +
100A ILE* 1.3 65.8 + - - -
102A SER 3.1 0.7 + - - -
103A PHE* 2.9 34.2 + - - -
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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
----------------------------------------------------------
73A ALA 4.0 1.8 + - - -
75A THR* 4.1 10.8 - - + -
96A MET* 2.8 31.7 + - + +
97A VAL 3.8 3.4 - - - +
99A GLY* 1.3 70.1 - - - +
101A THR* 1.3 53.2 + - - +
103A PHE* 4.0 1.4 - - - +
104A GLY* 2.8 32.4 + - - -
129A TBA 3.6 39.6 - - + +
74D THR* 4.0 27.6 - - + +
103D PHE* 3.2 59.5 - - + -
107D THR* 5.2 0.3 + - - -
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Residues in contact with THR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 2.4 40.3 + - - +
98A ALA* 3.3 5.2 - - - -
100A ILE* 1.3 74.8 - - - +
102A SER* 1.3 57.5 + - - +
104A GLY* 3.1 2.9 + - - -
105A LEU* 2.8 35.1 + - + +
103D PHE* 5.1 4.2 - - - -
106D VAL* 5.9 7.9 - - + +
110D LEU* 4.4 13.6 - - + +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 3.9 26.2 + - - +
33A THR 5.2 0.4 - - - -
35A LEU* 5.5 0.9 - - - +
36A LEU* 3.5 38.8 + - - +
98A ALA* 2.7 26.5 + - - +
99A GLY 3.6 0.7 - - - -
101A THR* 1.3 73.3 - - - +
103A PHE* 1.3 59.0 + - - +
105A LEU* 2.9 24.4 - - - +
106A VAL* 3.0 13.7 + - - +
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.2 19.3 - - + -
73A ALA* 4.0 17.7 - - + -
74A THR* 4.5 9.9 - - + -
99A GLY* 2.9 33.0 + - - +
100A ILE* 4.0 3.1 - - - +
102A SER* 1.3 69.0 - - - +
104A GLY* 1.3 69.2 + - - +
105A LEU 2.9 1.9 + - - -
106A VAL* 2.9 12.8 + - + +
107A THR* 2.8 26.8 + - - +
129A TBA 5.3 10.3 - - + -
97B VAL* 4.1 26.9 - - + -
100B ILE* 3.2 54.3 - - + -
101B THR* 5.3 4.5 - - - -
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE 2.8 18.9 + - - -
101A THR* 3.5 2.7 - - - -
103A PHE* 1.3 76.6 - - - +
105A LEU* 1.3 60.7 + - - +
107A THR* 3.4 5.0 - - - -
108A ALA* 3.2 10.7 + - - +
129A TBA 5.1 8.2 - - - +
107D THR* 3.0 46.0 - - - +
110D LEU* 4.4 3.6 - - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.5 21.5 - - + +
29A ALA* 3.7 13.2 - - - -
32A ALA* 3.4 30.1 - - + -
101A THR* 2.8 13.1 + - + +
102A SER* 2.9 12.8 - - - +
104A GLY* 1.3 72.7 - - - +
106A VAL* 1.3 56.4 + - + +
107A THR 3.0 1.6 - - - -
108A ALA* 2.6 30.9 + - - +
109A ALA* 3.0 6.6 + - + +
110D LEU* 3.5 34.8 - - + -
113D TRP* 5.5 1.3 - - + -
114D PHE* 4.1 23.7 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.8 18.2 - - + +
32A ALA* 5.2 2.5 - - + -
33A THR* 5.6 4.3 - - - +
102A SER 3.5 13.2 - - - +
103A PHE* 2.9 14.5 + - + +
105A LEU* 1.3 85.3 - - + +
107A THR* 1.3 60.9 + - - +
109A ALA* 3.5 8.7 + - + +
110A LEU* 3.1 33.5 + - + +
101B THR* 6.0 7.0 - - + +
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 2.8 17.3 + - - +
104A GLY* 3.4 12.7 - - - -
106A VAL* 1.3 76.5 - - - +
108A ALA* 1.3 63.1 + - - +
110A LEU* 3.5 8.8 + - - +
111A ALA* 3.2 22.1 + - + +
129A TBA 5.8 2.8 - - - +
100B ILE* 5.2 0.9 + - - +
104B GLY* 3.1 42.4 - - - +
107B THR* 4.3 15.5 - - + -
108B ALA* 4.3 3.2 - - - +
107D THR* 4.2 13.9 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY 3.2 12.2 + - - +
