Contacts of the helix formed by residues 88 - 117 (chain A) in PDB entry 3R45
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 ALA 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP 3.3 2.0 + - - -
87A GLN* 1.3 72.7 - - - +
89A GLN* 1.3 62.3 + - + +
91A LEU* 3.2 6.1 + - - +
92A LEU* 3.0 33.3 + - + +
47C THR* 5.9 0.2 - - - -
48C PRO* 3.0 37.4 + - + +
50C VAL* 4.1 15.0 - - + +
57C TYR* 5.6 0.2 - - + -
66C TRP* 3.7 26.6 - - + -
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN* 3.1 5.0 - - + +
88A ALA* 1.3 78.7 - - + +
90A ALA* 1.3 59.1 + - - +
92A LEU* 3.9 22.9 - - - +
93A ALA* 3.0 28.1 + - - +
83B ALA* 3.7 4.3 - - + +
40C TYR* 3.3 28.6 + - - -
44C PHE* 3.6 54.0 - - + -
47C THR* 4.4 15.3 + - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 3.6 16.2 - - + -
87A GLN* 3.0 14.4 + - + +
89A GLN* 1.3 75.0 - - - +
91A LEU* 1.3 62.1 + - - +
93A ALA* 3.6 0.4 - - - +
94A LEU* 3.0 30.1 + - - +
81B VAL 3.6 13.2 - - - +
82B THR 3.5 28.9 - - - +
83B ALA* 3.8 10.2 - - - +
86B VAL* 3.6 9.6 - - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 4.3 7.3 - - + -
68A SER* 4.3 17.9 - - - -
71A ALA* 4.6 11.2 - - + -
86A TRP* 3.8 31.6 - - + -
87A GLN 3.2 3.2 + - - +
88A ALA 3.5 7.4 - - - +
90A ALA* 1.3 79.2 - - - +
92A LEU* 1.3 56.9 + - - +
94A LEU* 3.4 6.6 + - + +
95A GLN* 3.0 30.5 + - - +
50C VAL* 3.8 37.0 - - + -
52C MET* 4.1 20.4 - - + -
66C TRP* 3.9 27.4 - - + +
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Residues in contact with LEU 92 (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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59A HIS* 6.0 2.9 - - + +
60A LEU* 3.9 25.7 - - + +
64A LYS* 4.1 8.5 - - + +
88A ALA* 3.0 22.7 + - + +
89A GLN* 4.0 29.2 - - - +
91A LEU* 1.3 72.6 - - - +
93A ALA* 1.3 57.3 + - - +
95A GLN* 3.2 3.9 + - - +
96A GLU* 2.8 39.4 + - + +
40C TYR* 3.7 15.5 - - - +
66C TRP* 4.0 24.9 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN 3.0 20.4 + - - +
90A ALA* 3.6 7.0 - - - +
92A LEU* 1.3 75.1 - - - +
94A LEU* 1.3 63.2 + - - +
96A GLU* 3.6 1.2 + - - +
97A ALA* 3.1 25.6 + - - +
83B ALA* 4.7 2.5 - - + -
86B VAL* 4.0 17.9 - - + +
87B VAL* 5.6 0.2 - - + -
90B LEU* 4.7 4.6 - - + +
36C LEU* 4.7 2.3 - - - +
40C TYR* 3.6 38.5 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 4.1 9.6 - - + -
71A ALA* 3.9 24.2 - - + -
86A TRP* 3.8 28.7 - - + -
90A ALA 3.0 18.4 + - - +
91A LEU* 3.6 6.7 - - + +
93A ALA* 1.3 78.1 - - - +
95A GLN* 1.3 57.6 + - - +
97A ALA* 3.7 3.4 - - - +
98A ALA* 3.0 27.2 + - - +
61B PHE* 4.7 2.4 - - + -
62B LEU* 3.8 20.4 - - + -
65B VAL* 3.7 30.1 - - + -
66B ILE* 4.0 13.5 - - + -
86B VAL* 4.0 11.4 - - + +
90B LEU* 5.9 0.7 - - + -
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Residues in contact with GLN 95 (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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60A LEU* 3.9 18.5 - - + +
62A ILE* 2.6 38.3 + - + +
63A ARG 4.3 1.2 - - - -
64A LYS* 3.6 22.4 - - - +
67A PHE* 3.5 44.2 - - + -
91A LEU 3.0 15.6 + - - +
92A LEU* 3.2 6.1 + - - +
94A LEU* 1.3 73.8 - - - +
96A GLU* 1.3 66.4 + - - +
98A ALA* 3.2 2.1 + - - +
99A GLU* 2.9 49.2 + - + +
66C TRP* 5.5 1.4 + - - -
