Contacts of the strand formed by residues 127 - 134 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.5 6.9 - - - +
125A ALA* 3.7 1.0 - - - +
126A ASP* 1.3 94.8 + - - +
128A ALA* 1.3 60.0 + - - +
129A TYR* 3.6 41.6 + - + +
234A SER* 3.9 18.4 - - - -
280A SER 3.9 0.3 - - - +
281A LEU* 3.4 6.4 - - - +
282A TRP* 2.9 39.4 + - - +
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Residues in contact with ALA 128 (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 GLU* 6.3 1.7 - - + +
119A LEU* 3.4 13.1 - - + +
127A THR* 1.3 73.8 - - - +
129A TYR* 1.3 63.2 + - - +
130A PHE* 3.7 20.6 - - + -
234A SER* 3.3 3.9 - - - -
235A LEU* 3.1 29.6 + - + -
280A SER 3.5 5.6 - - - +
281A LEU* 3.8 17.3 - - + -
305A TYR* 5.8 0.2 - - - +
384A LEU* 3.9 14.6 - - + -
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Residues in contact with TYR 129 (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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127A THR* 3.6 27.0 + - + +
128A ALA* 1.3 72.3 - - - +
130A PHE* 1.3 63.6 + - - +
232A PHE* 3.6 34.8 - + + -
233A ASN* 3.5 9.6 - - - -
234A SER* 3.5 24.2 - - - -
278A HIS 3.5 0.5 - - - +
279A GLN* 3.4 7.4 - - - +
280A SER* 2.9 38.1 + - - +
282A TRP* 3.4 52.4 - + + -
501A IQ1 3.7 4.1 - - - +
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Residues in contact with PHE 130 (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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128A ALA* 3.7 24.5 - - + -
129A TYR* 1.3 78.2 - - - +
131A GLY* 1.3 61.4 + - - +
132A ALA* 4.2 1.3 + - - -
232A PHE* 3.3 4.9 - - - -
233A ASN 2.8 30.2 + - - +
235A LEU* 3.7 31.4 - - + -
238A ALA* 3.9 21.8 - - + +
277A CYS* 4.6 6.3 - - + -
278A HIS 3.4 3.1 - - - -
279A GLN* 3.7 35.2 - - + -
305A TYR* 4.4 7.6 - - - -
380A PHE* 3.5 60.6 - + + -
383A MET* 4.2 3.8 - - - -
384A LEU* 4.5 2.5 - - + -
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Residues in contact with GLY 131 (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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130A PHE* 1.3 73.4 - - - +
132A ALA* 1.3 59.2 + - - -
230A TYR 5.5 0.2 - - - -
232A PHE* 3.7 17.3 - - - -
276A HIS 3.5 1.4 - - - +
277A CYS* 3.4 3.2 - - - -
278A HIS* 2.7 42.8 + - - +
501A IQ1 3.6 27.4 - - - +
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Residues in contact with ALA 132 (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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130A PHE 4.1 1.4 + - - -
131A GLY* 1.3 74.6 - - - -
133A GLU* 1.3 65.4 + - - +
134A ALA 3.9 1.4 + - - -
228A ILE 5.0 0.7 - - - +
229A ASN* 4.6 6.4 + - - -
230A TYR* 4.6 23.3 + - + +
238A ALA* 6.5 0.4 - - + -
242A MET* 3.4 29.6 - - + -
275A MET* 4.4 5.4 - - + -
276A HIS 3.3 6.7 - - - +
277A CYS* 4.7 2.9 - - - -
380A PHE* 4.2 18.8 - - + -
501A IQ1 4.0 10.1 - - - +
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Residues in contact with GLU 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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132A ALA* 1.3 76.7 - - - +
134A ALA* 1.3 60.2 + - - +
135A GLU* 3.3 4.4 + - + +
227A GLU* 2.8 19.7 - - - +
228A ILE 5.1 0.7 - - - -
229A ASN* 3.9 12.8 - - - +
274A GLY 2.9 17.0 - - - +
275A MET* 3.1 12.6 - - - -
276A HIS* 3.0 28.0 + - + +
278A HIS* 2.9 15.5 + - - -
501A IQ1 4.1 10.3 - - + -
503A MG 2.3 27.7 - - - -
504A MG 1.8 33.0 - - - -
505A P3S 3.0 2.8 + - - -
506A PO4 2.9 11.7 + - - -
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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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132A ALA 3.9 2.4 + - - -
133A GLU* 1.3 69.7 - - - +
135A GLU* 1.3 65.3 + - - +
136A PHE* 3.6 5.5 - - - -
227A GLU* 4.7 3.9 - - - -
228A ILE 4.8 3.1 + - - -
230A TYR* 6.2 0.8 - - - -
242A MET* 3.6 27.2 - - + +
245A TYR* 2.9 48.7 + - + -
262A PHE* 3.8 6.1 - - + -
274A GLY 3.8 3.1 - - - -
275A MET* 4.4 1.3 - - + -
372A SER* 3.6 16.6 - - - +
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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