Contacts of the helix formed by residues 110 - 134 (chain B) in PDB entry 1UAZ
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 ASP 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 1.3 76.7 - - - +
111B ARG* 1.3 60.9 + - - +
112B VAL* 3.0 30.5 - - + +
113B SER* 2.8 43.6 + - - -
114B ILE* 3.1 10.4 + - - +
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL 3.7 1.0 + - - -
110B ASP* 1.3 73.0 - - - +
112B VAL* 1.3 59.8 + - + +
114B ILE* 4.1 12.5 - - + +
115B GLY* 2.8 26.8 + - - -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 3.2 23.8 - - + +
111B ARG* 1.3 77.3 - - + +
113B SER* 1.3 59.7 + - - +
115B GLY* 3.6 2.6 + - - -
116B THR* 2.8 26.7 + - - -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 3.8 17.2 - - - +
110B ASP* 2.8 35.1 + - - -
112B VAL* 1.3 76.0 - - - +
114B ILE* 1.3 57.6 + - - -
115B GLY 3.0 1.1 - - - -
116B THR* 2.6 29.5 + - - -
117B LEU* 2.8 16.0 + - - +
157B PHE* 5.9 0.5 - - - -
162B LEU* 5.7 3.1 - - - -
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 3.5 30.5 - - + -
104B ALA* 3.5 27.8 - - + +
105B LEU* 4.7 4.5 - - + +
109B VAL* 3.3 36.1 - - + +
110B ASP 3.1 6.3 + - - +
111B ARG* 4.1 10.1 - - + +
113B SER* 1.3 78.5 - - - +
115B GLY* 1.3 58.3 + - - +
117B LEU* 3.8 8.2 - - - +
118B VAL* 3.0 36.3 + - + +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG 2.8 20.3 + - - -
112B VAL* 3.8 5.2 - - - -
113B SER 3.0 0.2 - - - -
114B ILE* 1.3 77.9 - - - +
116B THR* 1.3 57.5 + - - +
118B VAL* 5.0 3.3 - - - +
119B GLY* 3.6 15.5 + - - -
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 2.8 17.5 + - - +
113B SER* 2.6 21.8 + - - -
115B GLY* 1.3 72.6 - - - +
117B LEU* 1.3 64.6 + - - +
118B VAL 3.2 0.7 - - - -
119B GLY* 3.1 0.8 + - - -
120B VAL* 3.0 38.0 + - + +
157B PHE* 3.7 28.5 - - + -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 3.7 30.3 - - + +
104B ALA* 4.8 14.4 - - + -
113B SER* 2.8 12.9 + - - +
114B ILE* 3.8 10.5 - - + +
116B THR* 1.3 78.8 - - - +
118B VAL* 1.3 60.0 + - + +
120B VAL* 3.6 3.3 - - + +
121B ASP* 2.8 31.5 + - - +
154B VAL* 4.3 21.0 - - + +
157B PHE* 3.6 39.0 - - + -
158B LEU* 4.0 3.4 - - + -
162B LEU* 3.5 30.7 - - + -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PRO* 3.9 41.7 - - + +
100B LEU* 5.0 2.9 - - + -
101B LEU* 4.9 7.0 - - + +
114B ILE* 3.0 28.3 + - + +
115B GLY* 5.0 2.9 - - - -
117B LEU* 1.3 78.0 - - + +
119B GLY* 1.3 63.8 + - - +
121B ASP* 4.3 5.8 - - - -
122B ALA* 3.0 24.7 + - + +
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLY 3.6 11.4 + - - -
116B THR* 3.1 9.3 + - - -
118B VAL* 1.3 77.9 - - - +
120B VAL* 1.3 61.6 + - - +
122B ALA* 3.7 3.9 - - - +
123B LEU* 3.1 21.1 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B THR* 3.0 29.1 + - + +
117B LEU* 3.6 4.0 - - + +
119B GLY* 1.3 72.0 - - - +
121B ASP* 1.3 54.1 + - - +
122B ALA 2.7 5.3 + - - -
123B LEU* 2.5 32.9 + - + +
124B MET* 2.9 10.4 + - - +
150B CYS* 4.1 25.6 - - + +
153B VAL* 4.3 18.8 - - + -
154B VAL* 3.3 23.3 - - + -
157B PHE* 5.4 2.0 - - + -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR* 2.8 29.4 + - - -
97B PRO* 3.6 9.5 - - + +
100B LEU* 3.4 21.8 - - + +
117B LEU 2.8 22.3 + - - +
118B VAL* 4.3 3.6 - - - -
120B VAL* 1.3 72.5 - - - +
122B ALA* 1.3 57.7 + - - +
124B MET* 3.6 12.9 - - - +
125B ILE* 3.4 18.7 + - - +
154B VAL* 3.5 12.7 - - + +
188B TRP* 3.1 33.1 - - - -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 4.8 17.8 - - + +
97B PRO* 5.3 6.1 - - + -
118B VAL* 3.0 24.1 + - + +
119B GLY* 3.7 5.6 - - - +
120B VAL 2.7 2.4 + - - -
121B ASP* 1.3 74.4 - - - +
123B LEU* 1.3 64.2 + - - +
124B MET 3.0 2.0 + - - -
125B ILE* 3.3 5.9 + - - +
126B VAL* 2.8 30.3 + - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLY 3.1 14.4 + - - +
120B VAL* 2.5 21.9 + - - +
122B ALA* 1.3 71.1 - - - +
