Contacts of the strand formed by residues 170 - 175 (chain F) in PDB entry 2Q9Q
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 170 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PHE* 5.0 3.4 - + - -
140E GLU 4.5 2.5 + - - -
141E ALA* 3.4 45.9 + - - +
161E THR* 3.2 36.7 - - + +
164E LEU* 3.7 43.7 - - + -
165E ASN* 2.7 27.5 + - - +
168E TYR* 4.3 17.4 - - + +
168F ASP 3.9 5.6 - - - -
169F SER* 1.3 75.4 - - - +
171F VAL* 1.3 64.3 + - - +
185F GLU 5.6 0.3 + - - -
186F PRO 5.2 0.7 + - - -
205F LEU* 4.3 4.0 - - + -
206F ILE* 3.4 25.1 - - - -
207F ARG* 3.5 27.8 + - + +
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Residues in contact with VAL 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E THR* 4.3 4.3 - - - -
39F PHE* 3.6 29.6 - - + +
41F PRO* 4.7 2.5 - - + -
169F SER* 4.2 3.6 - - - +
170F TYR* 1.3 82.5 - - - +
172F PHE* 1.3 69.1 + - - +
173F LEU* 5.0 1.3 - - + -
204F HIS 3.6 0.9 - - - +
205F LEU* 3.4 5.1 - - - +
206F ILE* 2.8 41.6 + - + +
208F TYR* 4.0 32.5 - - + -
211F ILE* 4.4 7.2 - - + -
222F LEU* 3.9 24.2 - - + -
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Residues in contact with PHE 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LEU* 6.6 0.2 - - + -
145E LEU* 3.9 39.9 - - + -
148E LEU* 5.7 2.0 - - + -
153E ILE* 3.8 32.1 - - + -
157E GLY* 3.7 29.6 - - - -
160E LEU* 4.5 13.9 - - + -
161E THR* 3.7 23.3 - - + -
39F PHE* 5.6 1.8 - - - +
171F VAL* 1.3 78.3 - - - +
173F LEU* 1.3 63.8 + - - +
204F HIS 3.1 5.6 - - - +
205F LEU* 3.9 25.4 - - + -
222F LEU* 3.4 25.8 - - - +
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F VAL* 5.0 1.6 - - + -
172F PHE* 1.3 77.3 - - - +
174F ARG* 1.3 60.4 + - - +
175F VAL* 4.0 15.7 - - + -
198F LEU* 4.5 4.5 - - + -
203F GLN* 3.2 7.6 - - - +
204F HIS* 2.8 55.6 + - + +
206F ILE* 4.2 13.5 - - + -
211F ILE* 3.9 34.5 - - + -
220F VAL* 3.6 41.1 - - + -
221F GLN 3.2 11.7 - - - +
222F LEU* 4.1 5.8 - - + +
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Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ASP 4.4 6.9 + - - -
173F LEU* 1.3 77.0 - - - +
175F VAL* 1.3 67.8 + - - +
176F ARG* 3.6 1.4 + - + +
201F GLY* 3.1 33.9 + - - +
202F SER 3.3 7.9 - - - +
203F GLN* 3.1 32.9 + - + +
220F VAL* 3.8 0.5 - - - -
221F GLN* 2.8 43.8 + - + +
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Residues in contact with VAL 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F LEU* 4.0 14.8 - - + -
174F ARG* 1.3 76.1 + - - +
176F ARG* 1.3 59.6 + - - +
177F GLU 3.1 32.8 - - - +
198F LEU* 3.7 30.7 - - + +
199F GLU 3.2 19.3 - - - +
200F LYS* 4.2 1.2 - - - +
201F GLY* 2.8 27.7 + - - -
202F SER* 2.8 34.2 + - - +
204F HIS* 4.1 3.1 - - + -
219F ALA 3.8 5.4 - - - +
220F VAL* 4.2 3.6 - - + -
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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