Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 4UQJ
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 LYS 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TRP 3.8 0.2 - - - -
131A ASP* 1.3 92.3 + - - +
133A PHE* 1.3 62.0 + - - +
159A GLN* 3.8 25.6 - - + +
189A GLU* 3.8 14.3 - - - +
191A ARG* 4.3 16.1 - - - +
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Residues in contact with PHE 133 (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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125A ILE* 3.7 25.6 - - + -
130A TRP* 3.4 37.9 - + + -
132A LYS* 1.3 81.0 - - - +
134A ALA* 1.3 66.2 + - - +
135A TYR* 4.6 6.1 - + + -
149A VAL* 5.0 5.2 - - + -
158A TRP* 3.8 33.4 - + + -
159A GLN 3.6 5.2 + - - +
160A VAL* 3.4 37.5 - - + -
161A THR* 3.1 21.0 + - - -
189A GLU* 3.5 8.7 + - - -
191A ARG* 3.3 14.4 - - + +
193A ILE* 3.6 23.3 - - + -
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Residues in contact with ALA 134 (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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133A PHE* 1.3 73.1 - - - +
135A TYR* 1.3 60.5 + - - +
136A LEU* 3.9 3.1 - - + -
161A THR* 3.7 9.9 - - - +
184A LEU* 3.7 31.4 - - + -
189A GLU* 3.5 11.2 + - + +
191A ARG 2.8 11.4 + - - +
192A VAL* 3.4 18.1 - - + -
193A ILE* 2.8 30.5 + - - +
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Residues in contact with TYR 135 (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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121A LEU* 4.5 5.8 - - + +
133A PHE* 4.0 2.9 + + + -
134A ALA* 1.3 72.9 - - - +
136A LEU* 1.3 60.7 + - - +
137A TYR* 3.4 21.5 + + + -
145A THR* 3.0 20.4 + - - -
146A LEU* 3.5 37.4 + - + -
149A VAL* 4.2 24.0 - - + -
160A VAL* 3.7 22.0 - - + -
161A THR 3.0 9.9 + - - -
162A ALA* 4.3 1.8 - - + -
163A ILE 3.1 21.1 + - - -
193A ILE* 3.8 36.1 - - + -
195A ASP* 2.7 34.6 + - + -
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Residues in contact with LEU 136 (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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134A ALA* 3.9 2.0 - - + -
135A TYR* 1.3 74.8 - - - +
137A TYR* 1.3 60.6 + - - +
163A ILE* 3.5 39.7 - - + +
165A VAL* 4.3 12.8 - - + -
180A LEU* 4.3 24.9 - - + -
181A PHE* 4.9 5.8 - - + -
184A LEU* 4.4 13.5 - - + -
192A VAL* 3.8 18.6 - - + -
193A ILE 3.0 6.4 + - - +
194A LEU* 3.6 28.3 - - + -
195A ASP* 2.9 27.9 + - - +
196A CYS* 4.0 1.6 - - - -
204A ILE* 4.5 12.6 - - + -
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Residues in contact with TYR 137 (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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135A TYR* 3.4 39.3 - + + -
136A LEU* 1.3 72.4 - - - +
138A ASP* 1.3 63.7 + - - +
139A SER 5.0 0.4 - - - -
143A LEU* 3.6 31.6 - - + -
146A LEU* 3.7 14.8 - - + +
162A ALA* 3.8 11.9 - - + -
163A ILE* 3.2 30.0 + - - -
164A ASN* 3.3 36.2 + - + +
165A VAL* 3.0 30.5 + - - +
195A ASP* 3.6 11.7 - - - +
147B GLN* 3.3 27.9 - - - +
150B LEU* 4.9 3.6 - - - +
151B ASP* 4.0 4.2 + - - -
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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