Contacts of the strand formed by residues 127 - 134 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119F LEU* 3.6 5.7 - - - +
125F ALA* 3.7 0.6 - - - +
126F ASP* 1.3 95.0 + - - +
128F ALA* 1.3 62.7 + - - +
129F TYR* 3.5 45.2 + - + +
234F SER* 3.9 17.9 - - - -
280F SER 3.9 0.3 - - - +
281F LEU* 3.4 6.8 - - - +
282F TRP* 2.9 37.0 + - - +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F GLU* 6.3 1.9 - - + +
119F LEU* 3.5 13.5 - - + +
127F THR* 1.3 72.9 - - - +
129F TYR* 1.3 63.7 + - - +
130F PHE* 3.7 19.5 - - + -
234F SER* 3.3 3.9 - - - -
235F LEU* 3.0 30.2 + - + +
280F SER 3.6 4.9 - - - +
281F LEU* 3.7 17.9 - - + -
305F TYR* 5.7 0.2 - - - +
384F LEU* 3.9 15.9 - - + -
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Residues in contact with TYR 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F THR* 3.5 26.1 + - + +
128F ALA* 1.3 72.0 - - - +
130F PHE* 1.3 63.5 + - - +
232F PHE* 3.6 35.7 - + + -
233F ASN* 3.5 22.0 - - - -
234F SER* 3.5 11.9 - - - -
278F HIS 3.5 0.5 - - - +
279F GLN* 3.4 7.4 - - - +
280F SER* 2.9 37.9 + - - +
282F TRP* 3.4 52.0 - + + -
501F IQ1 3.7 2.6 - - - +
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Residues in contact with PHE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ALA* 3.7 24.7 - - + -
129F TYR* 1.3 77.7 - - - +
131F GLY* 1.3 59.8 + - - +
132F ALA* 4.2 1.3 + - - +
232F PHE* 3.5 5.2 - - - -
233F ASN 2.9 29.3 + - - +
235F LEU* 3.7 31.9 - - + -
238F ALA* 3.8 21.7 - - + +
277F CYS* 4.6 6.7 - - + -
278F HIS 3.4 2.9 - - - -
279F GLN* 3.7 35.7 - - + -
305F TYR* 4.4 7.9 - - - -
380F PHE* 3.4 59.7 - + + -
383F MET* 4.1 4.0 - - - -
384F LEU* 4.5 2.9 - - + -
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Residues in contact with GLY 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PHE* 1.3 73.0 - - - +
132F ALA* 1.3 60.0 + - - -
230F TYR 5.6 0.2 - - - -
232F PHE* 3.7 17.9 - - - -
276F HIS 3.6 0.9 - - - +
277F CYS* 3.4 3.9 - - - -
278F HIS* 2.7 42.6 + - - +
501F IQ1 3.6 26.5 - - - +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PHE 4.1 1.2 + - - -
131F GLY* 1.3 75.4 - - - +
133F GLU* 1.3 65.8 + - - +
134F ALA 3.9 1.0 + - - -
228F ILE 5.0 1.4 - - - +
229F ASN* 4.4 8.0 + - - -
230F TYR* 4.7 21.5 + - + +
242F MET* 3.3 31.0 - - + -
275F MET* 4.3 5.2 - - + -
276F HIS 3.3 7.0 - - - +
277F CYS* 4.6 2.7 - - - -
380F PHE* 4.3 17.9 - - + -
501F IQ1 4.0 9.3 - - - +
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Residues in contact with GLU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA* 1.3 76.8 - - - +
134F ALA* 1.3 59.8 + - - +
135F GLU* 3.4 3.8 + - + +
227F GLU* 3.0 18.8 - - - +
228F ILE 5.1 0.2 - - - -
229F ASN* 3.8 13.2 - - - +
274F GLY 3.0 17.0 - - - +
275F MET* 3.0 11.8 - - - -
276F HIS* 3.0 26.7 + - + +
278F HIS* 3.0 14.5 + - - -
501F IQ1 4.0 10.1 - - + -
503F MG 2.2 27.9 - - - -
504F MG 1.9 33.6 - - - -
505F P3S 3.0 2.9 + - - -
506F PO4 2.9 11.9 + - - -
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA 3.9 2.2 + - - -
133F GLU* 1.3 69.1 - - - +
135F GLU* 1.3 64.8 + - - +
136F PHE* 3.6 5.2 - - - -
226F ALA 4.7 0.2 - - - +
227F GLU* 5.3 2.2 - - - +
228F ILE 4.8 4.4 + - - +
230F TYR* 6.2 1.0 - - - -
242F MET* 3.5 27.5 - - + +
245F TYR* 2.9 44.9 + - + -
246F LYS* 5.4 0.2 - - + -
262F PHE* 3.8 5.8 - - + -
274F GLY 3.8 4.0 - - - -
275F MET* 4.5 1.3 - - + +
372F SER* 3.6 17.0 - - - +
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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