Contacts of the strand formed by residues 169 - 176 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L ASP 5.3 1.2 + - - -
133L SER* 3.1 19.1 + - - +
135L ILE* 3.7 27.8 - - + -
164L LEU 3.4 19.3 - - - +
165L LYS* 5.9 0.3 - - - -
166L LYS* 3.3 45.1 + - + +
167L SER 3.6 0.6 - - - -
168L LYS* 1.4 78.3 - - - +
170L LEU* 1.3 63.2 + - - +
171L PHE* 3.8 13.0 - - + -
189L PHE* 4.0 11.3 - - - -
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Residues in contact with LEU 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L SER 3.0 6.5 + - - +
134L ASP* 3.4 13.0 - - - +
135L ILE* 3.0 25.5 + - - +
168L LYS 4.0 0.6 + - - -
169L THR* 1.3 76.3 - - - +
171L PHE* 1.3 66.7 + - - +
186L PHE* 3.3 32.8 - - + +
189L PHE* 3.5 20.0 - - + -
190L GLN* 3.7 31.0 - - + +
228L GLY 4.0 12.1 - - - +
230L ARG* 3.4 38.4 - - - +
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Residues in contact with PHE 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L ILE* 3.3 38.8 - - + -
137L PHE* 3.5 32.5 - + + -
161L MET* 3.5 48.5 - - + -
164L LEU* 3.7 31.2 - - + -
165L LYS* 4.7 2.2 - - - -
169L THR* 3.8 15.3 - - + -
170L LEU* 1.3 76.3 - - - +
172L SER* 1.3 61.8 + - - +
184L PHE* 3.8 4.7 - - + -
185L THR 3.8 1.2 - - - +
186L PHE* 3.5 11.8 - - - -
189L PHE* 3.2 53.9 - + + +
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Residues in contact with SER 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ILE 3.0 5.5 + - - -
136L ALA* 3.5 6.0 - - - -
137L PHE* 2.8 34.8 + - - +
171L PHE* 1.3 75.9 - - - +
173L LEU* 1.3 56.0 + - - +
184L PHE* 2.7 27.0 + - - -
185L THR* 3.5 8.8 - - - -
186L PHE* 3.7 28.4 + - - -
222L LEU* 3.4 22.4 - - - +
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Residues in contact with LEU 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L PHE* 3.4 19.3 - - + +
139L ILE* 3.7 28.9 - - + -
157L VAL* 3.8 31.4 - - + -
172L SER* 1.3 74.9 - - - +
174L MET* 1.3 59.8 + - - +
182L ILE* 3.6 4.7 - - - +
183L HIS* 2.9 56.0 + - + -
184L PHE* 3.1 34.7 + - + +
199L VAL* 4.6 0.4 - - + -
202L ILE* 3.8 22.0 - - + -
222L LEU* 4.2 3.8 - - - -
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Residues in contact with MET 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L PHE 2.8 11.7 + - - +
138L LEU* 3.4 18.7 - - + +
139L ILE* 3.0 24.9 + - - +
173L LEU* 1.3 77.4 - - - +
175L GLN* 1.3 62.2 + - - +
176L TYR* 4.2 0.2 - - + -
180L PHE* 3.8 36.6 - - + -
181L ARG 3.3 23.6 - - - +
182L ILE* 4.0 15.0 - - + -
214L GLY* 3.5 21.5 - - - +
217L LYS* 3.8 21.8 - - + +
218L VAL* 4.1 15.3 - - + -
221L GLU* 5.6 1.8 - - - +
222L LEU* 3.8 15.9 - - + +
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Residues in contact with GLN 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L ILE* 3.2 24.5 - - + +
141L GLY* 3.2 21.2 - - - -
150L PHE* 3.6 11.9 - - - -
174L MET* 1.3 75.0 - - - +
176L TYR* 1.3 63.0 + - - +
180L PHE* 3.5 3.3 - - - -
181L ARG 2.9 32.3 + - - +
183L HIS* 3.1 30.9 + - + +
202L ILE* 4.0 1.0 - - - +
203L THR 2.7 27.5 + - - -
204L GLN* 3.3 4.0 - - - -
205L LEU* 2.8 41.0 + - + +
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Residues in contact with TYR 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L LEU* 3.6 37.2 - - + -
139L ILE 2.8 24.7 + - - -
140L ASP* 3.5 29.7 + - + +
141L GLY 2.7 32.8 + - - -
174L MET* 4.2 0.4 - - + -
175L GLN* 1.3 75.2 - - - +
177L SER* 1.3 63.8 + - - +
179L GLU 3.4 5.8 - - - -
180L PHE* 3.4 20.4 - - + -
205L LEU* 4.1 2.7 - - - -
209L THR* 4.2 5.3 - - + +
210L HIS 3.5 22.9 - - - -
211L THR* 2.8 44.7 + - + +
214L GLY* 4.4 2.5 - - - -
239L VAL* 5.1 2.0 - - + +
240L ILE 4.5 1.3 - - - -
241L THR* 3.2 26.0 + - - -
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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