Contacts of the helix formed by residues 113 - 135 (chain B) in PDB entry 1YWT
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLU* 5.4 1.9 - - - +
41B ARG* 5.2 4.4 + - - +
111B ALA* 5.0 2.8 - - - +
112B GLY* 1.3 79.5 + - - +
114B ALA* 1.3 63.5 + - - +
115B GLU* 4.1 5.4 - - + +
116B SER* 2.9 37.6 + - - +
117B ARG* 3.1 12.3 + - - +
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Residues in contact with ALA 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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112B GLY 3.5 1.2 + - - -
113B ASP* 1.3 72.2 - - - +
115B GLU* 1.3 59.5 + - + +
117B ARG* 3.3 14.2 + - - +
118B VAL* 2.9 37.0 + - - +
157B ILE* 4.2 2.7 - - + -
161B GLU* 3.4 49.8 + - + +
162B MET* 4.7 5.4 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 4.0 9.6 + - - +
113B ASP* 3.3 5.5 - - + +
114B ALA* 1.3 76.1 - - + +
116B SER* 1.3 59.8 + - - +
118B VAL* 3.9 0.7 - - - +
119B PHE* 2.9 31.4 + - - +
162B MET* 3.4 24.0 - - + -
166B ASN* 3.6 19.5 + - - +
167B PRO* 5.9 0.5 - - - +
168B ILE* 2.9 30.8 - - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU 5.8 1.6 - - - -
41B ARG* 3.8 27.5 - - - +
111B ALA* 3.7 16.1 - - - +
113B ASP* 2.9 42.9 + - - +
115B GLU* 1.3 79.5 - - - +
117B ARG* 1.3 59.7 + - - +
119B PHE* 3.6 1.2 - - - +
120B TYR* 2.8 43.4 + - - -
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Residues in contact with ARG 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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109B LYS* 3.7 48.2 + - + +
111B ALA* 4.9 4.3 - - + +
112B GLY 3.2 23.7 + - - +
113B ASP 3.1 10.3 + - - +
114B ALA* 3.7 17.3 - - - +
115B GLU 3.2 0.2 - - - -
116B SER* 1.3 82.3 + - - +
118B VAL* 1.3 64.6 + - - +
120B TYR* 3.5 5.2 + - - +
121B LEU* 3.1 33.7 + - + +
157B ILE* 3.6 36.6 - - + +
161B GLU* 3.6 23.2 + - - -
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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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114B ALA 2.9 22.1 + - - +
115B GLU 3.9 2.7 - - - +
117B ARG* 1.3 73.2 - - - +
119B PHE* 1.3 62.3 + - - +
121B LEU* 3.3 1.9 + - - +
122B LYS* 2.8 29.9 + - + +
154B ALA* 3.7 16.8 - - + +
157B ILE* 3.5 26.0 - - + -
158B SER* 4.1 5.4 - - - +
162B MET* 4.0 16.4 - - - -
168B ILE* 4.0 18.8 - - + +
172B LEU* 3.7 33.2 - - + -
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Residues in contact with PHE 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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41B ARG* 3.6 57.0 - - + +
42B ASN* 4.2 16.6 - - - -
44B LEU* 5.8 0.4 - - + -
45B SER* 3.7 24.2 - - - -
115B GLU 2.9 19.1 + - - +
116B SER 3.6 5.2 - - - +
118B VAL* 1.3 78.0 - - - +
120B TYR* 1.3 67.0 + + - +
122B LYS* 3.3 10.3 + - + +
123B MET* 3.0 46.8 + - + +
168B ILE* 4.1 23.1 - - + +
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Residues in contact with TYR 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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35B GLU* 6.6 0.2 - - + -
36B LEU* 3.4 27.6 + - - +
41B ARG* 3.1 38.0 + - + +
44B LEU* 4.7 6.1 - - + -
103B LEU* 3.8 14.2 - - + +
107B LEU* 3.6 54.4 - - + +
108B ILE* 4.0 23.2 - - + +
109B LYS 5.4 0.2 - - - -
111B ALA* 5.4 6.5 - - + -
116B SER* 2.8 34.1 + - - +
117B ARG* 4.0 4.3 - - - +
119B PHE* 1.3 84.4 - + - +
121B LEU* 1.3 58.2 + - - +
123B MET* 3.2 7.5 + - - +
124B LYS* 3.0 26.5 + - - +
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Residues in contact with LEU 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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108B ILE* 4.1 32.8 - - + -
109B LYS* 6.2 0.4 - - + +
117B ARG* 3.1 22.9 + - + +
