Contacts of the helix formed by residues 83 - 109 (chain A) in PDB entry 2CXF
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 MSE 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ALA* 1.3 65.5 + - - +
85A ASN* 3.0 16.8 + - - +
86A GLU* 3.0 33.4 + - + +
87A ARG* 3.1 18.4 + - - +
132A HIS* 3.0 35.0 - - + +
215A ASN* 3.8 29.2 - - + +
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Residues in contact with ALA 84 (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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83A MSE 1.3 78.0 - - - +
85A ASN* 1.3 66.5 + - - +
87A ARG* 3.1 32.3 + - - +
88A MSE 3.5 18.2 + - - +
222A GLU* 4.8 1.4 - - - +
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Residues in contact with ASN 85 (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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83A MSE 3.0 9.0 + - - +
84A ALA* 1.3 82.9 + - - +
86A GLU* 1.3 60.9 + - - +
87A ARG 3.0 3.0 + - - -
88A MSE 3.1 16.5 + - - +
89A ASN* 2.6 27.7 + - - +
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Residues in contact with GLU 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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83A MSE 3.0 31.2 + - + +
85A ASN* 1.3 78.4 - - - +
87A ARG* 1.3 61.8 + - - +
89A ASN* 3.1 23.4 - - - +
90A LEU* 3.6 13.8 + - + +
132A HIS* 3.6 23.0 - - + +
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Residues in contact with ARG 87 (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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83A MSE 3.1 36.0 + - - +
84A ALA* 3.1 32.0 + - - +
85A ASN 3.1 0.8 - - - -
86A GLU* 1.3 74.5 - - - +
88A MSE 1.3 66.8 + - - +
90A LEU* 3.2 9.1 + - - +
91A MSE 3.1 19.4 + - - +
132A HIS* 3.4 22.9 - - + +
215A ASN* 3.7 12.2 + - - +
216A ALA 3.7 13.7 - - - -
217A LEU* 3.9 11.2 - - + +
220A GLU* 3.2 45.9 + - - +
222A GLU* 3.2 26.5 + - + +
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Residues in contact with MSE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 3.5 10.1 + - - +
85A ASN* 3.1 11.0 + - - +
87A ARG* 1.3 78.0 - - - +
89A ASN* 1.3 63.2 + - - +
91A MSE 3.2 24.3 + - + +
92A ASN* 2.9 47.2 + - - +
222A GLU* 4.2 8.6 + - + +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 2.6 29.0 + - - +
86A GLU* 3.1 20.7 - - - +
88A MSE 1.3 77.4 - - - +
90A LEU* 1.3 65.3 + - + +
92A ASN* 4.2 5.0 - - - +
93A MSE 3.1 26.6 + - - +
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Residues in contact with LEU 90 (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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86A GLU* 3.6 16.8 - - + +
87A ARG 3.2 6.6 + - - +
89A ASN* 1.3 79.1 - - + +
91A MSE 1.3 54.7 - - - +
93A MSE 3.1 31.9 + - + +
94A ALA* 2.7 37.9 + - - +
125A VAL* 4.5 0.2 - - - +
128A HIS* 3.5 34.3 - - + +
129A CYS* 4.0 8.9 - - - +
132A HIS* 3.8 17.5 - - + -
217A LEU* 3.4 31.4 - - + -
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Residues in contact with MSE 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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87A ARG 3.1 3.4 + - - -
88A MSE 3.2 31.4 + - + +
90A LEU* 1.3 76.5 - - - +
92A ASN* 1.3 68.5 + - - +
94A ALA* 2.6 25.1 + - - +
95A LYS* 2.8 51.2 + - + +
217A LEU* 5.1 0.2 - - - +
221A GLU* 5.5 3.4 - - - +
222A GLU* 3.7 37.9 - - + +
225A ILE* 4.1 20.2 - - + -
226A ILE* 3.8 26.1 - - + +
