Contacts of the strand formed by residues 141 - 149 (chain E) in PDB entry 2WNU
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 TYR 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E ILE* 3.5 25.9 - - + +
125E ASN* 4.7 0.5 + - - -
133E PHE* 3.6 27.1 - + - -
135E CYS* 4.0 14.3 - - - -
136E LYS 5.0 0.2 + - - -
137E VAL* 2.6 31.9 + - - +
139E GLY 3.4 18.4 - - - -
140E LEU* 1.3 73.4 - - - +
142E TYR* 1.3 58.8 + - - +
143E PHE* 3.6 23.6 - + + -
185E MET 3.7 0.3 - - - +
186E VAL* 3.3 4.5 - - - +
187E LEU* 2.8 35.4 + - - +
189E LEU* 3.7 16.6 - - + -
218E PHE* 3.3 10.1 - - - +
219E LEU* 3.5 41.4 - - + +
220E LEU* 3.8 4.0 - - - -
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Residues in contact with TYR 142 (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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138D TYR* 5.2 3.1 - + - -
140D THR* 3.4 29.1 - - + +
142D GLN* 4.2 4.5 + - - -
215D SER* 4.5 4.7 - - - -
217D PHE* 3.8 17.3 - + + -
141E TYR* 1.3 72.7 - - - +
143E PHE* 1.3 66.5 + - - +
144E THR* 3.7 29.2 + - + -
184E GLY* 4.0 8.3 - - - -
185E MET* 3.4 32.3 - - - -
186E VAL* 3.8 13.5 - - + -
217E GLY* 3.1 4.2 - - - -
218E PHE* 2.9 72.2 + + + -
220E LEU* 3.8 12.4 - - + +
139F TYR* 4.4 11.9 + + - -
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Residues in contact with PHE 143 (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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97E PHE* 3.7 30.5 - + - -
133E PHE* 3.5 34.1 - + + -
141E TYR* 3.6 26.7 - + + -
142E TYR* 1.3 76.5 - - - +
144E THR* 1.3 62.2 + - - +
157E LEU* 4.7 13.2 - - + +
184E GLY* 3.1 3.8 - - - -
185E MET* 2.8 38.7 + - + +
187E LEU* 3.8 21.8 - - + -
189E LEU* 3.7 13.2 - - + -
195E VAL* 3.8 23.3 - - + -
215E PHE* 4.2 11.0 - + + -
216E SER 3.6 3.6 - - - +
217E GLY* 3.9 13.2 - - - -
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Residues in contact with THR 144 (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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142D GLN* 5.5 0.9 + - - -
142E TYR* 3.7 25.9 + - + -
143E PHE* 1.3 77.7 - - - +
145E TYR* 1.3 67.4 + - - +
146E HIS* 4.5 7.8 + - + +
182E THR* 4.2 6.9 + - - -
183E GLY 3.1 14.4 + - - -
184E GLY* 4.1 0.2 - - - -
215E PHE* 3.4 5.5 - - - -
216E SER* 2.9 54.5 + - - +
218E PHE* 5.3 2.0 - - + -
139F TYR* 3.6 27.0 + - + +
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Residues in contact with TYR 145 (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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115E PHE* 5.2 2.5 - + + -
144E THR* 1.3 80.6 + - - +
146E HIS* 1.3 67.5 + - - +
147E ALA* 4.0 21.8 - - + -
153E LEU* 5.6 1.1 - - + -
155E VAL* 2.9 34.3 - - + +
157E LEU* 6.2 0.4 - - + -
170E PHE* 3.2 29.0 + + - +
181E THR* 4.4 9.1 - - + +
182E THR* 2.6 38.2 + - - -
183E GLY* 3.1 33.6 + - - -
197E LEU* 3.9 38.6 - - + -
214E ILE* 3.1 18.4 - - - +
215E PHE* 4.1 1.8 - + + -
216E SER* 4.8 0.4 - - - +
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Residues in contact with HIS 146 (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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115E PHE* 5.3 0.5 - - - -
144E THR* 4.5 6.5 + - + +
145E TYR* 1.3 79.9 + - - +
147E ALA* 1.3 60.2 + - - +
180E VAL* 4.3 1.3 - - + -
181E THR 3.1 6.7 - - - +
182E THR* 3.2 18.5 + - + -
213E SER* 3.2 4.2 - - - -
214E ILE* 2.9 43.5 + - + +
139F TYR* 4.5 6.1 + - - -
141F VAL* 4.3 11.8 - - + +
143F HIS* 5.3 1.6 - + - -
164F PHE* 3.8 20.3 - - + -
176F SER* 2.9 35.8 + - - +
177F GLY* 3.3 28.8 + - - -
178F GLY* 3.4 19.8 + - - -
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Residues in contact with ALA 147 (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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115E PHE* 6.3 1.1 - - + -
145E TYR* 4.0 17.2 - - + -
146E HIS* 1.3 73.6 - - - +
148E SER* 1.3 62.5 + - - +
149E SER* 3.9 1.2 + - - -
153E LEU* 3.6 28.0 - - + -
179E GLN* 3.9 0.7 - - - +
180E VAL* 3.3 4.1 - - - -
181E THR* 2.8 37.9 + - + +
205E LEU* 3.7 18.4 - - + -
213E SER* 3.5 5.4 - - - +
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Residues in contact with SER 148 (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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147E ALA* 1.3 75.1 - - - +
149E SER* 1.3 60.9 + - - +
179E GLN 3.3 9.0 - - - -
180E VAL* 4.3 3.8 - - - +
205E LEU* 3.6 5.0 - - - +
206E LEU* 2.9 31.7 + - - -
211E ALA* 3.5 31.4 - - - -
212E ASN 2.6 26.0 + - - -
213E SER* 3.1 7.2 + - - -
163F THR 4.5 0.2 + - - -
164F PHE* 4.0 11.4 - - - -
165F CYS 4.9 3.0 + - - -
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Residues in contact with SER 149 (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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147E ALA 4.8 1.3 - - - -
148E SER* 1.3 74.0 - - - +
150E ARG* 1.3 59.6 + - - +
151E GLY 2.6 28.8 + - - -
153E LEU* 4.2 9.8 - - - +
178E PHE* 3.4 6.8 - - - +
179E GLN* 2.8 49.6 + - - +
181E THR* 6.0 0.2 - - - -
204E SER 3.0 22.1 + - - -
206E LEU* 4.0 11.9 - - - +
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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