Contacts of the strand formed by residues 153 - 163 (chain E) in PDB entry 2XTJ
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 THR 153 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 5.2 3.3 - - - -
148E SER 3.8 1.2 - - - +
149E THR* 3.2 5.8 - - - +
150E SER* 2.8 46.1 + - - -
151E GLY* 3.4 0.7 - - - -
152E GLY* 1.3 80.5 + - - +
154E ALA* 1.3 59.8 + - - +
201E THR* 3.7 30.1 - - + +
202E VAL* 3.3 17.0 - - - +
203E PRO* 5.2 0.2 - - + -
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Residues in contact with ALA 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PRO* 4.6 8.3 - - + -
148E SER 3.4 4.5 - - - +
149E THR* 3.8 16.2 - - - +
152E GLY 4.1 0.6 + - - -
153E THR* 1.3 74.8 - - - +
155E ALA* 1.3 61.4 + - - +
200E VAL 3.8 0.3 - - - +
201E THR* 3.4 3.8 - - - -
202E VAL* 2.7 40.8 + - - +
204E SER* 4.1 18.2 - - - -
207E LEU* 4.2 22.7 - - + -
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PHE* 4.1 20.4 - - + -
117C PHE* 3.7 6.7 - - + -
134C LEU* 4.2 14.8 - - + -
144E PRO* 3.7 6.1 - - - +
148E SER* 2.8 43.7 + - - +
154E ALA* 1.3 71.7 - - - +
156E LEU* 1.3 63.1 + - - +
199E VAL* 5.7 0.4 - - + -
200E VAL 3.4 7.4 - - - +
201E THR* 3.9 17.9 - - + +
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Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 4.5 2.7 - - - -
142E LEU* 3.4 14.4 - - - +
144E PRO* 3.7 26.2 - - + -
154E ALA 4.0 0.4 + - - +
155E ALA* 1.3 74.3 - - - +
157E GLY* 1.3 59.8 + - - +
172E TRP* 3.7 29.2 - - + -
199E VAL* 3.3 7.7 - - - +
200E VAL* 2.8 43.4 + - + +
202E VAL* 3.9 21.3 - - + -
207E LEU* 4.4 4.7 - - + -
212E TYR* 3.6 34.8 - - + -
229E VAL* 3.9 14.8 - - + +
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Residues in contact with GLY 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 2.7 45.8 + - - +
156E LEU* 1.3 78.1 - - - +
158E CYS* 1.3 60.7 + - - -
172E TRP* 3.7 10.3 - - - -
198E SER 3.1 12.6 - - - -
199E VAL* 4.0 1.3 - - - -
229E VAL* 3.5 13.9 - - - +
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Residues in contact with CYS 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E VAL* 3.9 12.3 - - + -
140E PHE 3.4 8.3 - - - +
142E LEU* 3.9 5.9 - - - +
157E GLY* 1.3 79.6 - - - -
159E LEU* 1.3 59.9 + - - +
160E VAL* 3.9 6.9 + - + +
170E VAL* 5.6 0.2 - - + -
172E TRP* 3.8 4.5 - - + -
197E SER* 3.4 6.9 - - - -
198E SER* 2.8 35.8 + - - +
214E CYS* 2.0 52.9 - - + -
227E LYS* 4.5 1.8 - - - -
229E VAL* 3.9 13.9 - - - -
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Residues in contact with LEU 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 4.0 14.4 - - - +
130C SER* 3.8 31.0 - - - +
132C VAL* 4.3 22.2 - - + -
177C THR* 4.9 7.9 - - + +
138E SER 3.2 6.8 - - - +
139E VAL* 3.4 0.8 - - - -
140E PHE* 2.8 53.1 + - + +
142E LEU* 4.3 13.0 - - + +
158E CYS* 1.3 72.2 - - - +
160E VAL* 1.3 58.6 + - - +
161E LYS* 3.4 14.3 + - + -
195E SER* 4.3 12.6 - - - +
196E LEU 4.0 11.0 - - - +
197E SER* 4.3 10.8 - - - -
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E PRO* 3.6 29.4 - - + -
138E SER 3.6 4.3 - - - +
139E VAL* 4.7 4.5 - - + +
158E CYS* 4.7 9.4 - - + +
159E LEU* 1.3 68.8 - - - +
161E LYS* 1.3 59.0 + - - +
163E TYR* 4.0 10.3 - - + -
168E VAL* 4.1 13.0 - - + -
170E VAL* 3.9 26.0 - - + -
195E SER* 3.4 3.6 + - - -
196E LEU* 2.8 53.8 + - + +
198E SER* 5.6 0.4 - - - +
216E VAL* 3.9 22.7 - - + -
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Residues in contact with LYS 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 3.9 14.1 - - - +
128C THR* 4.7 13.9 + - - +
130C SER* 3.3 23.1 - - - +
177C THR* 6.3 0.2 - - - -
179C THR* 5.0 7.5 + - - +
137E PRO* 3.3 1.9 - - - +
138E SER* 2.9 39.5 + - - +
140E PHE* 4.2 20.2 - - + -
159E LEU* 4.2 14.1 - - + +
160E VAL* 1.3 75.8 - - - +
162E ASP* 1.3 103.9 + - + +
163E TYR 3.6 1.8 - - - -
189E GLN* 3.4 16.8 + - - -
195E SER* 3.5 16.2 - - - +
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Residues in contact with ASP 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C THR* 5.1 3.3 + - - -
135E LYS* 2.5 42.2 + - - +
136E GLY 3.3 1.0 - - - +
138E SER* 5.9 1.3 - - - +
161E LYS* 1.3 110.6 + - - +
163E TYR* 1.3 59.3 + - - +
189E GLN* 3.1 15.4 + - - -
191E SER* 4.6 2.8 + - - -
193E LEU* 3.6 26.8 - - + +
194E TYR 3.1 11.5 + - - -
195E SER* 4.4 0.2 - - - -
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Residues in contact with TYR 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E LYS* 3.4 15.0 - - - +
137E PRO* 3.7 32.5 - - + -
160E VAL* 4.0 16.4 - - + -
162E ASP* 1.3 77.7 - - - +
164E PHE* 1.3 62.9 + - - +
165E PRO 3.3 24.7 - - - -
166E GLU* 2.8 26.2 + - - -
168E VAL* 3.2 28.9 - - + +
186E ALA* 3.2 17.2 - - - +
193E LEU* 3.6 2.8 - - - -
194E TYR* 2.7 66.9 + - + +
195E SER* 4.0 3.4 - - - -
196E LEU* 4.2 2.6 - - - +
218E HIS* 3.5 12.6 - + - +
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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