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Residues in contact with ASN 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 MSE 2.9 42.1 + - - +
89A ASN* 4.2 4.2 - - - +
91A MSE 1.3 83.0 - - - +
93A MSE 1.3 62.0 + - - +
95A LYS* 3.1 44.0 + - + +
96A LEU* 3.3 21.4 + - + +
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Residues in contact with MSE 93 (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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89A ASN* 3.1 20.1 + - - +
90A LEU* 3.2 39.3 - - + +
91A MSE 3.0 0.6 - - - -
92A ASN* 1.3 78.0 - - - +
94A ALA* 1.3 52.8 + - - +
96A LEU* 3.9 9.9 + - - +
97A SER* 2.8 30.4 + - - -
125A VAL* 3.5 42.6 - - + +
128A HIS* 4.4 10.3 - - + -
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Residues in contact with ALA 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 LEU 2.7 11.2 + - - +
91A MSE 2.6 17.0 + - - +
93A MSE 1.3 71.6 - - - +
95A LYS* 1.3 62.7 + - - +
97A SER* 3.1 5.0 + - - -
98A ILE* 2.9 29.9 + - + +
122A PHE* 6.3 2.0 - - + -
125A VAL* 3.7 17.2 - - + +
126A MSE 5.8 2.7 - - + -
129A CYS* 4.4 4.5 - - - -
226A ILE* 3.9 33.7 - - + -
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Residues in contact with LYS 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 MSE 2.8 60.8 + - + +
92A ASN* 3.1 24.9 + - - +
94A ALA* 1.3 77.1 - - - +
96A LEU* 1.3 60.6 + - + +
98A ILE* 3.3 7.1 + - - +
99A LYS* 2.8 39.5 + - - +
225A ILE* 4.7 9.4 - - - +
226A ILE* 5.9 1.1 - - + -
229A LEU* 4.2 21.1 - - + -
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Residues in contact with LEU 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 ASN* 3.3 14.7 + - + +
93A MSE 4.1 8.7 - - - +
95A LYS* 1.3 80.5 - - + +
97A SER* 1.3 57.5 + - - +
99A LYS* 3.9 28.0 - - - +
100A GLY* 2.7 32.9 + - - -
121A GLN* 5.4 3.5 + - - +
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Residues in contact with SER 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 MSE 2.8 18.9 + - - -
94A ALA* 3.1 11.4 + - - -
96A LEU* 1.3 77.7 - - - +
98A ILE* 1.3 54.5 + - - +
101A LEU* 2.7 39.8 + - - +
118A PRO 5.5 0.8 - - - +
121A GLN* 4.5 16.7 + - - +
122A PHE* 4.0 28.9 - - - +
125A VAL* 3.2 23.7 - - - +
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Residues in contact with ILE 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 ALA* 2.9 16.7 + - + +
95A LYS* 3.8 6.1 - - - +
97A SER* 1.3 72.7 - - - +
99A LYS* 1.3 66.8 + - - +
101A LEU* 2.9 4.3 + - - +
102A ILE* 2.8 38.1 + - + +
122A PHE* 3.9 21.1 - - + -
226A ILE* 4.3 13.0 - - + +
229A LEU* 3.7 25.6 - - + +
230A LEU* 3.4 34.1 - - + +
233A LEU* 3.5 31.4 - - + -
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Residues in contact with LYS 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 LYS* 2.8 21.6 + - + +
96A LEU* 3.9 31.9 - - - +
98A ILE* 1.3 74.3 - - - +
100A GLY* 1.3 59.5 + - - +
102A ILE* 3.2 11.0 + - - +
103A GLU* 2.9 30.8 + - + +
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Residues in contact with GLY 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 LEU* 2.7 23.2 + - - +
99A LYS* 1.3 76.8 - - - +
101A LEU* 1.3 49.2 + - - +
103A GLU* 3.2 6.8 + - - +
104A SER* 2.7 44.9 + - - -
118A PRO* 6.0 0.2 - - - -
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Residues in contact with LEU 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 SER 2.7 22.8 + - - +
