Contacts of the helix formed by residues 85 - 114 (chain A) in PDB entry 6T7B
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 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG 3.9 1.4 + - - -
84A PHE* 1.3 75.8 - - - +
86A SER* 1.3 67.6 + - - +
87A SER 3.2 3.6 - - - +
88A ALA* 3.2 4.6 + - - +
89A VAL* 3.2 18.5 + - - -
81B VAL 3.3 18.4 + - - -
82B THR* 5.7 1.1 - - - +
48I C 3.6 21.0 - - - -
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Residues in contact with SER 86 (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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84A PHE 3.7 2.0 + - - -
85A GLN* 1.3 72.5 - - - +
87A SER* 1.3 57.2 + - - +
89A VAL* 3.4 2.1 + - - +
90A MET* 2.9 25.5 + - - -
48I C 3.5 13.8 + - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLN* 3.2 1.2 - - - +
86A SER* 1.3 77.5 - - - +
88A ALA* 1.3 55.3 + - - +
90A MET* 3.4 1.8 + - - +
91A ALA* 2.9 24.9 + - - -
83B ALA* 4.6 7.6 - - - -
48I C 4.9 1.6 + - - -
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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
----------------------------------------------------------
85A GLN* 3.2 10.7 + - - +
87A SER* 1.3 74.0 - - - +
89A VAL* 1.3 58.0 + - - +
91A ALA* 3.3 2.0 + - - +
92A LEU* 3.0 24.8 + - - -
81B VAL 4.9 2.7 - - - -
82B THR 4.3 5.8 - - - -
83B ALA* 3.8 26.9 - - - +
86B VAL* 6.2 0.6 - - - +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 6.3 2.9 - - - +
85A GLN 3.2 13.7 + - - -
86A SER* 3.9 2.2 - - - +
88A ALA* 1.3 76.2 - - - +
90A MET* 1.3 57.2 + - - +
92A LEU* 3.4 2.3 + - - +
93A GLN* 2.9 24.3 + - - -
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER 2.9 16.2 + - - -
87A SER* 3.4 2.9 + - - +
89A VAL* 1.3 78.3 - - - +
91A ALA* 1.3 56.2 + - - +
93A GLN* 3.1 2.5 + - - +
94A GLU* 2.9 24.6 + - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER 2.9 16.6 + - - -
88A ALA* 3.3 2.0 + - - +
90A MET* 1.3 75.1 - - - +
92A LEU* 1.3 57.8 + - - +
94A GLU* 3.3 1.8 + - - +
95A ALA* 3.0 26.0 + - - -
83B ALA* 6.4 0.7 - - - +
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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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88A ALA 3.0 15.1 + - - -
89A VAL* 3.7 4.0 - - - +
91A ALA* 1.3 75.0 - - - +
93A GLN* 1.3 57.0 + - - +
95A ALA* 4.1 0.8 - - - +
96A SER* 2.9 26.2 + - - -
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL 2.9 15.3 + - - -
90A MET* 3.1 4.6 + - - +
92A LEU* 1.3 75.3 - - - +
94A GLU* 1.3 60.0 + - - +
96A SER* 3.8 0.8 - - - +
97A GLU* 2.9 26.3 + - - -
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Residues in contact with GLU 94 (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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90A MET 2.9 13.6 + - - -
91A ALA* 3.8 3.1 - - - +
93A GLN* 1.3 77.4 - - - +
95A ALA* 1.3 56.0 + - - +
97A GLU* 3.8 0.9 - - - +
98A ALA* 2.9 25.3 + - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.0 15.5 + - - -
92A LEU* 4.1 0.9 - - - +
94A GLU* 1.3 74.5 - - - +
96A SER* 1.3 57.7 + - - +
98A ALA* 3.8 1.7 - - - +
99A TYR* 2.9 26.5 + - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 2.9 18.9 + - - -
93A GLN* 3.8 1.3 - - - +
95A ALA* 1.3 73.5 - - - +
97A GLU* 1.3 59.5 + - - +
99A TYR* 3.4 0.9 + - - +
100A LEU* 3.0 25.8 + - - -
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Residues in contact with GLU 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 GLN 2.9 16.6 + - - -
94A GLU 3.9 1.1 - - - -
96A SER* 1.3 75.1 - - - +
98A ALA* 1.3 56.5 + - - +
100A LEU* 3.5 1.2 + - - +
101A VAL* 2.9 27.2 + - - -
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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
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94A GLU 2.9 16.0 + - - -
95A ALA* 3.4 2.7 + - - +
97A GLU* 1.3 77.2 - - - +
99A TYR* 1.3 56.8 + - - +
101A VAL* 3.4 1.3 + - - +
102A GLY* 3.0 26.9 + - - -
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Residues in contact with TYR 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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95A ALA 2.9 16.4 + - - -
96A SER* 3.9 1.6 - - - +
98A ALA* 1.3 74.8 - - - +
100A LEU* 1.3 57.6 + - - +
102A GLY* 3.4 1.3 + - - -
103A LEU* 2.9 25.5 + - - -
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Residues in contact with LEU 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 SER 3.0 16.2 + - - -
97A GLU* 3.9 1.1 - - - +
99A TYR* 1.3 75.5 - - - +
101A VAL* 1.3 58.7 + - - +
103A LEU* 3.4 1.7 + - - +
104A PHE* 2.9 25.6 + - - -
37B LEU* 4.8 5.3 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU 2.9 17.6 + - - -
98A ALA* 3.9 1.3 - - - +
100A LEU* 1.3 76.8 - - - +
102A GLY* 1.3 55.6 + - - +
104A PHE* 3.3 1.8 + - - +
105A GLU* 2.9 25.1 + - - -
37B LEU* 4.3 15.5 - - - +
41B GLY* 4.1 13.2 - - - +
