Contacts of the helix formed by residues 90 - 118 (chain A) in PDB entry 2A19
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 SER 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG 4.0 1.0 + - - -
89A VAL* 1.3 78.7 - - - +
91A SER* 1.3 59.6 + - - +
92A GLU* 3.6 11.3 - - - +
93A ASP* 3.0 34.9 + - - +
94A ILE* 3.1 27.0 + - - +
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Residues in contact with SER 91 (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 SER* 1.3 71.5 - - - +
92A GLU* 1.3 65.5 + - - +
94A ILE* 3.3 13.6 + - - +
95A ILE* 3.2 35.1 + - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER* 3.6 11.1 + - - +
91A SER* 1.3 79.6 - - - +
93A ASP* 1.3 64.3 + - - +
95A ILE* 3.4 7.9 + - - +
96A LYS* 3.1 53.0 + - - +
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.0 32.4 - - + +
88A ARG 4.1 4.9 - - - +
89A VAL* 3.7 17.0 - - + -
90A SER* 3.0 37.7 + - - +
92A GLU* 1.3 80.2 - - - +
94A ILE* 1.3 55.2 + - - +
96A LYS* 3.7 7.2 - - - +
97A CYS* 2.7 38.7 + - - +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 6.2 0.2 - - - +
69A VAL* 4.1 24.7 - - + +
89A VAL* 3.8 17.0 - - + +
90A SER 3.1 19.8 + - - +
91A SER* 3.3 14.8 + - - +
93A ASP* 1.3 75.0 - - - +
95A ILE* 1.3 63.1 + - + +
97A CYS* 3.2 2.9 + - - +
98A GLU* 2.8 36.3 + - + +
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Residues in contact with ILE 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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91A SER* 3.2 23.1 + - - +
92A GLU* 3.8 8.7 - - - +
94A ILE* 1.3 79.3 - - + +
96A LYS* 1.3 55.0 + - + +
98A GLU* 3.0 8.4 + - - +
99A GLU* 2.8 55.4 + - + +
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Residues in contact with LYS 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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92A GLU* 3.1 43.4 + - - +
93A ASP* 4.0 7.6 - - - +
95A ILE* 1.3 79.4 - - + +
97A CYS* 1.3 63.2 + - - +
99A GLU* 3.9 14.4 - - - +
100A LYS* 3.2 24.8 + - - +
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Residues in contact with CYS 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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18A ILE* 3.8 25.1 - - + +
19A VAL 3.6 31.0 - - - -
20A MET* 3.7 12.1 - - - -
37A GLU* 5.0 3.5 - - - +
69A VAL* 3.8 21.3 - - + -
93A ASP 2.7 22.2 + - - +
94A ILE 3.6 3.6 - - - +
96A LYS* 1.3 74.5 - - - +
98A GLU* 1.3 56.1 + - - +
100A LYS* 3.9 7.1 - - - +
101A TYR* 3.0 32.1 + - - +
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Residues in contact with GLU 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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20A MET* 3.7 17.5 - - + +
67A ASN* 5.5 1.0 - - - +
69A VAL* 5.5 0.7 - - + -
94A ILE* 2.8 27.4 + - + +
95A ILE* 3.0 7.2 + - - +
97A CYS* 1.3 72.1 - - - +
99A GLU* 1.3 59.2 + - + +
101A TYR* 3.6 14.4 - - - +
102A GLN* 2.8 70.7 + - - +
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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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95A ILE* 2.8 43.2 + - + +
96A LYS* 3.9 12.5 - - - +
98A GLU* 1.3 73.6 - - + +
100A LYS* 1.3 63.2 + - - +
102A GLN* 3.3 5.5 + - - +
103A LYS* 3.0 43.7 + - + +
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Residues in contact with LYS 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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8A TYR* 3.2 44.7 - - - +
18A ILE 5.5 7.2 - - - +
37A GLU* 4.2 5.8 - - - +
96A LYS 3.2 14.7 + - - +
97A CYS* 3.9 7.4 - - - +
99A GLU* 1.3 78.4 - - - +
101A TYR* 1.3 58.1 + - - +
103A LYS* 3.3 8.7 + - - +
104A SER* 2.8 33.1 + - - -
139A HIS* 3.8 17.3 + - + -
