Contacts of the strand formed by residues 133 - 138 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE 3.2 6.5 - - - +
122A LYS* 2.9 45.5 + - - +
129A ASP 3.9 0.7 - - - +
132A LEU* 1.3 84.4 - - - +
134A ILE* 1.3 66.7 + - - +
135A VAL* 4.0 8.4 + - + -
198A MET* 6.1 0.3 - - - +
322A PHE* 3.4 6.1 - - + -
323A ASN 2.9 31.6 + - - +
324A ILE* 4.6 5.5 - - - +
326A ASN* 2.7 34.7 + - - -
327A GLN* 4.0 9.7 + - - -
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Residues in contact with ILE 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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119A PHE 3.9 1.6 - - - +
120A SER* 3.4 3.3 - - - -
121A ILE* 2.9 40.9 + - + +
123A PHE* 3.7 32.8 - - + -
132A LEU* 4.1 9.4 - - + -
133A ASP* 1.3 77.1 - - - +
135A VAL* 1.3 63.7 + - - +
136A MET* 3.6 30.6 - - + +
194A SER* 4.4 2.7 - - - -
212A TYR* 3.9 51.4 - - + -
271A LEU* 4.0 14.4 - - + -
303A LEU* 5.0 0.2 - - + -
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Residues in contact with VAL 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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120A SER* 3.4 7.4 - - - +
133A ASP* 4.3 6.3 - - + -
134A ILE* 1.3 81.5 - - - +
136A MET* 1.3 63.4 + - - +
194A SER* 3.8 11.0 - - - +
322A PHE* 4.1 21.3 - - + +
323A ASN 4.6 0.9 - - - +
324A ILE* 3.7 26.5 - - + +
349A ARG* 3.4 22.4 + - - +
353A TYR* 4.6 4.0 - - + +
999A HEM 3.3 56.1 - - + +
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Residues in contact with MET 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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118A SER* 3.3 9.0 - - - -
119A PHE* 2.8 75.7 + - + +
134A ILE* 3.6 23.8 - - + -
135A VAL* 1.3 79.3 - - - +
137A ASN* 1.3 61.6 + - - +
192A TYR* 3.6 12.1 - - + +
193A TYR 3.0 16.2 - - - +
194A SER* 3.4 20.9 - - - +
212A TYR 4.0 1.3 - - - -
213A ARG* 3.5 28.5 - - - -
214A ALA* 3.8 11.9 - - + -
271A LEU* 3.8 13.0 - - + -
999A HEM 3.3 4.7 - - - +
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Residues in contact with ASN 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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67A HIS* 2.9 22.4 + - - -
106A LEU* 3.7 21.5 - - - +
116A ALA* 5.0 6.2 - - + +
117A ARG 3.4 7.9 - - - +
118A SER* 3.4 12.0 - - - -
136A MET* 1.3 74.7 - - - +
138A THR* 1.3 72.6 + - - +
139A GLY 3.6 1.4 + - - +
142A ASN* 5.8 2.8 - - - +
192A TYR* 4.1 3.4 - - - -
193A TYR* 2.8 30.4 + - - +
195A GLN* 4.3 7.5 + - - +
999A HEM 3.4 38.9 - - + +
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Residues in contact with THR 138 (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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116A ALA* 3.5 1.9 - - - +
117A ARG* 2.8 41.0 + - + +
137A ASN* 1.3 83.4 - - - +
139A GLY* 1.3 59.4 + - - +
179A ALA* 2.7 40.5 + - - +
181A ARG* 3.9 21.5 - - - +
190A LEU* 4.3 8.3 - - + -
191A TYR 3.3 22.0 - - - +
192A TYR* 3.8 13.2 - - + -
195A GLN* 4.1 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