Contacts of the strand formed by residues 381 - 388 (chain A) in PDB entry 1YQZ
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 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A HIS* 3.4 18.5 - - - +
372A VAL* 4.0 17.5 - - + -
373A TYR 3.6 10.3 - - - +
374A TYR* 4.3 0.9 - - - +
380A GLN* 1.3 75.8 - - - +
382A LEU* 1.3 61.7 + - - +
383A ARG 4.0 9.0 - - - +
384A ALA* 5.0 3.6 - - + -
399A LEU* 4.4 9.6 - - + -
402A ALA* 4.7 9.6 - - + -
403A MET* 3.8 32.3 - - + +
406A GLN* 5.5 2.0 - - - -
407A LEU 3.4 20.7 + - - +
408A THR 4.1 8.7 - - - +
409A VAL* 3.9 15.7 - - + +
412A LEU* 4.0 32.1 - - + -
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Residues in contact with LEU 382 (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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285A HIS* 3.0 21.2 + - - -
286A VAL* 3.7 22.0 - - + -
337A GLY* 3.4 1.0 - - - -
338A VAL* 3.1 26.1 + - + +
343A LEU* 4.6 5.6 - - + -
346A PHE* 3.7 48.5 - - + -
348A TYR* 3.8 12.6 - - + -
373A TYR* 2.8 14.0 + - + +
374A TYR* 3.8 5.2 - - - +
375A ASP* 3.6 39.5 - - + +
380A GLN* 4.0 2.7 - - + +
381A ILE* 1.3 76.3 - - - +
383A ARG* 1.3 60.4 + - - +
403A MET* 3.7 3.1 - - - -
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU 3.0 25.5 + - - -
188A ASP* 2.9 40.6 + - - +
335A SER* 3.8 19.7 + - - -
336A VAL 3.2 13.5 + - - +
337A GLY 4.6 2.0 + - - -
338A VAL* 2.9 32.8 + - + +
339A LYS* 3.9 2.0 - - - +
340A PRO* 3.7 21.4 - - - +
343A LEU* 4.0 16.4 - - + +
372A VAL* 3.5 0.9 - - - -
373A TYR* 2.8 53.3 + - + +
381A ILE* 3.7 6.5 - - - +
382A LEU* 1.3 81.6 - - - +
384A ALA* 1.3 69.0 + - - +
385A ALA* 4.5 3.0 - - - +
403A MET* 4.2 1.3 - - - -
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Residues in contact with ALA 384 (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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335A SER* 3.2 4.9 - - - -
336A VAL* 2.9 41.1 + - + +
370A LEU* 5.1 0.2 - - + -
371A ARG 3.2 11.4 - - - +
372A VAL* 4.1 4.3 - - + -
373A TYR* 5.2 0.4 - - - -
381A ILE* 5.0 5.2 - - + -
383A ARG* 1.3 79.7 - - - +
385A ALA* 1.3 61.0 + - - +
396A ILE* 3.8 9.0 - - + -
399A LEU* 3.6 33.0 - - + -
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Residues in contact with ALA 385 (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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187A MET* 3.8 24.9 - - + -
188A ASP* 4.5 13.5 - - - +
191A MET* 3.6 17.8 - - + +
334A ALA 3.4 7.4 - - - +
335A SER* 4.2 5.2 - - - -
370A LEU* 3.5 1.2 - - - +
371A ARG* 2.8 36.4 + - + +
373A TYR* 5.7 1.1 - - + -
383A ARG* 4.5 2.2 - - - +
384A ALA* 1.3 75.6 - - - +
386A ALA* 1.3 61.2 + - - +
396A ILE* 3.8 2.5 - - - -
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Residues in contact with ALA 386 (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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187A MET* 4.3 0.2 - - - +
191A MET* 4.0 0.2 - - - -
333A PHE* 3.7 0.3 - - - -
334A ALA 2.8 33.4 + - - -
368A LEU* 4.4 4.3 - - + -
369A HIS 3.2 10.8 - - - +
370A LEU* 4.0 10.8 - - + -
385A ALA* 1.3 76.1 - - - +
387A VAL* 1.3 65.7 + - - +
392A ALA* 3.8 23.4 - - + +
395A ARG* 4.9 2.7 - - + -
396A ILE* 3.6 21.8 - - + -
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Residues in contact with VAL 387 (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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187A MET* 3.8 20.0 - - + -
191A MET* 3.5 31.6 - - + +
194A PRO* 4.0 15.3 - - + -
331A TYR* 4.2 6.7 - - + -
332A THR 3.3 6.7 - - - +
333A PHE* 3.7 35.7 - - + -
367A PRO 4.2 1.0 - - - +
368A LEU* 3.8 3.9 - - - -
369A HIS* 3.0 34.1 + - + +
386A ALA* 1.3 80.3 - - - +
388A GLY* 1.3 63.1 + - - +
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Residues in contact with GLY 388 (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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331A TYR* 3.9 15.0 - - - -
332A THR* 3.0 31.1 + - - +
367A PRO 4.0 13.7 - - - -
368A LEU* 4.0 10.3 - - - +
387A VAL* 1.3 78.0 - - - +
389A LYS* 1.3 64.4 + - - -
390A GLU* 3.2 4.3 + - - -
392A ALA* 4.3 2.0 - - - +
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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