98A ILE 3.3 3.6 - - - +
100A GLY* 1.3 72.0 - - - +
102A ILE* 1.3 58.0 + - - +
104A SER* 3.4 4.0 + - - -
105A ALA* 2.9 30.3 + - - +
112A LEU* 4.8 4.7 - - + -
116A TYR* 4.3 7.6 - - + -
118A PRO* 3.5 17.3 - - + +
119A LEU* 3.5 47.8 - - + +
122A PHE* 3.7 33.0 - - + -
189A LEU* 5.8 1.8 - - + -
233A LEU* 4.1 19.3 - - + -
236A ILE* 5.3 8.5 - - + -
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Residues in contact with ILE 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 ILE* 2.8 34.5 + - + +
99A LYS* 3.5 9.4 - - - +
101A LEU* 1.3 73.8 - - - +
103A GLU* 1.3 55.0 + - - +
105A ALA* 3.0 1.9 + - - +
106A LEU* 2.7 37.5 + - + +
229A LEU 5.1 0.4 - - - +
232A GLY* 3.1 45.5 - - - +
233A LEU* 3.6 11.9 - - + -
235A VAL* 4.4 11.7 - - + -
236A ILE* 4.0 8.5 - - + -
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Residues in contact with GLU 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 LYS* 2.9 19.9 + - + +
100A GLY* 3.7 7.0 - - - +
102A ILE* 1.3 77.0 - - - +
104A SER* 1.3 60.3 + - - +
106A LEU* 3.3 31.6 + - - +
107A ASN* 3.1 35.7 + - - +
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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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100A GLY* 2.7 25.4 + - - -
101A LEU* 3.7 7.2 - - - -
103A GLU* 1.3 78.3 - - - +
105A ALA* 1.3 59.7 + - - +
106A LEU 3.4 0.2 - - - -
107A ASN* 4.3 2.9 + - - +
108A LEU* 3.2 24.3 + - - +
116A TYR* 3.3 27.2 + - - -
118A PRO* 4.7 8.7 - - - +
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Residues in contact with ALA 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 LEU 2.9 18.7 + - - +
102A ILE 3.0 1.1 + - - +
104A SER* 1.3 77.0 - - - +
106A LEU* 1.3 66.9 + - - +
108A LEU* 3.6 7.1 - - - +
109A GLY* 3.1 17.2 + - - -
110A ARG 4.7 3.0 + - - +
112A LEU* 4.0 23.3 - - + -
116A TYR* 5.0 0.9 - - - -
236A ILE* 3.4 28.9 - - + -
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Residues in contact with LEU 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 ILE* 2.7 19.7 + - + +
103A GLU* 3.3 25.8 - - - +
104A SER 3.4 0.2 - - - -
105A ALA* 1.3 80.0 - - - +
107A ASN* 1.3 73.2 + - - +
109A GLY* 3.1 10.9 + - - -
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Residues in contact with ASN 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 GLU* 3.1 34.0 + - - +
104A SER* 4.8 1.9 - - - +
106A LEU* 1.3 86.7 - - - +
108A LEU* 1.3 69.0 + - - +
109A GLY* 3.1 1.7 + - - -
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Residues in contact with LEU 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 SER 3.2 19.8 + - - +
105A ALA* 3.6 8.3 - - - +
106A LEU 3.2 0.2 - - - -
107A ASN* 1.3 78.4 - - - +
109A GLY* 1.3 68.1 + - - +
110A ARG* 3.4 32.3 - - + +
112A LEU* 4.0 19.7 - - + -
116A TYR* 4.4 19.1 - - + +
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Residues in contact with GLY 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 ALA 3.1 12.4 + - - -
106A LEU 3.1 9.4 + - - -
107A ASN 3.1 3.9 - - - -
108A LEU* 1.3 79.3 - - - +
110A ARG* 1.3 65.3 + - - +
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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
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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) + - + + + + + -
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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