Contacts of the helix formed by residues 138 - 162 (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 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B GLY* 1.3 71.0 - - - +
139B ASP* 1.3 66.3 + - - +
140B LYS 3.0 2.3 - - - +
141B LYS* 3.2 41.5 + - - +
142B ARG* 3.0 23.4 + - - +
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Residues in contact with ASP 139 (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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135B ALA* 4.4 7.2 - - + -
136B THR* 3.5 10.2 + - - +
137B GLY 2.6 15.4 + - - +
138B ASP* 1.3 75.3 - - - +
140B LYS* 1.3 60.7 + - - +
142B ARG* 3.5 28.3 + - - +
143B ILE* 3.0 34.6 + - + +
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Residues in contact with LYS 140 (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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132B ALA* 3.5 24.7 - - - +
133B GLU* 5.3 4.1 + - - +
135B ALA* 3.3 28.5 + - + +
136B THR* 3.3 20.6 + - - -
137B GLY* 4.1 4.7 - - - +
138B ASP 4.6 0.2 - - - +
139B ASP* 1.3 77.2 - - - +
141B LYS* 1.3 58.3 + - + +
143B ILE* 3.2 3.3 + - - +
144B ILE* 2.7 60.2 + - + +
183B ILE* 5.5 7.2 - - - -
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY* 5.4 1.8 - - - -
138B ASP* 3.2 43.3 + - - +
140B LYS* 1.3 79.1 - - + +
142B ARG* 1.3 62.1 + - - +
144B ILE* 4.3 8.3 - - + -
145B ASP* 2.6 35.4 + - - +
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Residues in contact with ARG 142 (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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138B ASP 3.0 15.2 + - - +
139B ASP* 3.7 39.2 + - - +
141B LYS* 1.3 75.7 - - - +
143B ILE* 1.3 91.3 + - - +
145B ASP* 3.3 5.9 + - - +
146B SER* 3.1 23.8 + - - +
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Residues in contact with ILE 143 (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* 6.4 0.2 - - - +
128B TYR* 3.1 39.0 - - + +
131B LEU* 3.9 22.4 - - + +
132B ALA* 3.5 12.6 - - + +
135B ALA* 3.8 21.5 - - + -
139B ASP* 3.0 20.9 + - + +
140B LYS* 3.6 3.8 - - - +
142B ARG* 1.3 100.3 - - - +
144B ILE* 1.3 63.3 + - - +
146B SER* 2.8 20.5 + - - -
147B ALA* 3.0 11.6 + - - +
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Residues in contact with ILE 144 (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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132B ALA* 4.0 9.9 - - + -
140B LYS* 2.7 45.5 + - + +
141B LYS* 3.8 7.4 - - + +
143B ILE* 1.3 72.9 - - - +
145B ASP* 1.3 66.6 + - - +
147B ALA* 3.3 7.8 + - - +
148B ARG* 3.1 32.9 + - - +
179B PHE* 3.6 21.9 - - + -
183B ILE* 3.6 36.3 - - + +
184B ALA* 5.1 6.3 - - - -
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Residues in contact with ASP 145 (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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141B LYS* 2.6 29.6 + - - +
142B ARG* 3.8 4.9 - - - +
144B ILE* 1.3 82.1 - - - +
146B SER* 1.3 64.1 + - - +
148B ARG* 3.5 14.7 + - - +
149B SER* 3.2 23.6 + - - -
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Residues in contact with SER 146 (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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124B LYS* 5.4 1.4 - - - -
128B TYR* 3.1 40.8 - - - -
142B ARG* 3.1 14.7 + - - +
143B ILE* 2.8 20.4 + - - -
145B ASP* 1.3 76.5 - - - +
147B ALA* 1.3 60.7 + - - +
149B SER* 3.2 16.4 + - - -
150B ALA* 3.5 12.8 + - - +
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Residues in contact with ALA 147 (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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125B GLY* 3.8 14.3 - - - +
128B TYR* 3.5 22.2 - - + -
129B ARG* 4.0 6.5 - - - +
132B ALA* 5.8 0.2 - - + -
143B ILE 3.0 12.9 + - - +
144B ILE* 3.4 11.7 - - - +
145B ASP 3.2 0.2 - - - -
146B SER* 1.3 78.9 + - - +
148B ARG* 1.3 58.9 + - - +
150B ALA* 3.3 4.5 + - - +
151B TYR* 3.1 32.7 + - + -
179B PHE* 3.9 16.2 - - + -
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Residues in contact with ARG 148 (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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144B ILE* 3.1 26.1 + - - +
145B ASP* 4.0 14.2 + - - +
147B ALA* 1.3 75.4 - - - +
149B SER* 1.3 60.6 + - - +
151B TYR* 3.2 5.4 + - - +
152B GLN* 2.7 33.9 + - + +
176B PHE* 4.4 9.8 - - + -
179B PHE* 3.7 34.1 - - + -
180B HIS* 3.8 27.9 + - - -
184B ALA* 3.9 16.4 - - - +
186B SER* 4.9 1.2 + - - -
189B GLU* 4.5 11.7 + - - -
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Residues in contact with SER 149 (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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145B ASP 3.2 12.6 + - - -
146B SER* 3.2 15.4 + - - -
148B ARG* 1.3 79.8 - - - +
150B ALA* 1.3 59.1 + - - +
152B GLN* 4.0 5.3 - - - +
153B GLU* 3.0 32.7 + - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.7 29.3 - - + +
124B LYS* 3.9 21.1 - - + -
125B GLY* 3.8 11.0 - - - +
146B SER 3.5 10.3 + - - +
147B ALA 3.3 9.6 + - - +
148B ARG 3.1 0.4 - - - -
149B SER* 1.3 80.4 + - - +
151B TYR* 1.3 65.7 + - - +
