Contacts of the helix formed by residues 87 - 116 (chain A) in PDB entry 5ZBX
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 GLN 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 1.3 74.1 - - - +
88A ALA* 1.3 66.2 + - - +
89A GLN* 4.3 8.6 - - + +
90A ALA* 3.1 19.0 + - + +
91A LEU* 3.2 14.1 + - - +
80B THR* 3.9 12.1 - - + +
81B VAL 3.1 20.6 + - - +
82B THR* 3.4 29.4 - - - +
83B ALA* 3.4 18.9 + - - +
49I C 3.0 21.1 - - - +
249J G 5.9 0.4 + - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 6.3 1.8 - - - +
68A GLN* 5.2 3.2 + - - +
86A TRP 3.6 3.1 + - - -
87A GLN* 1.3 71.6 - - - +
89A GLN* 1.3 64.3 + - - +
91A LEU* 3.0 14.8 + - - +
92A LEU* 3.0 20.9 + - - +
49I C 3.6 18.7 + - - +
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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* 3.3 9.5 - - - +
88A ALA* 1.3 77.9 - - - +
90A ALA* 1.3 57.6 + - - +
92A LEU* 3.3 10.2 + - - +
93A ALA* 2.9 30.1 + - - +
83B ALA* 4.1 13.2 - - + -
99B GLY 5.1 4.4 + - - -
100B PHE* 3.5 35.1 - - + +
57H LYS* 5.6 5.7 - - - +
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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* 4.3 9.9 - - + -
87A GLN* 3.1 20.0 + - + +
88A ALA 3.1 1.0 - - - -
89A GLN* 1.3 78.8 - - - +
91A LEU* 1.3 56.3 + - - +
93A ALA* 3.3 3.4 + - - +
94A LEU* 3.0 27.7 + - - +
81B VAL 3.8 6.5 - - - +
82B THR 3.4 31.0 - - - +
83B ALA* 3.8 10.7 - - - +
86B VAL* 3.8 13.0 - - + +
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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* 4.1 4.4 - - + -
68A GLN* 3.8 39.3 - - + +
71A VAL* 3.6 28.7 - - + -
72A ARG* 3.6 28.9 - - + +
86A TRP* 3.5 38.6 - - + +
87A GLN 3.2 9.1 + - - +
88A ALA* 3.0 12.8 + - - +
90A ALA* 1.3 74.3 - - - +
92A LEU* 1.3 65.2 + - - +
94A LEU* 3.4 5.6 + - - +
95A GLN* 3.0 24.2 + - - +
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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
----------------------------------------------------------
60A LEU* 3.5 29.4 - - + -
64A LYS* 6.0 7.0 - - - -
68A GLN* 5.2 2.3 - - - +
88A ALA 3.0 12.7 + - - +
89A GLN* 3.6 16.6 - - - +
91A LEU* 1.3 77.1 - - - +
93A ALA* 1.3 56.9 + - - +
95A GLN* 3.2 8.6 + - - +
96A GLU* 2.9 47.9 + - + +
100B PHE* 3.1 33.2 - - + -
57H LYS* 6.1 3.6 - - - +
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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 2.9 18.1 + - - +
90A ALA* 3.6 7.2 - - - +
92A LEU* 1.3 76.1 - - - +
94A LEU* 1.3 63.6 + - - +
96A GLU* 3.3 3.2 + - - +
97A ALA* 3.0 23.9 + - - +
83B ALA* 4.8 3.4 - - + +
86B VAL* 4.2 15.3 - - + -
87B VAL* 5.3 0.4 - - + -
97B LEU* 4.0 13.6 - - + +
100B PHE* 3.6 34.9 - - + -
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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* 4.0 6.5 - - + -
71A VAL* 3.9 34.3 - - + -
86A TRP* 4.0 9.2 - - + -
90A ALA 3.0 12.8 + - - +
91A LEU* 3.6 9.4 - - - +
93A ALA* 1.3 75.9 - - - +
95A GLN* 1.3 57.4 + - - +
97A ALA* 3.3 9.2 + - + +
98A ALA* 2.9 29.6 + - - +
61B PHE* 5.1 1.3 - - + -
62B LEU* 4.5 10.8 - - + -
65B VAL* 3.6 33.9 - - + -
66B ILE* 3.9 20.2 - - + -
86B VAL* 3.8 20.3 - - + +
