Contacts of the strand formed by residues 136 - 139 (chain F) in PDB entry 3ZXR
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 PHE 136 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F ALA 3.6 13.5 - - - -
135F GLU* 1.3 75.7 - - - +
137F TYR* 1.3 63.0 + - - +
138F ILE* 3.7 28.7 - - + -
202F MET* 3.9 15.3 - - + -
225F GLN* 3.3 6.7 - - - +
226F ALA* 2.6 62.8 + - + -
228F ILE* 4.4 10.3 - - + -
245F TYR* 3.4 19.5 - - - -
249F ILE* 3.5 34.5 - - + -
260F VAL* 3.8 10.5 - - + -
261F THR 3.6 13.9 - - - +
262F PHE* 3.6 21.1 - + + -
273F SER* 4.0 4.0 - - - -
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F PHE* 1.3 74.7 - - - +
138F ILE* 1.3 61.8 + - - +
139F PHE* 3.5 38.7 + + + -
221F GLY* 3.2 17.2 - - - -
222F SER 3.1 21.3 - - - -
223F GLY 3.7 3.4 - - - -
224F GLY 3.7 0.9 - - - -
225F GLN* 3.4 45.6 - - + -
260F VAL* 3.3 8.0 - - - +
261F THR* 3.1 32.2 + - + +
263F MET 5.3 0.2 - - - -
266F PRO* 3.6 25.1 - - + -
267F LEU* 3.6 16.7 - - + +
271F ASN 2.7 26.2 + - - -
273F SER* 3.5 15.7 - - - -
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Residues in contact with ILE 138 (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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136F PHE* 3.7 28.9 - - + -
137F TYR* 1.3 71.4 - - - +
139F PHE* 1.3 59.5 + - - +
140F ASP* 5.0 0.2 - - - +
157F ALA* 4.3 0.7 - - - +
195F TYR* 3.9 43.4 + - + -
198F LEU* 3.7 28.0 - - + -
199F ARG* 4.3 8.3 - - + -
202F MET* 4.1 12.8 - - + -
223F GLY 3.4 13.2 - - - +
224F GLY* 2.8 21.0 + - - +
226F ALA* 4.3 8.5 - - + -
258F LYS* 3.7 22.2 - - + -
259F THR 4.0 1.8 - - - -
260F VAL* 4.0 10.1 - - + -
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Residues in contact with PHE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F TYR* 3.5 28.6 + + + -
138F ILE* 1.3 77.0 - - - +
140F ASP* 1.3 60.8 + - - +
141F SER 4.1 5.4 - - - +
142F VAL* 5.6 2.2 - - + -
155F VAL* 3.7 42.0 - - + -
156F ASP 3.5 8.7 - - - +
157F ALA* 3.9 10.5 - - + -
162F TRP* 4.9 2.5 - + - -
223F GLY 3.4 24.9 - - - -
258F LYS* 3.6 6.2 - - - +
259F THR* 2.8 49.9 + - + +
261F THR* 3.6 30.7 - - + -
266F PRO* 3.9 13.7 - - + -
267F LEU* 4.1 10.8 - - + -
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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