Contacts of the helix formed by residues 124 - 149 (chain X) in PDB entry 2O5B
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 GLY 124 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116X HIS* 5.7 0.4 - - - -
121X GLY 6.1 1.1 - - - -
122X ASP 4.0 1.6 + - - -
123X PHE* 1.3 73.3 - - - +
125X ALA* 1.3 67.9 + - - -
126X ASP* 3.1 13.2 + - - -
127X ALA* 4.0 8.7 - - - +
128X GLN* 2.9 26.8 + - - +
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Residues in contact with ALA 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X GLY* 1.3 70.2 - - - +
126X ASP* 1.3 59.0 + - + +
128X GLN* 3.7 12.7 - - - +
129X GLY* 3.1 25.1 + - - -
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Residues in contact with ASP 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X GLN* 2.7 40.2 + - - +
124X GLY* 3.8 12.6 - - - -
125X ALA* 1.3 74.0 + - + +
127X ALA* 1.3 72.1 + - - +
129X GLY* 3.5 2.4 + - - -
130X ALA* 3.2 20.8 + - - +
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Residues in contact with ALA 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X GLN* 3.8 27.3 - - + +
13X VAL* 3.9 26.6 - - + +
122X ASP 5.8 0.4 - - - +
123X PHE* 3.8 11.7 - - + -
124X GLY 3.3 11.3 + - - +
126X ASP* 1.3 83.2 + - - +
128X GLN* 1.3 57.3 + - - +
130X ALA* 3.3 3.6 + - - +
131X MET* 3.0 29.5 + - - +
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Residues in contact with GLN 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X ILE* 3.7 17.2 - - - +
116X HIS* 3.0 32.3 + - + +
123X PHE* 3.5 26.0 - - + -
124X GLY 2.9 17.1 + - - +
125X ALA* 3.7 11.8 + - - +
127X ALA* 1.3 77.6 - - - +
129X GLY* 1.3 57.6 + - - +
131X MET* 4.1 0.7 - - - +
132X THR* 2.7 41.1 + - - +
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Residues in contact with GLY 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X GLU* 6.0 0.7 - - - -
125X ALA 3.1 12.1 + - - -
126X ASP 3.9 3.1 - - - -
128X GLN* 1.3 81.8 - - - +
130X ALA* 1.3 56.5 + - - +
132X THR* 3.6 6.4 + - - -
133X LYS* 3.0 33.8 + - - +
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Residues in contact with ALA 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X LEU* 3.8 1.4 - - - +
6X GLU* 3.4 49.3 - - + +
9X GLN* 4.1 8.7 - - + +
10X VAL* 3.3 12.1 - - + +
126X ASP 3.2 16.0 + - - +
127X ALA 3.3 4.0 + - - +
129X GLY* 1.3 72.4 - - - +
131X MET* 1.3 59.9 + - - +
133X LYS* 3.2 7.8 + - - +
134X ALA* 2.8 25.1 + - - +
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Residues in contact with MET 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X VAL* 3.6 45.7 - - + +
13X VAL* 3.7 22.9 - - + -
14X TRP* 4.6 15.7 - - + -
76X LEU* 4.3 11.9 - - - -
111X ILE* 5.2 2.9 - - + -
112X ILE* 3.8 13.2 - - + -
115X LEU* 3.8 21.8 - - + -
123X PHE* 4.2 6.1 - - + -
127X ALA 3.0 17.1 + - - +
128X GLN 4.1 2.7 - - - +
130X ALA* 1.3 71.6 - - - +
132X THR* 1.3 67.8 + - - +
134X ALA* 3.1 3.4 + - - +
135X LEU* 2.8 44.8 + - + +
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Residues in contact with THR 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X ILE* 3.5 21.4 - - + +
128X GLN* 2.7 29.8 + - - +
129X GLY* 3.7 6.9 - - - -
131X MET* 1.3 78.3 - - - +
133X LYS* 1.3 56.5 + - - -
135X LEU* 3.4 5.1 + - + +
136X GLU* 2.9 50.7 + - + +
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Residues in contact with LYS 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X GLY 3.3 22.4 + - - -