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Residues in contact with TYR 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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7A PHE* 4.2 15.0 - + - -
20A MET* 3.8 27.6 - - + -
36A LEU* 3.3 41.2 - - + +
37A GLU* 4.2 21.4 + - + +
67A ASN* 4.1 13.8 + - - -
97A CYS 3.0 19.7 + - - +
98A GLU* 3.6 10.1 - - - +
100A LYS* 1.3 77.1 - - - +
102A GLN* 1.3 77.0 + - - +
104A SER* 3.1 4.7 + - - -
105A LYS* 2.7 64.3 + - + +
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Residues in contact with GLN 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 GLU* 2.8 56.9 + - - +
99A GLU* 3.8 4.7 - - - +
101A TYR* 1.3 90.2 - - - +
103A LYS* 1.3 64.5 + - + +
105A LYS* 3.3 15.1 + - - +
106A THR* 3.0 27.8 + - - -
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Residues in contact with LYS 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 GLU* 3.0 35.8 + - + +
100A LYS* 3.7 6.7 - - - +
102A GLN* 1.3 77.5 - - + +
104A SER* 1.3 56.7 + - - +
106A THR* 3.3 3.1 + - - -
107A VAL* 3.0 31.9 + - - +
139A HIS* 3.9 14.8 - - + -
141A TYR* 3.4 45.0 - - + -
142A GLU* 2.6 32.9 + - - -
145A LYS* 5.7 0.4 - - - +
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Residues in contact with SER 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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7A PHE* 3.3 33.6 - - - -
8A TYR* 3.0 21.4 + - - -
100A LYS 2.8 13.6 + - - -
101A TYR* 3.5 4.5 - - - -
103A LYS* 1.3 74.7 - - - +
105A LYS* 1.3 64.0 + - - +
107A VAL* 3.4 3.9 + - - +
108A HIS* 3.0 25.3 + - - +
126A TYR* 4.6 0.7 + - - -
139A HIS* 2.8 29.4 + - - -
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Residues in contact with LYS 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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7A PHE* 4.2 7.8 - - + -
101A TYR* 2.7 55.3 + - + +
102A GLN* 3.7 17.5 + - - +
104A SER* 1.3 74.0 - - - +
106A THR* 1.3 56.5 + - - +
108A HIS* 3.4 8.1 - - + +
109A SER* 2.9 30.2 + - - -
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Residues in contact with THR 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 GLN 3.0 14.1 + - - -
103A LYS 3.5 8.1 - - - -
105A LYS* 1.3 74.0 - - - +
107A VAL* 1.3 67.5 + - - +
109A SER* 3.1 7.3 + - - -
110A ILE* 2.9 46.3 + - + +
141A TYR* 3.7 27.1 - - + -
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Residues in contact with VAL 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 LYS 3.0 17.3 + - - +
104A SER* 3.8 6.1 - - - +
106A THR* 1.3 74.8 - - + +
108A HIS* 1.3 55.1 + - - +
110A ILE* 3.1 10.1 + - - +
111A LEU* 2.7 56.1 + - + +
126A TYR* 4.4 11.4 - - + +
139A HIS* 4.2 5.2 - - + -
140A ALA* 4.2 19.1 - - + -
141A TYR* 3.8 35.4 - - + +
144A PHE* 4.3 14.4 - - + -
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Residues in contact with HIS 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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3A SER 3.8 12.0 + - - -
4A HIS* 4.8 0.7 - - - -
5A CYS 3.6 20.6 + - - -
7A PHE* 3.5 24.9 - + + -
104A SER 3.0 16.2 + - - +
105A LYS* 3.4 6.5 - - + +
107A VAL* 1.3 77.7 - - - +
109A SER* 1.3 54.7 + - - +
111A LEU* 3.7 0.9 - - - +
112A ARG* 2.8 66.7 + - - +
122A LEU* 3.7 20.6 - - + +
126A TYR* 3.2 29.8 + - - +
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Residues in contact with SER 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 LYS* 2.9 18.3 + - - -
106A THR* 3.1 8.5 + - - -
108A HIS* 1.3 79.3 - - - +
110A ILE* 1.3 65.9 + - - +
112A ARG* 3.7 21.0 + - - +
113A TYR* 3.1 21.1 + - - +
171A TYR* 4.5 10.0 + - - -
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Residues in contact with ILE 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 THR* 2.9 36.6 + - + +
107A VAL* 3.4 6.1 - - - +
109A SER* 1.3 75.4 - - - +