124B MET* 1.3 48.1 + - - +
126B VAL* 2.9 23.3 - - + +
127B THR* 2.7 46.6 + - + +
146B PHE* 3.6 18.8 - - + -
150B CYS* 3.3 26.2 - - - -
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Residues in contact with MET 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR* 4.7 0.7 - - + -
120B VAL 2.9 6.2 + - - +
121B ASP* 3.6 34.1 - - - +
123B LEU* 1.3 75.0 - - - +
125B ILE* 1.3 83.6 + - + +
127B THR* 2.7 21.9 + - - -
128B GLY* 2.8 14.7 + - - -
147B SER* 3.2 22.3 + - - +
150B CYS* 3.9 16.5 - - + +
151B MET* 3.3 39.7 - - - -
154B VAL* 5.4 0.9 - - - -
188B TRP* 4.1 5.6 - - + -
255B RET 3.6 33.0 - - + -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR* 3.2 39.2 - - + +
92B TRP* 3.8 21.3 - - + +
93B LEU* 3.5 19.3 - - + +
96B THR* 3.7 16.2 - - - +
121B ASP 3.4 15.9 - - - +
122B ALA* 3.3 6.6 + - - +
124B MET* 1.3 96.8 - - + +
126B VAL* 1.3 57.6 + - - +
128B GLY* 3.5 1.4 + - - -
129B LEU* 3.0 25.3 + - - +
255B RET 4.2 25.6 - - + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 5.5 11.2 - - + +
122B ALA 2.8 26.8 + - - +
123B LEU* 2.9 28.5 - - + +
125B ILE* 1.3 75.3 - - - +
127B THR* 1.3 69.5 + - + +
129B LEU* 2.8 24.4 + - + +
130B VAL* 2.9 22.5 + - + +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 2.7 41.5 + - + +
124B MET* 2.7 21.3 + - - -
126B VAL* 1.3 75.3 - - + +
128B GLY* 1.3 51.2 + - - +
130B VAL* 2.8 15.8 + - + +
131B GLY* 2.7 33.4 + - - -
143B TRP* 3.8 24.7 - - + +
146B PHE* 3.8 16.2 - - + -
147B SER* 3.4 23.0 + - - -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B TYR* 3.8 8.2 - - - -
124B MET 2.8 16.6 + - - -
125B ILE 3.8 1.8 - - - -
127B THR* 1.3 78.1 + - - +
129B LEU* 1.3 61.1 + - - +
131B GLY* 3.1 3.6 + - - -
132B ALA* 2.9 22.7 + - - +
143B TRP* 5.6 1.1 - - - -
144B TRP* 6.0 0.4 - - - -
147B SER* 3.6 14.1 + - - -
195B TRP* 4.2 4.0 - - - -
255B RET 4.1 17.5 - - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE* 5.8 0.4 - - + -
86B TYR* 4.3 16.4 - - + +
89B TYR* 3.4 44.6 - - + -
93B LEU* 6.4 2.2 - - + -
125B ILE 3.0 13.2 + - - +
126B VAL* 2.8 18.2 + - + +
128B GLY* 1.3 74.8 - - - +
130B VAL* 1.3 65.0 + - + +
132B ALA* 3.1 6.1 + - + +
133B LEU* 3.0 48.3 + - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 2.9 25.7 + - + +
127B THR* 2.8 19.7 + - + +
129B LEU* 1.3 77.4 - - + +
131B GLY* 1.3 64.9 + - - +
133B LEU* 2.9 11.5 + - + +
134B SER* 2.8 20.2 + - - +
143B TRP* 3.4 42.0 - - + +
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR 2.7 14.9 + - - -
128B GLY* 3.1 5.5 + - - -
130B VAL* 1.3 69.9 - - - +
132B ALA* 1.3 53.0 + - - +
133B LEU 2.6 2.1 + - - -
134B SER* 2.6 38.9 + - - -
140B ARG* 3.7 12.9 - - - +
143B TRP* 3.6 17.9 - - - +
144B TRP 5.0 1.3 - - - -
195B TRP* 4.1 11.9 - - - -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.1 1.0 - - - +
84B ILE* 3.9 29.0 - - + +
89B TYR* 3.2 34.5 - - + +
128B GLY 2.9 9.3 + - - +
129B LEU* 3.3 10.3 - - + +
131B GLY* 1.3 72.5 - - - +
133B LEU* 1.3 59.5 - - + +
140B ARG* 2.8 27.2 + - - +
195B TRP* 3.4 16.1 - - + -
200B GLU* 4.9 0.2 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B THR* 5.0 7.6 - - + -
75B VAL* 3.7 30.8 - - + +
84B ILE* 4.5 11.7 - - + -
86B TYR* 5.9 4.0 - - + -
129B LEU* 3.3 42.0 - - + +
130B VAL* 2.9 11.4 + - - +
131B GLY 2.6 4.0 + - - -
132B ALA* 1.3 77.4 - - + +
134B SER* 1.3 63.8 + - - +
135B HIS* 3.4 11.1 + - - -
140B ARG* 4.0 0.7 - - - -
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.6 1.9 - - - +
130B VAL* 2.8 17.5 + - - +
131B GLY* 2.6 17.4 + - - -
133B LEU* 1.3 69.8 - - - +
135B HIS* 1.3 59.9 + - - +
136B THR 3.5 0.2 - - - -
139B ALA* 3.7 10.5 - - - -
140B ARG* 2.6 56.3 + - - +
143B TRP* 3.0 26.2 + - - -
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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