Contacts of the strand formed by residues 419 - 425 (chain A) in PDB entry 1UA4
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A LEU* 3.5 27.8 - - + -
331A ALA* 3.6 32.2 + - + +
332A LYS* 3.9 25.8 + - + +
336A VAL 5.4 3.1 - - - -
337A LYS 5.9 0.4 - - - -
350A LEU* 3.6 25.4 - - + -
351A THR* 3.3 20.0 - - - +
352A GLU* 3.8 21.1 - - + +
415A GLU* 3.2 6.7 - - - +
416A VAL* 2.8 36.3 + - - +
417A GLU* 3.7 14.1 - - + -
418A GLY* 1.3 78.6 - - - +
420A GLN* 1.3 60.8 + - - +
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Residues in contact with GLN 420 (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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349A ALA 3.5 1.6 + - - +
350A LEU* 3.4 5.8 - - - +
351A THR* 2.9 34.5 + - - +
353A TYR 3.5 16.1 + - - +
354A LYS* 3.5 14.2 - - + +
355A GLY* 3.0 45.7 + - - +
358A VAL* 3.8 21.0 - - - +
413A ILE* 3.6 26.4 - - + +
414A GLY 3.3 13.2 - - - +
415A GLU* 4.4 4.4 - - + +
418A GLY 4.0 0.8 + - - -
419A TYR* 1.3 73.8 - - - +
421A ILE* 1.3 66.2 + - - +
422A ALA* 4.5 6.2 - - - +
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Residues in contact with ILE 421 (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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324A THR* 4.0 26.2 - - + +
327A MET* 5.0 2.9 - - - -
348A LEU* 4.4 18.4 - - + -
349A ALA 3.9 12.1 - - - +
350A LEU* 4.2 15.3 - - + +
403A LEU* 5.3 3.1 - - + -
407A TYR* 4.5 13.0 - - + -
409A ILE* 3.9 16.0 - - + +
412A GLY 3.6 2.6 - - - +
413A ILE* 3.6 0.9 - - - -
414A GLY* 2.8 55.3 + - - +
415A GLU* 3.9 6.1 - - - +
416A VAL* 4.3 16.4 - - + -
419A TYR 3.9 0.4 + - - -
420A GLN* 1.3 75.2 - - - +
422A ALA* 1.3 70.0 + - - +
423A PHE* 5.7 0.4 - - + -
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Residues in contact with ALA 422 (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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348A LEU* 3.2 9.0 - - - +
349A ALA* 2.8 42.0 + - + +
358A VAL* 4.1 22.9 - - + -
359A ARG* 4.4 14.1 - - + +
362A LEU* 4.0 9.4 - - + +
412A GLY 3.1 7.0 - - - +
413A ILE* 4.7 1.8 - - + +
420A GLN* 4.0 9.6 - - - +
421A ILE* 1.3 74.1 - - - +
423A PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 423 (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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4A TRP* 3.3 17.6 - + - -
346A TYR* 3.6 26.2 - + + -
347A TYR 3.6 4.3 - - - -
348A LEU* 3.5 17.3 - - + -
359A ARG* 4.2 1.2 - - - +
362A LEU* 4.9 0.4 - - - -
396A ALA 4.0 9.6 - - - -
399A VAL* 3.7 16.2 - - + -
400A GLU* 3.6 34.3 - - + -
403A LEU* 3.4 24.7 - - + -
409A ILE* 4.1 19.1 - - + -
412A GLY* 2.7 19.0 + - - +
421A ILE* 5.7 0.9 - - + -
422A ALA* 1.3 74.5 - - - +
424A ILE* 1.3 75.0 + - - +
425A PRO* 3.7 33.9 - - + -
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Residues in contact with ILE 424 (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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4A TRP* 4.0 2.5 - - + -
8A TYR* 4.3 2.5 - - - +
346A TYR* 3.2 22.5 - - - +
347A TYR* 3.3 35.2 + - + +
359A ARG* 3.7 24.2 - - + +
362A LEU* 3.2 39.7 - - + +
363A LEU* 3.6 24.9 - - + +
366A ALA* 3.8 15.0 - - + -
423A PHE* 1.3 87.9 - - - +
425A PRO* 1.3 68.4 - - + +
426A THR* 4.4 2.2 - - + -
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Residues in contact with PRO 425 (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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4A TRP* 3.4 51.1 - - + +
8A TYR* 2.6 27.9 + - + -
345A GLY 3.9 6.3 - - - +
392A VAL* 3.3 26.1 - - + +
396A ALA* 3.5 20.9 - - + +
400A GLU* 5.9 0.9 - - - +
423A PHE* 3.7 9.6 - - + -
424A ILE* 1.3 85.9 - - + +
426A THR* 1.3 54.2 + - - +
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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