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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
----------------------------------------------------------
60A LEU* 3.6 25.3 - - + +
62A ILE* 2.8 37.4 + - - +
63A ARG 4.3 1.4 + - - -
64A LYS* 4.4 15.2 - - - +
67A PHE* 3.5 44.3 - - + +
68A GLN* 5.3 3.1 + - - +
91A LEU 3.0 14.1 + - - +
92A LEU* 3.2 8.4 + - - +
94A LEU* 1.3 72.5 - - - +
96A GLU* 1.3 66.0 + - - +
98A ALA* 3.8 0.7 - - - +
99A GLU* 2.9 44.9 + - + +
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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
----------------------------------------------------------
58A THR 5.5 0.2 - - - +
60A LEU* 3.4 30.7 - - + +
92A LEU* 2.9 40.3 + - + +
93A ALA* 3.3 5.8 + - - +
95A GLN* 1.3 77.4 - - - +
97A ALA* 1.3 62.6 + - - +
99A GLU* 4.0 0.7 - - - +
100A ALA* 2.9 27.5 + - - +
97B LEU* 4.4 14.8 - - + -
100B PHE* 4.0 8.5 - - + -
103G ALA* 3.6 5.4 - - + -
104G GLN* 2.8 45.9 + - - +
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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 3.0 15.5 + - - +
94A LEU* 3.6 6.3 - - + +
96A GLU* 1.3 77.6 - - - +
98A ALA* 1.3 58.0 + - - +
100A ALA* 3.5 4.3 + - - +
101A PHE* 2.9 29.8 + - - +
61B PHE* 4.1 6.7 - - + -
90B LEU* 3.6 39.5 - - + -
95B ARG* 6.0 0.3 - - - -
97B LEU* 4.4 10.4 - - + +
101G THR* 5.1 2.7 - - - +
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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* 6.1 0.4 - - + -
67A PHE* 4.0 15.9 - - + -
94A LEU 2.9 18.1 + - - +
95A GLN 3.9 2.9 - - - +
97A ALA* 1.3 76.9 - - - +
99A GLU* 1.3 59.3 + - + +
101A PHE* 3.3 3.0 + - - +
102A LEU* 2.9 35.2 + - + +
58B LEU* 3.8 25.6 - - + -
61B PHE* 3.7 19.3 - - + -
62B LEU* 4.2 2.2 - - + -
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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
----------------------------------------------------------
59A GLU 4.4 0.3 - - - +
60A LEU* 3.3 21.2 - - + +
61A LEU* 2.8 30.1 + - - +
62A ILE* 2.9 44.9 + - + +
95A GLN* 2.9 38.0 + - + +
96A GLU* 4.1 2.0 - - - +
98A ALA* 1.3 73.9 - - + +
100A ALA* 1.3 61.1 + - - +
102A LEU* 3.8 2.9 - - - +
103A VAL* 2.9 36.9 + - + +
37B LEU* 3.9 14.4 - - + +
40B ARG* 4.7 4.9 + - - +
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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
----------------------------------------------------------
96A GLU 2.9 18.8 + - - +
97A ALA 3.8 3.6 - - - +
99A GLU* 1.3 74.7 - - - +
101A PHE* 1.3 66.1 + - - +
103A VAL* 3.4 4.7 + - - +
104A HIS* 3.0 39.4 + - + +
101G THR* 4.3 28.9 - - + +
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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
----------------------------------------------------------
97A ALA 2.9 17.8 + - - +
98A ALA 3.5 5.2 - - - +
100A ALA* 1.3 77.2 - - - +
102A LEU* 1.3 71.3 + - + +
104A HIS* 3.4 4.1 + - - +
105A LEU* 3.0 47.7 + - + +
130A ARG* 4.5 7.9 - - - -
133A ARG* 3.6 27.3 + - - -
135A GLU* 3.8 14.1 - - - -
57B VAL* 4.5 9.2 - - + -
58B LEU* 5.7 0.7 - - - -
61B PHE* 3.7 41.3 - + + -
95B ARG* 3.7 40.8 - - - +
101G THR* 6.0 0.2 - - - +
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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