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Residues in contact with GLU 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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59A HIS* 4.6 15.9 + - + +
60A LEU* 3.7 24.2 - - + +
92A LEU* 2.8 21.1 + - + +
93A ALA 4.0 2.7 - - - +
95A GLN* 1.3 71.8 - - - +
97A ALA* 1.3 58.4 + - - +
99A GLU* 3.3 3.6 + - - +
100A ALA* 2.9 29.8 + - - +
32C ARG* 2.9 29.2 + - - +
36C LEU* 3.4 19.6 - - + +
39C LYS* 2.8 20.4 + - - -
40C TYR* 2.5 28.3 + - + +
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Residues in contact with ALA 97 (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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93A ALA 3.1 20.2 + - - +
94A LEU* 3.7 4.9 - - - +
95A GLN 3.2 0.2 - - - -
96A GLU* 1.3 77.8 - - - +
98A ALA* 1.3 56.7 + - - +
100A ALA* 3.5 3.0 + - - +
101A PHE* 3.0 27.9 + - - +
61B PHE* 3.9 7.1 - - + -
90B LEU* 3.8 32.8 - - + -
33C MET* 4.2 8.3 - - + +
36C LEU* 3.5 19.0 - - + +
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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
----------------------------------------------------------
62A ILE* 5.5 1.1 - - + -
67A PHE* 4.1 14.1 - - + -
94A LEU 3.0 18.0 + - - +
95A GLN 3.6 4.0 - - - +
97A ALA* 1.3 73.7 - - - +
99A GLU* 1.3 62.6 + - + +
101A PHE* 3.3 3.2 + - - +
102A LEU* 3.0 34.8 + - - +
58B LEU* 3.8 23.7 - - + +
61B PHE* 3.6 23.5 - - + -
62B LEU* 4.4 0.9 - - + -
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Residues in contact with GLU 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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59A HIS 4.2 2.1 - - - +
60A LEU* 3.7 17.2 - - - +
61A LEU* 2.9 34.9 + - - +
62A ILE* 2.9 43.5 + - + +
95A GLN* 2.9 33.7 + - - +
96A GLU* 3.7 4.5 - - - +
98A ALA* 1.3 74.9 - - - +
100A ALA* 1.3 66.1 + - - +
102A LEU* 3.2 2.6 + - - +
103A VAL* 2.9 32.6 + - + +
37B LEU* 4.0 13.0 - - + +
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Residues in contact with ALA 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 GLU 2.9 18.9 + - - +
97A ALA* 3.7 5.2 - - - +
98A ALA 3.4 0.2 - - - -
99A GLU* 1.3 75.2 - - - +
101A PHE* 1.3 62.8 + - - +
103A VAL* 3.5 5.6 + - - +
104A HIS* 3.0 25.6 + - - +
29C PHE* 3.7 5.6 - - + -
32C ARG* 4.1 32.1 - - + +
33C MET* 4.2 14.6 - - - -
36C LEU* 4.6 1.8 - - + -
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Residues in contact with PHE 101 (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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97A ALA 3.0 17.7 + - - +
98A ALA 3.4 5.4 - - - +
100A ALA* 1.3 78.3 - - - +
102A LEU* 1.3 67.9 + - + +
104A HIS* 3.4 7.2 + + - +
105A LEU* 2.9 38.6 + - + +
130A ARG* 4.3 18.4 - - - -
133A ARG* 4.6 23.1 - - + -
57B VAL* 3.7 26.5 - - + -
58B LEU* 6.4 0.2 - - + -
61B PHE* 3.5 44.2 - + + -
29C PHE* 3.8 27.8 - + + -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.7 5.2 - - + -
98A ALA 3.0 21.7 + - - +
99A GLU 3.8 3.1 - - - +
101A PHE* 1.3 80.1 - - + +
103A VAL* 1.3 60.0 + - - +
105A LEU* 3.2 8.6 + - + +
106A PHE* 2.9 46.3 + - + -
37B LEU* 3.8 27.1 - - + -
54B THR* 4.2 26.0 - - + +
57B VAL* 3.9 27.8 - - + -
58B LEU* 4.1 30.3 - - + +