120B TYR* 1.3 72.8 - - - +
122B LYS* 1.3 65.5 + - - +
124B LYS* 3.2 16.8 + - + +
125B GLY* 3.0 17.0 + - - -
150B ALA* 3.7 20.7 - - - +
153B GLU* 4.0 34.5 - - + +
154B ALA* 3.7 18.2 - - + +
157B ILE* 3.9 26.0 - - + -
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Residues in contact with LYS 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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118B VAL* 2.8 19.3 + - + +
119B PHE* 3.5 12.6 - - + +
121B LEU* 1.3 76.1 - - - +
123B MET* 1.3 58.9 + - - +
125B GLY* 2.9 3.7 + - - +
126B ASP* 2.8 59.0 + - - +
151B TYR* 3.7 5.8 - - + -
154B ALA* 4.1 1.0 - - - +
168B ILE* 4.6 7.9 - - + +
171B GLY* 3.4 32.5 - - - -
172B LEU* 3.7 38.1 - - + +
175B ASN* 3.1 4.2 - - - +
7D TYR* 2.7 28.1 + - - -
8D PRO* 4.0 7.0 - - - +
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Residues in contact with MET 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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44B LEU* 4.1 31.6 - - + +
45B SER* 4.2 20.9 - - - -
48B TYR* 4.8 4.5 - - + -
99B VAL* 3.7 22.7 - - + -
103B LEU* 4.0 19.3 - - + -
119B PHE* 3.0 35.5 + - + +
120B TYR* 3.3 12.1 - - - +
122B LYS* 1.3 78.0 - - - +
124B LYS* 1.3 61.4 + - - +
126B ASP* 3.4 9.4 + - - +
127B TYR* 3.0 50.0 + - + +
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Residues in contact with LYS 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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100B LEU* 3.8 10.1 - - + +
103B LEU* 3.8 11.4 - - + +
104B ASP* 2.5 32.0 + - - +
108B ILE* 3.3 25.9 - - + +
120B TYR 3.0 12.8 + - - +
121B LEU* 3.4 16.2 - - + +
122B LYS 3.1 0.2 - - - -
123B MET* 1.3 75.9 - - - +
125B GLY* 1.3 63.0 + - - +
127B TYR 3.5 0.2 + - - -
128B TYR* 3.1 61.6 + - + -
146B SER 5.4 1.3 - - - -
150B ALA* 3.9 15.0 - - + -
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Residues in contact with GLY 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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121B LEU 3.0 9.6 + - - -
122B LYS 2.9 7.5 + - - -
124B LYS* 1.3 76.8 - - - +
126B ASP* 1.3 54.9 + - - +
128B TYR* 3.3 2.6 + - - +
129B ARG* 2.8 30.1 + - - +
147B ALA* 3.8 20.5 - - - +
150B ALA* 3.8 4.6 - - - +
151B TYR* 3.3 21.8 - - - -
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Residues in contact with ASP 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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122B LYS* 2.8 46.5 + - - +
123B MET* 3.7 10.3 - - - +
124B LYS 3.4 0.2 - - - -
125B GLY* 1.3 73.9 - - - +
127B TYR* 1.3 62.7 + - + +
129B ARG* 3.1 8.2 + - - +
130B TYR* 2.9 52.3 + - + +
151B TYR* 2.5 31.2 + - - -
175B ASN* 2.9 24.2 + - - +
8D PRO* 5.4 1.7 - - - +
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Residues in contact with TYR 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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45B SER* 4.5 2.9 + - - -
48B TYR* 3.3 33.4 + - + +
49B LYS* 3.4 9.4 + - - +
52B VAL* 4.2 14.8 - - + +
95B VAL* 5.0 1.3 - - + -
96B CYS* 3.9 18.1 - - + -
99B VAL* 3.6 40.8 - - + -
100B LEU* 4.0 24.5 - - + -
123B MET* 3.0 43.8 + - + +
126B ASP* 1.3 77.3 - - + +
128B TYR* 1.3 65.6 + - - +
130B TYR* 3.4 30.0 + + - +
131B LEU* 3.1 27.5 + - - +
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Residues in contact with TYR 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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100B LEU* 3.6 34.3 - - + +
104B ASP* 6.2 0.2 - - - -
124B LYS* 3.1 54.5 + - + +
125B GLY 3.8 0.2 - - - +
127B TYR* 1.3 76.3 - - - +
129B ARG* 1.3 58.9 + - - +
131B LEU* 3.1 9.5 + - + -
132B ALA* 2.8 25.5 + - - +
