Contacts of the strand formed by residues 361 - 367 (chain A) 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 TYR 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A GLU* 4.5 6.4 + - - -
333A ASN 5.5 3.1 - - - -
335A LEU* 3.5 38.5 + - + +
338A SER* 3.5 26.9 + - - -
356A VAL* 5.2 1.1 - - + -
358A THR* 2.7 70.7 + - + +
360A TYR* 1.3 85.3 - - + +
362A LEU* 1.3 68.0 + - - +
363A MSE 4.4 17.7 - - + -
418A VAL* 3.9 16.4 - - + -
438A VAL* 3.9 23.6 - - + -
439A ILE 3.0 15.7 - - - +
441A THR* 3.5 4.0 - - - +
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Residues in contact with LEU 362 (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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355A GLN* 5.4 0.9 - - - +
356A VAL 3.4 4.9 - - - +
357A HIS* 3.6 27.8 - - + -
358A THR 4.1 1.1 - - - +
361A TYR* 1.3 81.3 - - - +
363A MSE 1.3 61.9 + - - +
381A LEU* 3.4 45.3 - - + +
385A THR* 3.7 14.4 - - + -
437A VAL 4.0 0.2 - - - +
438A VAL* 3.3 6.2 - - - +
439A ILE* 2.8 41.0 + - + +
441A THR* 3.6 20.2 - - + -
457A ILE* 3.6 28.7 - - + -
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Residues in contact with MSE 363 (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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338A SER* 3.5 31.2 - - - +
339A ILE* 3.6 30.3 - - - -
354A LEU 3.7 0.3 - - - +
355A GLN* 3.2 7.6 - - - +
356A VAL* 2.8 73.9 + - + +
361A TYR* 4.4 13.2 - - + -
362A LEU* 1.3 77.6 - - - +
364A TYR* 1.3 71.7 + - - +
365A ILE* 4.0 13.5 - - + -
381A LEU* 3.9 6.5 - - - -
436A VAL* 4.1 7.9 - - + -
437A VAL 3.1 12.1 - - - +
438A VAL* 3.9 11.9 - - + -
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Residues in contact with TYR 364 (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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305A SER* 5.3 4.9 + - - -
353A ILE* 3.4 31.0 - - + -
354A LEU 3.3 12.6 - - - -
355A GLN* 3.7 21.8 - - + -
363A MSE 1.3 72.6 - - - +
365A ILE* 1.3 66.0 + - - +
366A THR* 4.9 1.8 - - + -
377A LEU* 3.5 42.6 - - + -
380A SER* 2.8 26.3 + - - -
381A LEU* 3.4 30.2 - - + +
435A LYS 4.2 0.7 - - - -
436A VAL* 3.3 4.5 - - - -
437A VAL* 2.8 39.4 + - + +
461A ALA* 3.2 19.1 + - + +
462A PHE* 4.3 0.9 + - - -
465A TYR* 3.8 9.7 - + - +
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Residues in contact with ILE 365 (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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339A ILE* 3.9 8.7 - - - +
342A GLY* 3.5 14.4 - - - -
343A MSE 3.4 37.5 - - + +
346A LEU* 3.7 20.4 - - + +
353A ILE* 3.5 2.9 - - - +
354A LEU* 2.9 44.1 + - + +
356A VAL* 5.8 0.4 - - + -
363A MSE 4.0 24.9 - - + -
364A TYR* 1.3 79.4 - - - +
366A THR* 1.3 64.1 + - - +
434A TYR* 4.2 16.8 - - + -
435A LYS 3.1 8.1 - - - +
436A VAL* 4.2 10.1 - - + -
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Residues in contact with THR 366 (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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346A LEU* 3.9 9.0 - - - -
352A GLU 4.0 5.2 - - - -
353A ILE* 3.8 26.9 - - + -
364A TYR* 4.9 0.7 - - + -
365A ILE* 1.3 77.3 - - - +
367A HIS* 1.3 71.9 + - - +
370A ASN* 3.7 19.2 - - - +
377A LEU* 3.9 21.8 - - + -
434A TYR* 3.1 11.3 - - - -
435A LYS* 2.8 48.3 + - - +
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Residues in contact with HIS 367 (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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346A LEU* 3.9 24.2 - - + +
347A ASP* 5.7 0.4 - - - -
350A ASN* 3.5 20.6 + - - -
351A PHE 2.7 24.7 + - - -
352A GLU* 3.3 28.0 + - + -
366A THR* 1.3 88.3 + - - +
368A ARG* 1.3 66.8 + - + +
369A ASP* 3.1 17.9 - - - +
370A ASN* 3.0 15.0 + - + +
433A GLU 3.8 4.9 + - - +
434A TYR* 4.0 16.9 + + - -
435A LYS* 4.0 1.1 - - - -
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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