111A LEU* 1.3 65.3 + - - +
113A TYR* 3.0 15.8 + - - +
114A CYS* 3.3 12.7 + - - -
141A TYR* 6.4 0.2 - - + -
144A PHE* 4.1 22.7 - - + -
168A LEU* 3.7 28.7 - - + -
171A TYR* 3.6 47.1 - - + -
172A ILE* 4.9 8.5 - - + -
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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 VAL* 2.7 27.7 + - + +
108A HIS 4.0 1.8 - - - +
110A ILE* 1.3 73.1 - - - +
112A ARG* 1.3 61.2 + - - +
114A CYS* 3.3 3.8 + - - -
115A ALA 3.0 19.6 + - - -
122A LEU* 3.4 16.7 - - + +
125A LEU* 3.3 33.8 - - + +
126A TYR* 3.9 28.0 - - + -
129A ILE* 5.1 6.3 - - + -
130A ALA* 3.8 28.3 - - + -
144A PHE* 4.2 9.0 - - + -
168A LEU* 4.0 28.0 - - + -
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Residues in contact with ARG 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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2A SER 5.2 0.2 - - - +
3A SER* 3.7 26.8 + - - +
108A HIS* 2.8 47.0 + - - +
109A SER* 3.7 19.4 + - - +
110A ILE 3.1 0.2 - - - -
111A LEU* 1.3 73.8 - - - +
113A TYR* 1.3 56.6 + - - +
115A ALA* 3.9 1.3 - - - +
116A GLU* 2.9 57.4 + - - +
122A LEU* 3.7 13.8 - - + +
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Residues in contact with TYR 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 SER 3.1 11.6 + - - +
110A ILE 3.0 8.7 + - - +
112A ARG* 1.3 77.2 - - - +
114A CYS* 1.3 65.3 + - - +
116A GLU* 4.0 7.3 - - - +
117A LYS* 3.0 59.1 + - + +
167A GLU* 3.7 22.3 + - - -
171A TYR* 3.5 39.7 - + + +
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Residues in contact with CYS 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 ILE* 3.3 16.3 + - - -
111A LEU* 3.6 8.7 - - + +
112A ARG 3.2 0.4 - - - -
113A TYR* 1.3 81.0 - - - +
115A ALA* 1.3 59.4 + - - +
117A LYS* 3.1 4.8 + - - -
118A PHE* 2.9 39.0 + - + +
125A LEU* 3.8 12.6 - - + -
164A VAL* 3.9 12.1 - - + -
167A GLU* 4.2 12.3 - - - -
168A LEU* 4.0 40.4 - - - -
171A TYR* 5.4 1.1 - - - -
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Residues in contact with ALA 115 (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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2A SER 4.0 8.1 - - - +
111A LEU 3.0 14.6 + - - +
112A ARG 3.9 3.1 - - - +
114A CYS* 1.3 77.7 - - - +
116A GLU* 1.3 57.5 + - - +
119A GLN* 2.9 23.9 + - - -
120A ILE* 2.9 37.4 + - - +
121A PRO 4.2 0.2 - - - -
122A LEU* 3.7 19.7 - - + +
125A LEU* 3.5 16.2 - - + +
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Residues in contact with GLU 116 (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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2A SER 4.2 6.5 - - - +
3A SER* 3.1 28.7 + - - +
112A ARG* 2.9 45.5 + - - +
113A TYR* 4.1 5.4 - - - +
115A ALA* 1.3 73.3 - - - +
117A LYS* 1.3 68.4 + - - +
119A GLN* 3.1 28.4 + - - +
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Residues in contact with LYS 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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113A TYR* 3.0 47.0 + - + +
114A CYS* 3.1 4.9 + - - +
116A GLU* 1.3 80.3 - - - +
118A PHE* 1.3 71.4 + - + +
119A GLN* 3.2 6.1 + - - +
167A GLU* 3.4 38.8 + - + +
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Residues in contact with PHE 118 (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 CYS 2.9 21.9 + - - +
115A ALA 3.7 0.2 - - - -
117A LYS* 1.3 85.0 - - + +
119A GLN* 1.3 66.3 + - - +
120A ILE* 2.9 26.4 + - + +
161A SER* 5.0 2.5 - - - -
163A ASP* 3.1 50.5 - - + -
164A VAL* 3.9 17.5 - - + -
167A GLU* 3.2 44.6 - - + -
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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
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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