105A LEU* 2.6 21.1 + - - +
107A THR* 1.3 69.6 - - - +
109A ALA* 1.3 57.0 + - - +
111A ALA* 3.1 4.9 + - - +
112A THR* 2.8 32.7 + - - +
107D THR* 4.1 3.3 - - - +
110D LEU* 4.1 10.3 - - + -
111D ALA* 3.5 39.7 - - + +
114D PHE* 4.1 6.5 - - + -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 3.7 22.0 + - + +
26A TRP* 4.5 14.0 - - + -
29A ALA* 5.0 11.0 - - + -
105A LEU* 3.0 9.3 + - + +
106A VAL* 3.9 11.4 - - + +
107A THR 3.4 0.2 - - - -
108A ALA* 1.3 76.6 - - - +
110A LEU* 1.3 64.0 + - - +
112A THR* 3.1 12.6 - - - +
113A TRP* 3.1 26.4 + - - +
114D PHE* 3.9 10.2 - - + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 5.2 8.7 - - + -
106A VAL* 3.1 29.7 + - + +
107A THR* 3.6 7.2 - - - +
109A ALA* 1.3 76.2 - - - +
111A ALA* 1.3 60.8 + - - +
113A TRP* 3.4 37.1 - - + -
114A PHE* 3.3 20.3 + - - -
101B THR* 4.4 15.3 - - + +
104B GLY 4.4 3.1 - - - -
105B LEU* 3.7 46.9 - - + +
108B ALA* 4.2 8.3 - - + -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.2 11.1 + - + +
108A ALA* 3.1 9.4 + - - +
109A ALA 3.1 0.4 - - - -
110A LEU* 1.3 76.8 - - - +
112A THR* 1.3 53.4 + - - +
113A TRP 2.8 5.7 + - - -
114A PHE* 2.6 28.7 + - - +
115A VAL* 3.1 15.8 + - + +
108B ALA* 3.6 28.3 - - + +
111B ALA* 5.3 6.3 - - + -
112B THR* 5.6 1.6 - - - -
111D ALA* 5.2 6.1 - - + -
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 3.1 41.4 - - + +
108A ALA 2.8 18.1 + - - +
109A ALA* 3.1 11.7 - - - +
111A ALA* 1.3 71.8 - - - +
113A TRP* 1.3 58.4 + - - +
115A VAL* 3.7 6.0 + - - +
116A GLY* 3.5 13.2 + - - -
111D ALA* 4.3 3.5 - - - +
114D PHE* 3.2 34.6 + - + +
115D VAL* 3.2 28.2 - - - +
118D GLU* 4.4 7.4 - - - +
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Residues in contact with TRP 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 4.2 7.9 - + - +
26A TRP* 3.5 36.2 - + + -
109A ALA 3.1 19.2 + - - +
110A LEU* 3.4 37.0 - - + +
112A THR* 1.3 76.8 - - - +
114A PHE* 1.3 83.0 + + - +
115A VAL 3.2 0.4 - - - -
116A GLY* 2.7 25.7 + - - +
117A ARG* 3.4 9.5 + - + +
28B ALA* 5.9 2.7 - - + -
105B LEU* 5.6 1.3 - - + -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU 3.3 11.2 + - - -
111A ALA 2.6 15.5 + - - +
113A TRP* 1.3 101.3 - + - +
115A VAL* 1.3 54.8 + - - +
116A GLY 3.0 5.2 - - - -
117A ARG* 3.4 6.1 + - + +
118A GLU* 3.2 24.8 + - - +
25B HIS* 3.8 32.5 + - + +
28B ALA* 3.7 26.9 - - + -
105B LEU* 4.0 18.4 - - + -
108B ALA* 4.1 11.2 - - + -
109B ALA* 4.0 21.3 - - + -
112B THR* 3.3 34.2 + - + +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 3.1 12.9 + - + +
112A THR* 4.0 11.2 - - - +
113A TRP 3.2 0.2 - - - -
114A PHE* 1.3 74.3 - - - +
116A GLY* 1.3 59.6 + - - +
117A ARG 3.4 0.2 - - - -
118A GLU* 3.7 11.7 - - + -
119A GLN* 3.4 37.2 + - + +
112B THR* 3.5 25.8 - - - +
115B VAL* 4.6 24.5 - - + -
115C VAL* 6.1 0.4 - - + -
115D VAL* 4.4 27.1 - - + -
119D GLN* 5.0 1.5 - - - +
----------------------------------------------------------
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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