2X LEU* 3.8 14.9 - - + +
3X SER 4.9 0.2 - - - +
6X GLU* 3.0 42.6 + - + +
129X GLY 3.0 20.8 + - - +
130X ALA* 3.2 8.0 + - - +
132X THR* 1.3 72.3 - - + +
134X ALA* 1.3 62.4 + - - +
136X GLU* 3.5 15.6 + - - +
137X LEU* 3.1 23.0 + - - +
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Residues in contact with ALA 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X LEU* 3.9 9.1 - - + +
7X TRP* 3.9 19.5 - - + -
10X VAL* 3.7 20.0 - - + -
76X LEU* 4.0 18.7 - - + +
82X HIS* 5.6 0.5 - - - -
130X ALA 2.8 20.1 + - - +
131X MET* 3.1 6.0 + - - +
133X LYS* 1.3 75.1 - - - +
135X LEU* 1.4 57.4 + - - +
137X LEU* 3.5 5.9 + - - +
138X PHE* 3.1 25.6 + - - +
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Residues in contact with LEU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X LEU* 4.1 33.2 - - + -
76X LEU* 5.1 3.8 - - + -
108X SER* 3.6 42.8 + - - +
111X ILE* 4.3 15.9 - - + -
112X ILE* 3.9 21.1 - - + -
131X MET* 2.8 39.4 + - + +
132X THR* 3.9 4.3 - - + +
134X ALA* 1.4 69.5 - - - +
136X GLU* 1.3 61.0 + - - +
138X PHE* 3.4 11.0 - - + +
139X ARG* 3.0 35.4 + - - +
154X MNH 6.2 0.4 - - + -
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Residues in contact with GLU 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X THR* 2.9 38.5 + - + +
133X LYS* 3.6 20.5 + - - +
135X LEU* 1.3 77.1 - - - +
137X LEU* 1.3 50.6 + - - +
139X ARG* 3.4 29.3 + - - +
140X ASN* 2.7 37.0 + - - +
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Residues in contact with LEU 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X GLY* 5.3 15.9 - - - +
2X LEU* 4.5 7.9 - - + -
7X TRP* 3.9 33.7 - - + -
80X GLY* 4.0 9.4 - - - -
82X HIS* 4.0 20.2 - - + -
133X LYS 3.1 14.0 + - - +
134X ALA 3.6 7.0 - - - +
135X LEU 3.3 0.4 - - - -
136X GLU* 1.3 71.8 - - - +
138X PHE* 1.3 66.2 + - - +
140X ASN* 3.6 9.8 - - - +
141X ASP* 2.9 48.0 + - - +
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Residues in contact with PHE 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X LEU* 4.2 16.6 - - + -
75X ILE* 3.7 35.4 - - + -
76X LEU* 5.7 2.0 - - + -
82X HIS* 4.5 5.8 - - + -
86X LEU* 3.9 18.2 - - + +
89X LEU* 4.4 8.5 - - + -
104X LEU* 4.7 11.4 - - + -
107X ILE* 5.8 0.7 - - + -
108X SER* 5.2 6.3 - - - -
134X ALA 3.1 14.3 + - - +
135X LEU* 3.4 17.5 - - + +
137X LEU* 1.3 77.7 - - - +
139X ARG* 1.3 61.4 + - + +
141X ASP* 3.4 3.1 + - - +
142X ILE* 3.0 57.8 + - + +
154X MNH 3.6 42.4 - + + -
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Residues in contact with ARG 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ILE* 3.6 26.3 - - + +
104X LEU* 3.6 27.4 - - + -
105X GLU* 3.7 31.2 + - - +
108X SER* 2.9 29.4 + - - -
109X ASP* 5.5 2.6 + - - -
135X LEU* 3.0 28.9 + - - +
136X GLU* 3.5 28.9 + - - +
138X PHE* 1.3 78.8 - - + +
140X ASN* 1.3 54.1 + - - +
142X ILE* 3.3 4.5 + - - -
143X ALA* 2.8 36.2 + - - +
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Residues in contact with ASN 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X GLU 2.7 21.4 + - - +
137X LEU* 3.6 13.3 - - + +
139X ARG* 1.3 72.1 - - - +
141X ASP* 1.3 69.9 + - - +
143X ALA* 3.4 8.9 + - - +
144X ALA* 3.1 26.7 + - - +
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Residues in contact with ASP 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X HIS* 2.6 29.7 + - - +
