Contacts of the strand formed by residues 133 - 138 (chain B) in PDB entry 1U5U
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 ASP 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE 3.2 5.8 - - - +
122B LYS* 2.8 47.4 + - - +
129B ASP 4.1 0.7 - - - +
132B LEU* 1.3 83.9 - - - +
134B ILE* 1.3 66.3 + - - +
135B VAL* 4.1 7.9 + - + -
198B MET* 6.1 0.2 - - - +
322B PHE* 3.3 4.9 - - - -
323B ASN 2.9 31.6 + - - +
324B ILE* 4.7 5.2 - - - +
326B ASN* 2.7 33.9 + - - -
327B GLN* 3.9 10.4 + - - -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 5.0 0.9 - - + -
119B PHE* 3.9 1.7 - - - +
120B SER* 3.3 3.1 - - - -
121B ILE* 2.9 42.5 + - + +
123B PHE* 3.9 25.8 - - + -
132B LEU* 4.1 13.5 - - + -
133B ASP* 1.3 78.3 - - - +
135B VAL* 1.3 62.4 + - - +
136B MET* 3.5 32.1 - - + -
194B SER* 4.4 3.6 - - - -
212B TYR* 3.9 50.9 - - + -
271B LEU* 4.1 13.0 - - + -
324B ILE* 5.8 0.2 - - - -
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.3 8.3 - - - +
133B ASP* 4.3 5.6 - - + -
134B ILE* 1.3 82.6 - - - +
136B MET* 1.3 63.6 + - - +
194B SER* 3.8 11.2 - - - +
322B PHE* 4.0 26.9 - - + -
324B ILE* 3.9 22.4 - - + +
349B ARG* 3.5 17.3 + - - +
353B TYR* 4.7 3.8 - - + +
999B HEM 3.3 60.3 - - + +
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B SER* 3.2 10.0 - - - -
119B PHE* 2.8 68.3 + - + +
134B ILE* 3.5 26.5 - - + -
135B VAL* 1.3 79.7 - - - +
137B ASN* 1.3 62.7 + - - +
192B TYR* 3.5 29.2 - - + +
193B TYR 3.1 12.3 - - - +
194B SER* 3.5 17.0 - - - +
212B TYR 4.1 0.7 - - - -
213B ARG* 3.6 14.1 - - - +
214B ALA* 3.7 6.1 - - + -
271B LEU* 3.7 20.4 - - + -
999B HEM 3.3 5.6 - - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 2.9 22.3 + - - -
106B LEU* 3.6 22.7 - - - +
116B ALA* 4.9 6.5 - - + -
117B ARG 3.5 7.8 - - - +
118B SER* 3.4 12.7 - - - +
136B MET* 1.3 74.2 - - - +
138B THR* 1.3 71.2 + - - +
139B GLY 3.6 1.0 + - - +
142B ASN* 5.8 3.0 - - - +
192B TYR* 4.1 3.6 - - - -
193B TYR* 2.8 31.6 + - - +
195B GLN* 4.2 7.1 + - - +
999B HEM 3.5 37.9 + - + +
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.5 1.9 - - - -
117B ARG* 2.9 42.3 + - + +
137B ASN* 1.3 81.6 - - - +
139B GLY* 1.3 60.1 + - - +
179B ALA* 2.5 42.4 + - - +
181B ARG* 3.5 19.3 - - - +
190B LEU* 4.1 10.3 - - + -
191B TYR 3.4 20.0 - - - +
192B TYR* 3.9 14.1 - - + -
195B GLN* 4.0 3.1 + - - -
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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