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62A ILE* 4.6 6.5 - - + -
98A ALA 2.9 21.4 + - - +
99A GLU 3.9 3.4 - - - +
101A PHE* 1.3 86.2 - - + +
103A VAL* 1.3 59.0 + - - +
105A LEU* 3.4 7.4 + - + +
106A PHE* 2.9 40.8 + - + -
29B ILE* 6.2 1.3 - - + -
37B LEU* 3.7 30.3 - - + -
54B THR* 3.9 19.5 - - + -
57B VAL* 3.6 31.2 - - + -
58B LEU* 4.1 31.6 - - + -
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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
----------------------------------------------------------
99A GLU* 2.9 21.9 + - + +
100A ALA* 3.9 5.6 - - - +
102A LEU* 1.3 76.4 - - - +
104A HIS* 1.3 63.5 + - + +
106A PHE* 3.2 4.7 + - - +
107A GLU* 3.0 38.7 + - - +
37B LEU* 3.7 37.2 - - + +
40B ARG* 3.8 26.2 - - + +
41B GLY* 4.1 8.6 - - - +
107G VAL* 3.7 20.4 - - + -
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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 35.7 + - + +
101A PHE* 4.0 2.5 - - - +
103A VAL* 1.3 77.0 - - + +
105A LEU* 1.3 62.4 + - - +
107A GLU* 3.0 37.9 + - - +
108A ASP* 3.0 27.0 + - - +
133A ARG* 3.6 14.1 - - - +
84G GLN* 5.7 6.5 + - - -
101G THR* 5.1 12.0 - - + +
107G VAL* 4.6 12.9 - - + +
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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
----------------------------------------------------------
101A PHE* 3.0 26.5 + - + +
102A LEU* 3.7 7.9 - - + +
103A VAL 3.3 0.2 - - - -
104A HIS* 1.3 76.7 - - - +
106A PHE* 1.3 58.0 + - + +
108A ASP* 3.3 1.5 + - - +
109A ALA* 2.9 29.3 + - - +
126A ILE* 4.0 26.5 - - + +
129A ALA* 4.2 17.5 - - + -
130A ARG* 3.6 33.0 - - + -
133A ARG* 3.4 22.3 - - - +
57B VAL* 4.0 27.4 - - + -
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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
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102A LEU* 2.9 27.3 + - + -
103A VAL* 3.5 7.4 - - - +
105A LEU* 1.3 78.2 - - + +
107A GLU* 1.3 56.6 + - - +
109A ALA* 3.9 2.4 - - - +
110A TYR* 2.9 32.1 + - - +
121A ILE* 4.7 10.0 - - + +
126A ILE* 3.9 27.1 - - + -
34B ILE* 4.0 15.0 - - + -
37B LEU* 3.9 17.5 - - + -
38B ALA* 3.6 45.1 - - + -
41B GLY* 4.5 7.4 - - - -
43B VAL* 4.2 11.3 - - + +
50B ILE* 4.2 9.9 - - + -
54B THR* 3.6 29.8 - - + -
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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
----------------------------------------------------------
103A VAL* 3.0 21.3 + - - +
104A HIS* 3.0 37.1 + - - +
106A PHE* 1.3 76.6 - - - +
108A ASP* 1.3 67.5 + - - +
110A TYR* 3.2 4.5 + - - +
111A LEU* 3.0 28.2 + - + +
40B ARG 4.6 0.9 - - - +
41B GLY* 3.6 25.3 + - - +
107G VAL* 3.6 27.7 - - - +
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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
----------------------------------------------------------
104A HIS* 3.0 15.3 + - - +
105A LEU 3.7 6.5 - - - +
107A GLU* 1.3 78.9 - - - +
109A ALA* 1.3 63.3 + - - +
111A LEU* 3.1 27.3 + - - +
112A LEU* 3.2 14.9 + - - +
129A ALA* 4.1 16.2 - - + -
133A ARG* 2.7 36.2 + - - +
131E ARG* 5.6 0.9 - - - +
132E ILE* 4.2 24.1 - - + +
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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