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Residues in contact with VAL 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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61A LEU* 5.1 1.1 - - + -
99A GLU* 2.9 23.0 + - + +
100A ALA* 3.9 6.1 - - - +
102A LEU* 1.3 73.5 - - - +
104A HIS* 1.3 59.8 + - - +
106A PHE* 3.4 8.0 + - - +
107A GLU* 3.0 38.5 + - - +
37B LEU* 3.7 30.5 - - + +
40B ARG* 4.0 39.7 - - + +
41B GLY* 4.0 3.9 - - - -
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Residues in contact with HIS 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 ALA 3.0 18.2 + - - +
101A PHE* 3.6 9.2 - + - +
103A VAL* 1.3 77.3 - - - +
105A LEU* 1.3 66.9 + - + +
107A GLU* 3.3 9.2 + - - +
108A ASP* 3.0 41.3 + - - +
133A ARG* 5.0 14.7 - - + +
136A GLU* 5.4 1.8 + - - -
25C SER* 3.3 43.9 + - - -
26C ARG* 3.7 12.4 - - + +
29C PHE* 3.5 43.2 - + + +
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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
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101A PHE* 2.9 29.5 + - + +
102A LEU* 3.2 11.2 + - + +
104A HIS* 1.3 82.2 - - + +
106A PHE* 1.3 53.0 + - + +
108A ASP* 3.4 4.5 + - + +
109A ALA* 2.8 36.3 + - - +
126A VAL* 4.1 24.0 - - + +
129A ALA* 3.9 24.7 - - + +
130A ARG* 4.2 23.1 - - + +
133A ARG* 5.7 5.4 - - + +
57B VAL* 3.7 32.1 - - + -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.9 34.0 + - + +
103A VAL 3.6 5.2 - - - +
105A LEU* 1.3 75.5 - - + +
107A GLU* 1.3 60.1 + - - +
109A ALA* 3.4 2.3 + - - +
110A TYR* 2.9 32.4 + - - +
121A LEU* 3.7 30.3 - - + -
126A VAL* 5.0 9.4 - - + -
34B ILE* 4.1 8.3 - - + -
37B LEU* 3.7 18.6 - - + -
38B ALA* 3.6 37.9 - - + -
41B GLY* 4.3 10.1 - - - -
43B VAL* 3.9 10.6 - - + +
50B ILE* 4.1 7.2 - - + -
54B THR* 3.6 33.2 - - + -
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Residues in contact with GLU 107 (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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103A VAL* 3.0 30.6 + - - +
104A HIS* 3.5 12.8 - - - +
106A PHE* 1.3 74.1 - - - +
108A ASP* 1.3 63.5 + - - +
110A TYR* 3.2 4.5 + - - +
111A LEU* 3.1 29.2 + - + +
40B ARG 4.9 2.3 - - - +
41B GLY* 3.3 27.4 + - - +
25C SER* 3.5 14.7 + - - +
28C ARG* 2.8 39.2 + - - +
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Residues in contact with ASP 108 (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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104A HIS* 3.0 30.6 + - - +
105A LEU* 3.7 10.9 - - + +
107A GLU* 1.3 79.8 - - - +
109A ALA* 1.3 63.5 + - - +
110A TYR 3.3 0.7 + - - -
111A LEU* 3.3 12.3 + - - +
112A LEU* 3.5 14.9 + - - +
129A ALA* 3.8 21.6 - - + +
132A ILE* 5.6 2.6 - - - +
133A ARG* 5.1 5.7 + - - +
136A GLU* 4.6 9.4 - - - +
22C LEU* 3.8 23.8 - - + +
25C SER* 2.6 34.5 + - - -
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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
----------------------------------------------------------
105A LEU 2.8 22.6 + - - +
106A PHE* 3.7 4.5 - - - +
108A ASP* 1.3 73.9 - - - +
110A TYR* 1.3 62.3 + - - +
112A LEU* 3.1 16.2 + - - +
113A THR* 3.2 12.8 + - - -
121A LEU* 3.6 21.3 - - + -
125A ASP* 3.5 24.4 - - - +
126A VAL* 3.8 18.4 - - + -