143B ILE* 3.1 26.5 - - + +
146B SER* 3.1 41.2 - - - -
147B ALA* 3.5 21.3 - - + +
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Residues in contact with ARG 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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56B ARG* 4.2 4.6 - - - +
125B GLY 2.8 14.1 + - - +
126B ASP* 3.1 31.2 + - - +
128B TYR* 1.3 78.6 - - - +
130B TYR* 1.3 73.4 + - + +
132B ALA* 3.1 10.0 + - - +
133B GLU* 3.0 30.1 + - - +
147B ALA* 4.0 5.1 - - - +
151B TYR* 2.9 20.0 + - + +
175B ASN* 3.4 16.5 + - - +
178B VAL* 4.0 17.1 - - - +
179B PHE* 3.9 32.1 - - + +
182B GLU* 5.6 0.4 + - - -
183B ILE* 3.8 18.1 - - + +
6D SEP 2.8 43.6 + - - -
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Residues in contact with TYR 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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49B LYS* 3.5 16.5 - - - +
52B VAL* 3.9 17.3 - - + -
56B ARG* 3.2 46.9 - - + -
92B LEU* 4.5 7.9 - - + +
96B CYS* 4.0 9.9 - - - -
126B ASP* 2.9 35.4 + - + +
127B TYR* 3.6 42.5 - + - +
128B TYR 3.2 0.2 - - - -
129B ARG* 1.3 86.7 - - - +
131B LEU* 1.3 66.4 + - - +
133B GLU* 3.0 26.4 + - - +
134B VAL* 3.7 10.2 + - - +
6D SEP 2.6 24.9 + - - -
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Residues in contact with LEU 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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92B LEU* 4.7 0.9 - - + -
93B GLN* 3.8 37.7 + - + +
96B CYS* 3.5 22.4 - - + -
97B ASP* 4.1 12.3 - - - +
100B LEU* 3.6 31.2 - - + -
127B TYR 3.1 14.0 + - - +
128B TYR* 3.4 17.9 - - + +
130B TYR* 1.3 76.1 - - - +
132B ALA* 1.3 61.7 + - - +
134B VAL* 3.4 9.9 + - - +
135B ALA* 3.3 21.8 + - - +
143B ILE* 3.9 20.8 - - + +
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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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128B TYR 2.8 12.7 + - - +
129B ARG* 3.3 13.0 - - - +
130B TYR 3.1 0.2 - - - -
131B LEU* 1.3 76.2 - - - +
133B GLU* 1.3 64.6 + - - +
134B VAL 3.2 0.9 + - - -
135B ALA* 3.4 12.4 + - - -
140B LYS* 3.5 21.7 - - + +
143B ILE* 3.5 15.2 - - + +
144B ILE* 4.0 26.2 - - + +
147B ALA* 5.8 0.2 - - + -
183B ILE* 4.0 13.2 - - + -
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Residues in contact with GLU 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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56B ARG* 3.0 52.3 + - - +
59B TRP* 3.5 23.4 - - + -
60B ARG* 5.2 4.1 + - - +
129B ARG* 3.0 25.8 + - + +
130B TYR* 3.0 16.1 + - - +
132B ALA* 1.3 77.3 - - - +
134B VAL* 1.3 63.7 + - + +
135B ALA 4.9 1.4 - - - +
140B LYS* 5.3 3.6 + - - +
182B GLU* 5.2 5.5 - - - +
183B ILE* 3.9 18.7 - - + +
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Residues in contact with VAL 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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59B TRP* 3.6 41.0 - - + +
89B GLU* 3.6 32.6 - - + +
92B LEU* 4.7 16.6 - - + -
93B GLN* 3.6 32.7 + - + +
130B TYR 4.0 10.8 - - - +
131B LEU* 3.4 10.1 + - - +
132B ALA 3.1 0.4 - - - -
133B GLU* 1.3 86.3 - - + +
135B ALA* 1.3 62.9 + - - +
136B THR* 4.2 5.2 + - - +
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Residues in contact with ALA 135 (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 GLN* 5.5 4.0 - - - +
131B LEU 3.3 15.6 + - - +
132B ALA* 3.4 5.5 + - - +
133B GLU 4.9 1.0 - - - +
134B VAL* 1.3 82.9 - - + +
136B THR* 1.3 65.8 + - - +
139B ASP* 4.4 4.5 - - + -
140B LYS* 3.3 40.5 + - + +
143B ILE* 3.8 21.8 - - + -
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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