Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 1YRT
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TRP* 4.3 4.9 - + - -
79A ASN* 4.6 4.3 - - - -
81A ASN* 4.0 12.3 - - + -
82A LEU* 3.9 22.7 - - + -
86A PHE* 3.8 29.4 - + - -
143A GLY 2.9 15.0 + - - +
144A TYR* 3.3 27.0 - - - +
145A GLU 3.6 0.6 - - - -
146A GLN* 1.3 85.4 - - + +
148A GLU* 1.3 67.4 + - - +
149A PHE* 3.6 22.9 - - + -
163A TYR* 3.7 31.6 - + + -
164A ARG 3.4 9.9 - - - +
165A ARG* 3.2 43.3 - - + -
166A LYS* 4.0 1.3 - - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 6.6 0.7 - - + -
144A TYR* 5.8 1.3 - - - +
147A PHE* 1.3 76.9 - - - +
149A PHE* 1.3 63.8 + - - +
163A TYR* 3.1 7.4 - - - +
164A ARG* 2.7 75.0 + - - +
166A LYS* 3.2 14.0 - - + +
167A GLY 3.1 28.4 + - - -
171A PHE* 3.6 14.0 - - + -
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TRP* 3.9 21.8 - + - -
71A LEU* 3.9 12.8 - - + -
72A GLN* 4.1 15.5 - - - -
82A LEU* 4.4 6.1 - - + -
136A VAL* 4.1 7.3 - - - +
137A VAL* 3.4 37.0 + - + +
144A TYR* 3.3 42.1 - + - -
147A PHE* 3.6 36.1 - + + -
148A GLU* 1.3 76.1 - - - +
150A ARG* 1.3 65.6 + - - +
161A VAL* 4.8 1.3 - - + -
162A GLN 3.1 9.4 - - - +
163A TYR* 3.5 26.0 - + + -
171A PHE* 4.2 3.7 - - - -
174A VAL* 4.4 13.0 - - + -
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 4.3 6.4 - - - +
135A GLY 3.3 17.7 - - - +
136A VAL* 4.3 7.9 - - + -
137A VAL* 4.5 2.2 - - - +
149A PHE* 1.3 76.4 - - - +
151A VAL* 1.3 64.5 + - - +
152A LYS* 4.4 20.0 - - + +
161A VAL* 3.9 1.6 - - - -
162A GLN* 2.9 59.2 + - + +
170A ASP* 5.4 3.4 + - - -
171A PHE* 3.5 53.9 + - + +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 4.8 15.3 - - + -
115A LEU* 5.0 1.6 - - + -
120A LEU* 4.8 3.6 - - + -
132A MET* 3.8 25.8 - - + -
134A ASP 5.2 1.6 - - - +
135A GLY* 3.1 18.6 + - - +
137A VAL* 5.1 0.7 - - + -
150A ARG* 1.3 77.1 - - - +
152A LYS* 1.3 71.7 + - - +
153A GLU 5.0 0.2 - - - +
159A TYR* 3.1 50.9 - - + +
160A ALA 3.2 17.0 - - - +
161A VAL* 4.3 11.2 - - + -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 4.4 19.8 - - + +
151A VAL* 1.3 85.8 - - - +
153A GLU* 1.3 69.3 + - - +
154A THR* 3.3 1.2 + - - +
159A TYR* 4.1 2.5 - - - -
160A ALA* 3.0 39.0 + - + +
162A GLN* 3.4 32.7 + - - +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS* 3.2 18.7 + - - -
152A LYS* 1.3 77.6 - - - +
154A THR* 1.3 75.9 + - - +
157A GLY* 3.9 5.8 - - - +
158A ARG 3.2 12.1 - - - +
159A TYR* 3.2 36.8 + - + -
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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