129A ALA* 3.7 4.0 - - + +
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Residues in contact with TYR 110 (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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106A PHE 2.9 18.5 + - - +
107A GLU* 3.2 6.0 + - - +
109A ALA* 1.3 73.1 - - - +
111A LEU* 1.3 60.4 + - + +
112A LEU 3.1 1.8 - - - -
113A THR* 2.9 24.0 + - + -
114A LEU* 2.8 55.8 + - + +
119A VAL* 2.8 41.5 + - - +
121A LEU* 4.3 3.8 - - + -
41B GLY 4.8 2.2 - - - +
42B GLY 3.2 25.1 - - - -
43B VAL* 3.6 31.0 - - + -
44B LYS* 3.3 27.7 - - + +
45B ARG 4.5 1.3 - - - -
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Residues in contact with LEU 111 (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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107A GLU* 3.1 16.3 + - + +
108A ASP* 3.5 7.9 - - - +
110A TYR* 1.3 75.6 - - + +
112A LEU* 1.3 57.9 + - - +
114A LEU* 3.6 17.5 + - + +
115A HIS* 2.9 28.1 + - - +
18C LEU* 3.9 17.0 - - + +
21C LYS* 3.6 55.6 - - + +
22C LEU* 3.7 18.8 - - + +
25C SER* 4.6 6.3 - - - -
28C ARG* 6.3 0.2 - - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP 3.5 16.2 - - - +
109A ALA 3.2 5.4 - - - +
110A TYR 3.1 0.6 - - - -
111A LEU* 1.3 74.2 - - - +
113A THR* 1.3 61.1 + - - +
115A HIS* 3.2 9.0 + - + +
116A ALA* 2.8 30.0 + - - +
125A ASP* 3.3 33.6 - - + +
128A LEU* 3.9 21.5 - - + -
129A ALA* 3.7 21.1 - - + +
132A ILE* 4.2 19.5 - - + -
18C LEU* 4.2 26.0 - - + -
22C LEU* 5.1 4.0 - - + -
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA 3.2 12.3 + - - -
110A TYR* 2.9 17.3 + - + -
112A LEU* 1.3 76.7 - - - +
114A LEU* 1.3 59.8 + - - +
116A ALA* 3.0 9.7 + - - +
118A ARG* 2.9 49.7 + - - +
119A VAL 3.8 4.3 - - - -
120A THR 3.3 31.6 - - - +
121A LEU* 3.5 13.2 - - - +
125A ASP* 3.0 20.8 + - - -
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Residues in contact with LEU 114 (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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110A TYR* 2.8 48.5 + - + +
111A LEU* 3.9 17.3 - - + +
113A THR* 1.3 73.8 - - - +
115A HIS* 1.3 61.3 + - - +
117A GLY* 3.1 13.7 + - - -
118A ARG 3.4 15.7 + - - +
119A VAL* 4.2 15.9 - - + -
14C GLU* 3.9 17.7 - - - +
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU 2.9 19.8 + - - +
112A LEU* 3.4 12.8 - - + +
113A THR 3.1 0.2 - - - -
114A LEU* 1.3 72.7 - - - +
116A ALA* 1.3 61.7 + - - +
117A GLY 3.1 5.2 + - - -
14C GLU* 3.2 43.6 + - + +
15C ASP* 3.7 29.8 + - + -
18C LEU* 3.9 21.9 - - + +
84C SO4 4.2 9.7 + - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 2.8 13.4 + - - +
113A THR 3.0 10.0 + - - +
115A HIS* 1.3 76.8 - - - +
117A GLY* 1.3 58.6 + - - +
118A ARG* 3.4 29.8 - - - +
143A SO4 3.8 20.3 + - - +
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Residues in contact with GLY 117 (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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114A LEU 3.1 9.9 + - - -
115A HIS 3.1 6.0 + - - -
116A ALA* 1.3 80.3 - - - +
118A ARG* 1.3 62.8 + - - +
119A VAL* 5.7 0.5 - - - +
144A SO4 4.2 2.3 + - - -
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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