86X LEU* 3.5 21.1 - - + +
137X LEU* 2.9 32.5 + - - +
138X PHE 3.9 1.8 - - - +
140X ASN* 1.3 84.6 + - - +
142X ILE* 1.3 65.8 + - - +
144X ALA* 3.6 10.8 + - - +
145X LYS* 3.4 21.8 + - - +
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Residues in contact with ILE 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X LEU* 4.1 13.7 - - + -
89X LEU* 5.4 3.8 - - + -
90X ALA* 4.2 20.2 - - + +
93X HIS* 5.9 0.4 - - + -
101X ILE* 3.7 14.4 - - + -
104X LEU* 3.9 12.3 - - + -
138X PHE* 3.0 64.1 + - + +
139X ARG* 3.7 6.7 - - - +
141X ASP* 1.3 76.1 - - - +
143X ALA* 1.4 65.6 + - - +
144X ALA 3.2 0.2 + - - -
145X LYS* 3.2 4.2 + - - +
146X TYR* 2.9 50.4 + - + +
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Residues in contact with ALA 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ILE* 3.9 19.3 - - + +
139X ARG 2.8 21.2 + - - +
140X ASN* 3.6 11.4 - - - +
141X ASP 3.4 0.2 - - - -
142X ILE* 1.4 73.5 - - - +
144X ALA* 1.3 55.8 + - - +
146X TYR* 3.3 9.4 - - - +
147X LYS* 2.9 28.8 + - - +
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Residues in contact with ALA 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X ASN* 3.1 16.9 + - - +
141X ASP* 3.9 8.3 - - - +
142X ILE 3.2 0.6 - - - -
143X ALA* 1.3 77.2 - - - +
145X LYS* 1.3 59.4 + - + +
147X LYS* 3.3 8.6 + - - +
148X GLU* 3.2 27.2 + - - +
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Residues in contact with LYS 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X GLU* 2.9 43.3 + - - -
86X LEU* 4.7 4.0 - - + -
87X LYS* 3.6 22.7 - - + +
90X ALA* 3.7 23.6 - - + -
91X GLN* 5.7 3.4 - - + +
141X ASP 3.4 16.4 + - - +
142X ILE 3.2 6.0 + - - +
144X ALA* 1.3 73.3 - - + +
146X TYR* 1.3 65.4 + - - +
148X GLU* 3.4 26.3 + - - +
149X LEU* 3.1 35.0 + - + +
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Residues in contact with TYR 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X ALA* 3.5 24.7 - - + -
93X HIS* 3.3 22.0 - - - +
94X ALA* 3.6 12.3 - - + -
99X ILE 2.6 29.6 + - - -
101X ILE* 3.7 28.9 - - + -
104X LEU* 4.1 7.2 - - + +
142X ILE* 2.9 35.0 + - + +
143X ALA* 3.3 11.4 - - - +
145X LYS* 1.3 75.0 - - - +
147X LYS* 1.3 64.9 + - - +
149X LEU* 3.2 4.4 + - - +
150X GLY 3.1 4.3 + - - -
151X PHE* 3.0 62.8 + + + +
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Residues in contact with LYS 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143X ALA 2.9 14.5 + - - +
144X ALA* 3.3 10.0 + - - +
146X TYR* 1.3 72.9 - - - +
148X GLU* 1.3 66.1 + - - +
150X GLY* 3.1 13.2 + - - -
151X PHE 5.1 1.8 - - - +
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Residues in contact with GLU 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X LYS* 5.8 2.8 + - - -
91X GLN* 4.9 10.0 + - - -
144X ALA 3.2 9.9 + - - +
145X LYS* 3.4 37.2 + - - +
147X LYS* 1.3 77.7 - - - +
149X LEU* 1.3 70.5 + - + +
150X GLY 3.3 1.4 + - - -
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Residues in contact with LEU 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X ALA 4.7 1.3 - - - +
91X GLN* 4.2 41.5 - - + +
94X ALA* 3.9 26.5 - - + -
95X THR* 4.5 11.2 - - - +
145X LYS* 3.1 25.6 + - + +
146X TYR* 3.8 4.3 - - - +
147X LYS 3.2 0.6 - - - -
148X GLU* 1.3 88.1 - - + +
150X GLY* 1.3 60.2 + - - +
151X PHE* 3.4 3.1 + - + +
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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