153B GLU* 3.4 5.8 + - - +
154B ALA* 3.0 23.9 + - - +
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Residues in contact with TYR 151 (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* 3.7 15.7 - - + -
125B GLY* 3.3 21.1 - - - -
126B ASP* 2.5 35.2 + - - -
129B ARG* 2.9 21.8 + - + -
147B ALA 3.1 25.0 + - - +
148B ARG 3.7 0.7 - - - +
150B ALA* 1.3 76.0 - - - +
152B GLN* 1.3 53.2 + - - +
154B ALA* 3.1 6.5 + - - +
155B MET* 2.8 36.1 + - - +
172B LEU* 3.7 23.0 - - + +
175B ASN* 4.0 15.1 - - + +
176B PHE* 3.6 37.0 - + + -
179B PHE* 3.9 28.0 - + + -
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Residues in contact with GLN 152 (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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148B ARG* 2.7 26.9 + - + +
149B SER* 4.0 6.1 - - - +
151B TYR* 1.3 74.4 - - - +
153B GLU* 1.3 57.3 + - - +
155B MET* 3.1 15.9 + - - +
156B ASP* 2.8 64.1 + - - +
176B PHE* 3.8 21.9 - - + -
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Residues in contact with GLU 153 (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* 4.0 28.1 - - + +
149B SER 3.0 20.6 + - - +
150B ALA* 3.9 5.0 - - - +
151B TYR 3.3 0.2 - - - -
152B GLN* 1.3 74.9 - - - +
154B ALA* 1.3 60.2 + - - +
156B ASP* 3.5 10.3 + - + +
157B ILE* 3.2 35.3 + - + +
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Residues in contact with ALA 154 (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* 3.7 18.3 - - + +
121B LEU* 3.7 23.8 - - + +
122B LYS 4.1 2.5 - - - +
150B ALA 3.0 13.8 + - - +
151B TYR 3.4 6.3 - - - +
153B GLU* 1.3 76.8 - - - +
155B MET* 1.3 58.9 + - - +
157B ILE* 3.5 4.0 + - - +
158B SER* 3.0 26.9 + - - -
172B LEU* 3.3 27.4 - - + +
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Residues in contact with MET 155 (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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151B TYR 2.8 13.1 + - - +
152B GLN* 3.3 21.3 - - - +
154B ALA* 1.3 75.5 - - - +
156B ASP* 1.3 65.3 + - - +
158B SER* 2.8 22.5 + - - -
159B LYS* 3.1 46.2 + - + +
169B ARG* 5.3 1.8 - - - +
172B LEU* 3.4 34.1 - - + +
173B ALA* 3.9 20.0 - - - +
176B PHE* 3.4 30.5 - - + -
193B LEU* 4.5 15.3 - - + -
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Residues in contact with ASP 156 (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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152B GLN* 2.8 49.3 + - - +
153B GLU* 3.8 10.3 - - + +
155B MET* 1.3 76.9 - - - +
157B ILE* 1.3 63.8 + - + +
159B LYS* 3.6 6.0 + - - +
160B LYS* 3.5 21.5 + - - +
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Residues in contact with ILE 157 (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* 4.2 3.6 - - + +
117B ARG* 3.6 41.7 - - + +
118B VAL* 3.5 19.1 - - + -
121B LEU* 3.9 22.9 - - + -
153B GLU* 3.2 25.7 + - + +
154B ALA* 3.8 5.4 - - - +
155B MET 3.2 0.6 - - - -
156B ASP* 1.3 78.9 - - + +
158B SER* 1.3 58.3 + - - +
160B LYS* 3.5 2.1 + - - -
161B GLU* 2.9 45.1 + - + +
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Residues in contact with SER 158 (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* 4.4 2.5 - - - -
154B ALA 3.0 14.7 + - - -
155B MET* 2.8 26.7 + - - +
157B ILE* 1.3 78.9 - - - +
159B LYS* 1.3 59.6 + - - +
162B MET* 2.8 60.3 + - - +
169B ARG* 3.6 25.8 + - - +
172B LEU* 3.8 7.3 - - - +
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Residues in contact with LYS 159 (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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155B MET* 3.1 44.1 + - + +
156B ASP* 4.1 5.4 - - - +
158B SER* 1.3 77.4 - - - +
160B LYS* 1.3 58.6 + - - +
162B MET 4.6 1.9 - - - +
169B ARG* 3.9 33.6 + - - +
193B LEU* 5.4 7.5 - - - +
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Residues in contact with LYS 160 (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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156B ASP 3.5 14.3 + - - +
157B ILE* 3.5 3.9 + - - +
158B SER 3.2 0.2 - - - -
159B LYS* 1.3 82.0 - - - +
161B GLU* 1.3 77.0 + - + +
162B MET 3.8 0.4 - - - -
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Residues in contact with GLU 161 (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* 3.4 35.1 + - + +
117B ARG* 3.6 11.5 + - - +
157B ILE* 2.9 28.5 + - + +
160B LYS* 1.3 107.4 - - + +
162B MET* 1.3 63.0 + - + +
163B PRO* 4.5 1.9 - - - +
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Residues in contact with MET 162 (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* 4.9 2.2 - - + +
115B GLU* 3.4 42.2 - - + -
118B VAL* 4.0 12.1 - - + -
158B SER* 2.8 40.9 + - - +
159B LYS 4.6 2.3 - - - +
160B LYS 3.8 0.4 - - - -
161B GLU* 1.3 86.4 - - + +
163B PRO* 1.3 64.5 - - + +
164B PRO* 4.3 0.2 - - - +
166B ASN* 3.2 35.9 - - + +
168B ILE* 3.8 14.4 - - + -
169B ARG* 2.5 38.1 + - - -
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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
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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