Contacts of the strand formed by residues 353 - 357 (chain B) in PDB entry 1U2X
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 ILE 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B ASP 2.9 8.1 + - - +
305B SER* 3.3 27.4 + - - +
306B VAL 3.0 25.3 + - - +
346B LEU* 4.6 0.9 - - - -
351B PHE* 3.3 8.6 - - - -
352B GLU* 1.3 81.1 - - + +
354B LEU* 1.3 62.5 + - - +
364B TYR* 3.3 39.3 - - + -
365B ILE 3.6 4.9 - - - +
366B THR* 3.3 28.7 - - + -
377B LEU* 3.6 14.6 - - + -
465B TYR* 3.6 37.7 - - + +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER* 6.0 0.2 - - - -
306B VAL* 3.5 22.7 - - + +
308B ILE* 3.8 26.9 - - + -
342B GLY* 3.6 40.6 - - - +
345B ILE* 4.3 12.8 - - + -
346B LEU* 4.6 4.4 - - + +
351B PHE* 3.8 23.1 - - + -
353B ILE* 1.3 74.5 - - - +
355B GLN* 1.3 62.3 + - - +
356B VAL* 4.2 15.9 - - + +
363B MSE 3.8 0.2 - - - +
364B TYR* 3.2 8.3 - - - -
365B ILE* 2.8 43.0 + - + +
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B HIS* 4.6 3.1 + - - +
305B SER* 5.4 3.8 - - - +
306B VAL 2.9 12.7 + - - +
307B GLY* 3.5 3.4 - - - -
308B ILE* 2.9 29.8 + - - +
354B LEU* 1.3 74.8 - - - +
356B VAL* 1.3 80.2 + - - +
357B HIS* 2.5 36.7 + - - +
362B LEU* 5.2 1.0 - - - +
363B MSE 3.2 10.1 - - - +
364B TYR* 3.7 17.3 - - + -
381B LEU* 3.9 19.5 - - + -
457B ILE* 4.2 9.6 - - - +
458B SER* 2.9 33.2 + - - -
461B ALA* 4.3 6.2 - - + +
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 3.3 20.2 - - + +
309B ASP 4.5 3.8 - - - -
310B GLU 4.6 0.2 - - - +
313B ILE* 3.8 27.4 - - + -
354B LEU* 4.2 15.9 - - + +
355B GLN* 1.3 82.9 + - - +
357B HIS* 1.3 61.4 + - - +
358B THR* 4.3 18.8 - - + -
361B TYR* 4.4 3.9 - - + +
362B LEU* 3.4 4.5 - - - -
363B MSE 2.9 64.8 + - + +
365B ILE* 5.5 0.2 - - + -
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Residues in contact with HIS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 3.2 27.4 + - - -
308B ILE 3.0 25.7 + - - -
309B ASP* 3.5 35.5 + - + +
310B GLU 3.8 0.7 + - - -
312B GLU* 5.4 0.6 + - - -
355B GLN* 2.5 22.9 + - - +
356B VAL* 1.3 72.3 - - - +
358B THR* 1.3 67.7 + - - +
362B LEU* 3.6 20.2 - - + -
454B GLY* 3.6 25.2 - - - -
457B ILE* 3.9 17.9 - - + +
458B SER* 3.4 11.3 + - - -
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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