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105A LEU 2.9 18.2 + - - +
106A PHE* 3.9 2.5 - - - +
108A ASP* 1.3 76.2 - - - +
110A TYR* 1.3 56.5 + - - +
112A LEU* 3.0 8.4 + - - +
113A THR* 2.9 26.0 + - - -
121A ILE* 3.5 22.2 - - + -
125A ASP* 3.6 25.0 - - - +
126A ILE* 3.8 18.8 - - + -
129A ALA* 3.9 4.6 - - + +
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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 19.0 + - - +
107A GLU* 3.7 6.1 - - - +
108A ASP 3.2 0.2 - - - -
109A ALA* 1.3 73.4 - - - +
111A LEU* 1.3 66.4 + - - +
113A THR* 3.1 14.7 + - + -
114A LEU* 2.9 58.5 + - + +
119A VAL* 2.9 38.5 + - - +
121A ILE* 4.0 5.3 - - + +
41B GLY 4.9 2.9 - - - +
42B GLY 3.3 25.8 - - - -
43B VAL* 3.7 28.3 - - + -
44B LYS* 3.3 18.9 + - - +
112G GLN* 5.0 7.4 - - + -
115G LEU* 3.6 23.3 - - + +
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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* 3.0 20.4 + - + +
108A ASP* 3.1 21.5 + - - +
110A TYR* 1.3 77.0 - - - +
112A LEU* 1.3 58.3 + - - +
114A LEU* 3.5 5.0 + - + +
115A HIS* 2.9 28.1 + - - +
128E LEU* 4.1 21.3 - - + +
131E ARG* 3.5 49.4 - - - +
132E ILE* 4.6 5.4 - - + -
112G GLN* 4.0 27.8 - - - +
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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 3.2 9.4 + - - +
109A ALA 3.0 8.9 + - - +
111A LEU* 1.3 74.8 - - - +
113A THR* 1.3 64.9 + - - +
115A HIS* 3.2 6.2 + - + +
116A ALA* 3.0 24.1 + - - +
125A ASP* 3.4 21.1 - - + +
128A LEU* 3.6 21.3 - - + +
129A ALA* 3.4 36.6 - - + +
132A ILE* 5.5 0.4 - - + -
112E LEU* 3.5 26.2 - - + -
115E HIS* 3.7 9.7 + - + +
128E LEU* 4.0 10.1 - - + -
132E ILE* 3.5 20.2 - - + -
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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 2.9 12.5 + - - -
110A TYR* 3.1 17.1 + - + -
112A LEU* 1.3 75.2 - - - +
114A LEU* 1.3 61.1 + - - +
116A ALA* 3.1 13.2 + - - +
118A ARG* 3.1 35.6 + - - +
119A VAL 3.8 3.6 - - - -
120A THR 3.3 41.5 - - - +
121A ILE* 3.3 14.4 - - - +
125A ASP* 2.7 23.2 + - - -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 2.9 56.2 + - + +
111A LEU* 4.0 5.8 - - + +
113A THR* 1.3 74.6 - - - +
115A HIS* 1.3 65.3 - - - +
117A LYS* 3.1 17.0 + - - +
118A ARG 3.6 16.2 - - - +
119A VAL* 4.9 0.7 - - + -
112G GLN* 3.5 47.3 - - + +
114G VAL* 3.8 22.9 - - + -
115G LEU* 4.1 3.6 - - + -
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU 2.9 19.1 + - - +
112A LEU* 3.2 8.6 + - + +
114A LEU* 1.3 76.6 - - - +
116A ALA* 1.3 56.0 + - - +
117A LYS* 3.2 18.2 + - - +
112E LEU* 3.5 31.7 + - + +
115E HIS* 5.2 4.2 - - - -
116E ALA* 4.0 14.4 + - + +
118E ARG* 3.6 14.8 + - - -
124E LYS* 3.7 30.5 + - + +
125E ASP* 2.8 33.5 + - - -
128E LEU* 3.6 23.5 - - + +
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 3.0 6.5 + - - +
113A THR 3.1 7.8 + - - +
115A HIS* 1.3 74.6 - - - +
117A LYS* 1.3 67.8 + - - +
118A ARG* 3.1 30.8 + - - +
115E HIS* 3.6 37.2 - - + +
116E ALA* 4.5 9.6 - - - +
117E LYS* 3.9 17.3 + - - -
----------------------------------------------------------
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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