Contacts of the strand formed by residues 133 - 140 (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 SER 133 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132L ASP* 1.4 75.7 + - - +
134L ASP* 1.4 63.4 + - - +
135L ILE* 4.0 9.4 - - - -
166L LYS* 6.0 1.1 - - - -
168L LYS 3.1 9.7 + - - +
169L THR* 3.1 20.2 - - - +
170L LEU 3.0 24.1 + - - +
230L ARG* 4.1 0.6 - - - +
234L PHE* 3.7 18.7 - - - +
236L ILE* 3.9 16.7 - - - +
316L ILE* 5.5 3.0 + - - +
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Residues in contact with ASP 134 (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* 1.4 69.8 - - - +
135L ILE* 1.3 62.0 + - - +
170L LEU* 3.4 21.5 - - - +
186L PHE* 3.7 22.1 - - + -
223L PHE* 3.7 10.0 - - + -
229L ALA* 4.0 1.7 - - - +
230L ARG* 2.7 58.7 + - - +
233L ALA* 3.4 13.6 - - + +
234L PHE 2.9 16.5 + - - +
235L LYS* 5.0 2.0 - - + +
236L ILE 3.0 27.7 + - - +
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Residues in contact with ILE 135 (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* 4.6 5.4 - - - -
134L ASP* 1.3 76.3 - - - +
136L ALA* 1.3 68.0 + - - +
137L PHE* 4.6 10.1 - - + -
160L VAL* 6.1 0.2 - - + -
164L LEU* 3.9 20.6 - - + -
169L THR* 3.7 21.3 - - + -
170L LEU 3.0 6.8 + - - +
171L PHE* 3.3 42.5 - - + -
172L SER 3.0 22.0 + - - +
186L PHE* 3.5 2.7 - - - -
236L ILE* 3.6 32.8 - - + -
238L VAL* 4.7 9.2 - - + -
316L ILE* 3.9 13.2 - - + -
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Residues in contact with ALA 136 (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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134L ASP 3.9 0.6 + - - -
135L ILE* 1.3 75.3 - - - +
137L PHE* 1.3 65.1 + - - +
172L SER* 3.5 6.7 - - - -
186L PHE* 4.3 4.9 - - + -
218L VAL* 4.3 1.6 - - + -
222L LEU* 4.0 22.2 - - + -
223L PHE* 3.7 28.5 - - + -
236L ILE 2.9 7.1 + - - +
237L LEU* 3.4 12.2 - - + +
238L VAL 3.0 24.4 + - - -
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Residues in contact with PHE 137 (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* 4.6 4.7 - - + -
136L ALA* 1.3 76.4 - - - +
138L LEU* 1.4 56.5 + - - +
139L ILE* 3.8 4.5 - - + -
156L PHE* 5.4 2.5 - + - -
157L VAL* 3.7 31.0 - - + -
160L VAL* 3.6 33.4 - - + -
161L MET* 3.7 17.7 - - + -
171L PHE* 3.5 33.2 - + - -
172L SER 2.8 24.1 + - - +
173L LEU* 3.4 17.7 - - + +
174L MET* 2.8 33.6 + - - +
184L PHE* 5.3 0.4 - + - -
222L LEU* 4.5 2.1 - - - +
237L LEU* 4.2 1.8 - - - -
238L VAL* 3.7 37.2 - - + -
240L ILE* 5.1 2.2 - - + -
312L LEU* 5.4 0.9 - - + -
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Residues in contact with LEU 138 (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* 1.4 69.3 - - - +
139L ILE* 1.3 60.9 + - - +
140L ASP 4.0 0.2 + - - -
174L MET* 3.5 39.0 - - + +
176L TYR* 3.6 27.6 - - + -
211L THR* 4.5 1.8 - - + +
214L GLY* 3.6 25.1 - - - +
215L ILE* 3.6 23.1 - - + +
218L VAL* 3.7 10.3 - - + -
237L LEU* 3.7 18.7 - - + +
238L VAL 2.8 11.3 + - - +
239L VAL* 3.5 16.2 - - + +
240L ILE 3.0 26.2 + - - +
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Residues in contact with ILE 139 (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* 5.0 1.8 - - + -
138L LEU* 1.3 76.7 - - - +
140L ASP* 1.4 58.0 + - - +
150L PHE* 4.2 12.3 - - + -
153L MET* 3.8 34.1 - - + -
154L LYS* 5.2 7.0 - - + -
157L VAL* 4.2 15.3 - - + -
173L LEU* 3.7 38.1 - - + -
174L MET 3.0 9.8 + - - +
175L GLN* 3.2 22.5 - - + -
176L TYR* 2.8 34.4 + - - -
202L ILE* 4.4 7.6 - - + -
240L ILE* 3.9 22.2 - - + -
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Residues in contact with ASP 140 (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* 1.4 68.7 - - - +
141L GLY* 1.3 57.2 + - - +
142L SER* 2.5 41.3 + - - -
145L ILE* 3.4 19.4 - - + +
150L PHE* 4.1 0.9 - - - -
153L MET* 3.5 21.1 - - - +
175L GLN* 4.7 0.4 - - - -
176L TYR* 3.5 25.4 + - + +
209L THR* 4.2 7.6 + - - +
240L ILE 3.1 20.8 + - - +
241L THR* 3.0 27.4 + - - -
242L ASP* 3.2 10.5 + - - +
243L GLY 4.0 1.9 + - - +
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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