Contacts of the strand formed by residues 127 - 134 (chain C) 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 THR 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C LEU* 3.6 5.4 - - - +
125C ALA* 3.7 1.0 - - - +
126C ASP* 1.3 95.7 + - - +
128C ALA* 1.3 60.6 + - - +
129C TYR* 3.6 40.1 + - + +
234C SER* 3.9 17.7 - - - -
280C SER 3.9 0.3 - - - +
281C LEU* 3.4 6.2 - - - +
282C TRP* 2.9 42.3 + - - +
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Residues in contact with ALA 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLU* 6.0 2.1 + - + +
119C LEU* 3.5 12.7 - - + +
127C THR* 1.3 73.3 - - - +
129C TYR* 1.3 62.5 + - - +
130C PHE* 3.6 20.2 - - + -
234C SER* 3.3 3.7 - - - -
235C LEU* 3.1 30.1 + - + -
280C SER 3.5 5.6 - - - +
281C LEU* 3.8 18.2 - - + -
305C TYR* 5.7 0.2 - - - +
384C LEU* 3.9 14.8 - - + -
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Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C THR* 3.6 25.8 + - + +
128C ALA* 1.3 71.2 - - - +
130C PHE* 1.3 63.5 + - - +
232C PHE* 3.6 34.3 - + + -
233C ASN* 3.5 22.2 - - - -
234C SER* 3.6 11.7 - - - -
278C HIS 3.5 0.7 - - - +
279C GLN* 3.3 8.3 - - - +
280C SER* 2.8 41.7 + - - +
282C TRP* 3.4 52.5 - + + -
501C IQ1 3.6 4.1 - - - +
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Residues in contact with PHE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ALA* 3.6 24.7 - - + -
129C TYR* 1.3 77.4 - - - +
131C GLY* 1.3 59.8 + - - +
132C ALA* 4.1 0.8 + - - -
232C PHE* 3.4 4.8 - - - +
233C ASN 2.8 29.5 + - - +
235C LEU* 3.7 31.9 - - + -
238C ALA* 3.8 21.9 - - + +
277C CYS* 4.6 6.1 - - + -
278C HIS 3.4 2.9 - - - -
279C GLN* 3.6 36.6 - - + -
305C TYR* 4.4 8.1 - - - -
380C PHE* 3.4 60.6 - + + -
383C MET* 4.2 3.6 - - - -
384C LEU* 4.4 2.7 - - + -
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Residues in contact with GLY 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C PHE* 1.3 73.4 - - - +
132C ALA* 1.3 60.0 + - - -
230C TYR 5.6 0.4 - - - -
232C PHE* 3.7 18.2 - - - -
276C HIS 3.5 1.2 - - - +
277C CYS* 3.4 2.6 - - - -
278C HIS* 2.7 44.9 + - - +
501C IQ1 3.6 25.2 - - - +
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Residues in contact with ALA 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C PHE 4.1 1.2 + - - -
131C GLY* 1.3 75.6 - - - -
133C GLU* 1.3 65.6 + - - +
134C ALA 3.9 1.1 + - - -
228C ILE 5.1 1.0 - - - +
229C ASN* 4.4 8.5 + - - -
230C TYR* 4.7 21.9 + - + +
238C ALA* 6.5 0.4 - - + -
242C MET* 3.4 28.9 - - + -
275C MET* 4.4 4.9 - - + -
276C HIS 3.2 7.4 - - - +
277C CYS* 4.7 2.9 - - - -
380C PHE* 4.2 18.8 - - + -
501C IQ1 4.0 9.2 - - - +
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Residues in contact with GLU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ALA* 1.3 78.2 - - - +
134C ALA* 1.3 60.0 + - - +
135C GLU* 3.3 5.3 + - + +
227C GLU* 3.0 19.7 - - - +
228C ILE 5.2 0.2 - - - -
229C ASN* 3.9 12.6 - - - +
274C GLY 3.0 17.0 - - - +
275C MET* 3.2 11.0 - - - -
276C HIS* 2.9 28.2 + - + +
278C HIS* 2.9 14.1 + - - -
501C IQ1 4.0 10.1 - - + -
503C MG 2.1 28.1 - - - -
504C MG 2.0 32.9 - - - -
505C P3S 3.0 2.8 + - - -
506C PO4 2.9 12.0 + - - -
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ALA 3.9 2.4 + - - -
133C GLU* 1.3 70.5 - - - +
135C GLU* 1.3 64.9 + - - +
136C PHE* 3.6 5.7 - - - -
226C ALA 4.6 0.2 - - - +
227C GLU* 5.2 2.0 - - - -
228C ILE 4.8 4.5 + - - -
230C TYR* 6.1 1.4 - - + -
242C MET* 3.6 26.6 - - + +
245C TYR* 3.0 44.1 + - + -
262C PHE* 3.7 6.9 - - + -
274C GLY 3.8 4.0 - - - -
275C MET* 4.4 1.8 - - + -
372C SER* 3.6 17.3 - - - +
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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