Contacts of the strand formed by residues 169 - 176 (chain E) in PDB entry 3Q3G
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 169 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ASP 5.1 1.9 + - - -
133E SER* 3.6 16.6 + - - -
135E ILE* 3.8 17.7 - - + -
164E LEU 3.5 18.6 - - - +
165E LYS* 6.0 0.2 - - - -
166E LYS* 3.3 47.6 + - - +
168E LYS* 1.3 76.4 - - - +
170E LEU* 1.3 64.1 + - - +
171E PHE* 3.7 24.6 - - + -
189E PHE* 3.9 13.2 - - - -
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Residues in contact with LEU 170 (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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133E SER 3.2 10.8 + - - +
134E ASP* 4.7 0.7 - - - +
135E ILE* 3.0 25.8 + - - +
169E THR* 1.3 75.0 - - - +
171E PHE* 1.3 67.2 + - - +
186E PHE* 3.4 36.5 - - + +
189E PHE* 3.6 18.8 - - + -
190E GLN* 3.6 32.5 - - + +
228E GLY 3.8 13.7 - - - +
230E ARG* 3.4 40.2 - - - +
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Residues in contact with PHE 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E ILE* 3.3 45.8 - - + -
137E PHE* 3.8 11.4 - + + -
161E MET* 3.7 60.6 - - + -
164E LEU* 3.8 26.0 - - + -
165E LYS* 4.8 2.5 - - - -
169E THR* 3.7 25.8 - - + -
170E LEU* 1.3 74.1 - - - +
172E SER* 1.3 60.7 + - - +
184E PHE* 3.9 5.1 - - + -
185E THR 3.6 1.6 - - - +
186E PHE* 3.3 23.4 - - - -
189E PHE* 3.3 45.6 - + + +
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Residues in contact with SER 172 (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 ILE 3.2 4.9 + - - +
136E ALA* 3.4 2.2 - - - -
137E PHE* 2.8 29.1 + - - -
171E PHE* 1.3 76.3 - - - +
173E LEU* 1.3 59.1 + - - +
184E PHE* 2.8 24.4 + - - -
185E THR* 3.4 10.4 - - - -
186E PHE* 3.5 28.7 + - - -
222E LEU* 3.3 28.0 - - - +
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Residues in contact with LEU 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E PHE* 3.6 17.7 - - + +
139E ILE* 3.9 25.1 - - + -
157E VAL* 3.8 29.8 - - + -
172E SER* 1.3 75.2 - - - +
174E MET* 1.3 70.1 + - - +
182E ILE* 3.6 4.9 - - - +
183E HIS* 2.9 42.1 + - + -
184E PHE* 3.1 36.4 + - + +
199E VAL* 4.8 1.3 - - + -
202E ILE* 3.8 31.0 - - + -
222E LEU* 4.2 3.1 - - - -
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Residues in contact with MET 174 (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 PHE 2.9 6.1 + - - -
138E LEU* 3.3 22.1 - - + +
139E ILE* 3.0 24.1 + - - +
173E LEU* 1.3 78.5 - - - +
175E GLN* 1.3 60.3 + - - +
176E TYR* 4.2 3.6 - - + -
180E PHE* 3.7 36.6 - - + -
181E ARG 3.4 22.9 - - - +
182E ILE* 4.0 15.0 - - + -
214E GLY* 3.5 20.6 - - - +
217E LYS* 3.8 21.1 - - + +
218E VAL* 4.1 15.3 - - + -
221E GLU* 5.7 1.6 - - - +
222E LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 175 (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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139E ILE* 3.3 26.9 - - + +
141E GLY* 3.2 20.8 - - - -
150E PHE* 3.6 12.1 - - - -
174E MET* 1.3 75.5 - - - +
176E TYR* 1.3 62.8 + - - +
180E PHE* 3.4 3.1 - - - -
181E ARG 2.9 31.6 + - - +
183E HIS* 3.2 30.2 + - + +
202E ILE* 4.0 1.0 - - - +
203E THR 2.7 27.3 + - - -
204E GLN* 3.4 3.6 - - - -
205E LEU* 2.8 41.4 + - + +
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Residues in contact with TYR 176 (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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138E LEU* 3.6 39.0 - - + -
139E ILE 3.0 15.3 + - - -
140E ASP* 3.5 25.7 + - + +
141E GLY 2.7 27.8 + - - -
174E MET* 4.2 0.2 - - + -
175E GLN* 1.3 75.1 - - - +
177E SER* 1.3 62.3 + - - +
179E GLU 3.4 5.8 - - - -
180E PHE* 3.4 21.8 - + + -
205E LEU* 4.1 2.9 - - - -
209E THR* 3.9 12.0 - - + +
210E HIS 3.5 18.6 - - - -
211E THR* 3.0 46.1 + - + +
214E GLY* 4.4 1.8 - - - -
239E VAL* 4.7 1.8 - - + -
240E ILE 4.6 0.9 - - - -
241E THR* 3.2 25.1 + - - -
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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