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Residues in contact with GLY 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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98A ALA 3.0 15.9 + - - -
99A TYR* 3.9 1.3 - - - -
101A VAL* 1.3 76.3 - - - +
103A LEU* 1.3 55.5 + - - +
105A GLU* 3.2 2.6 + - - -
106A ASP* 3.0 24.9 + - - -
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Residues in contact with LEU 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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99A TYR 2.9 16.5 + - - -
100A LEU* 3.8 2.0 - - - +
101A VAL 3.3 0.2 - - - -
102A GLY* 1.3 76.3 - - - +
104A PHE* 1.3 57.5 + - - +
106A ASP* 3.5 2.1 + - - +
107A THR* 2.9 24.4 + - - -
124A ILE* 6.0 1.6 - - - -
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Residues in contact with PHE 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 LEU 2.9 17.1 + - - -
101A VAL* 3.7 2.7 - - - +
102A GLY 3.2 0.2 - - - -
103A LEU* 1.3 73.7 - - - +
105A GLU* 1.3 60.7 + - - +
107A THR* 3.8 2.2 - - - +
108A ASN* 2.9 24.6 + - - -
38B ALA* 5.7 9.0 - - - +
41B GLY* 4.5 9.4 - - - +
43B VAL* 5.5 4.2 + - - -
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Residues in contact with GLU 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 VAL 2.9 14.0 + - - -
102A GLY* 3.2 4.0 + - - -
104A PHE* 1.3 77.7 - - - +
106A ASP* 1.3 57.3 + - - +
108A ASN* 3.2 3.0 + - - +
109A LEU* 2.9 24.3 + - - -
41B GLY* 3.8 16.5 + - - -
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Residues in contact with ASP 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 GLY 3.0 13.8 + - - -
103A LEU* 3.9 2.9 - - - +
105A GLU* 1.3 72.4 - - - +
107A THR* 1.3 60.6 + - - +
109A LEU* 3.3 2.6 + - - +
110A ALA* 2.9 25.1 + - - -
123A ASP 5.4 0.2 - - - +
127A ALA* 5.3 10.3 - - - +
130E ILE* 6.0 6.5 - - - +
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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
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103A LEU 2.9 16.5 + - - -
104A PHE* 3.4 4.0 + - - +
105A GLU 3.3 0.2 - - - -
106A ASP* 1.3 77.7 - - - +
108A ASN* 1.3 56.0 + - - +
110A ALA* 3.4 1.4 + - - +
111A ALA* 2.9 25.6 + - - -
119A ILE* 5.4 6.9 - - - -
123A ASP* 4.6 21.2 - - - -
124A ILE* 5.3 2.9 - - - +
127A ALA* 5.8 0.4 - - - +
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Residues in contact with ASN 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 PHE 2.9 15.3 + - - -
105A GLU* 3.2 4.0 + - - +
107A THR* 1.3 73.6 - - - +
109A LEU* 1.3 59.9 + - - +
111A ALA* 4.4 1.1 - - - +
112A ILE* 2.9 27.2 + - - -
42B GLY 6.4 0.9 - - - -
43B VAL* 5.9 6.7 - - - +
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Residues in contact with LEU 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 GLU 2.9 14.2 + - - -
106A ASP* 3.3 5.1 + - - +
108A ASN* 1.3 76.7 - - - +
110A ALA* 1.3 56.1 + - - +
112A ILE* 3.8 1.1 - - - +
113A HIS* 2.9 25.3 + - - -
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Residues in contact with ALA 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 ASP 2.9 15.4 + - - -
107A THR* 3.9 1.3 - - - +
108A ASN 3.3 0.2 - - - -
109A LEU* 1.3 76.6 - - - +
111A ALA* 1.3 60.5 + - - +
113A HIS* 3.3 2.3 + - - +
114A ALA* 3.2 18.9 + - - -
123A ASP* 5.9 7.6 - - - +
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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
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107A THR 2.9 16.7 + - - -
108A ASN* 3.8 1.3 - - - +
110A ALA* 1.3 74.0 - - - +
112A ILE* 1.3 62.1 + - - +
113A HIS 3.5 0.2 + - - -
114A ALA* 3.5 5.3 + - - +
115A LYS 3.6 0.2 + - - -
116A ARG* 2.8 35.8 + - - +
117A VAL 5.9 1.1 - - - -
118A THR 5.7 1.6 - - - -
119A ILE* 5.4 10.3 - - - +
123A ASP* 5.8 2.8 - - - +
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Residues in contact with ILE 112 (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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108A ASN 2.9 17.4 + - - -
109A LEU 3.8 1.6 - - - -
111A ALA* 1.3 75.2 - - - +
113A HIS* 1.3 63.0 + - - +
115A LYS* 3.0 14.7 + - - -
116A ARG 3.4 11.1 + - - -
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Residues in contact with HIS 113 (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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109A LEU 2.9 16.6 + - - -
110A ALA* 3.3 4.0 + - - +
111A ALA 3.2 0.2 - - - -
112A ILE* 1.3 77.8 - - - +
114A ALA* 1.3 55.3 + - - +
115A LYS 3.2 3.8 + - - -
114E ALA* 5.6 0.9 - - - -
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 3.2 13.4 + - - -
111A ALA* 3.5 3.1 + - - +
112A ILE 3.3 0.6 - - - -
113A HIS* 1.3 73.7 - - - +
115A LYS* 1.3 61.0 + - - +
116A ARG* 3.4 3.0 - - - -
113E HIS 5.6 0.7 - - - -
114E ALA* 4.5 23.3 - - - +
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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) + - + + + + + -
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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