Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 1CZY
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 VAL 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A THR* 2.9 24.7 + - - +
351A ASP* 3.0 28.6 + - - +
352A GLY* 1.3 80.8 - - - +
354A PHE* 1.3 65.4 + - - +
355A ILE* 5.3 0.9 - - + -
493A LYS* 3.8 28.7 - - - +
494A ALA 3.5 4.0 - - - +
495A ILE* 4.4 16.8 - - + -
496A VAL 5.9 0.2 - - - +
385C ARG* 5.6 0.2 - - - +
386C TYR* 4.2 12.4 + - + -
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Residues in contact with PHE 354 (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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347A ALA* 3.4 26.7 - - + -
349A THR* 4.2 2.2 - - - -
352A GLY 4.1 0.2 + - - -
353A VAL* 1.3 76.2 - - - +
355A ILE* 1.3 68.7 + - - +
356A TRP* 3.6 27.6 - + + -
378A SER* 3.7 17.3 - - - -
379A PRO* 3.7 31.4 - - + -
380A ALA 4.6 1.1 - - - -
381A PHE* 3.6 51.6 - + + -
392A LEU* 4.2 10.5 - - + -
492A ILE 3.8 0.3 - - - +
493A LYS* 3.2 5.9 - - - +
494A ALA* 2.8 38.1 + - + +
386C TYR* 3.3 14.8 - - - -
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL* 5.3 0.9 - - + -
354A PHE* 1.3 83.3 - - - +
356A TRP* 1.3 59.9 + - - +
357A LYS* 3.9 2.2 + - - +
435A LEU* 4.6 4.3 - - + -
491A PHE* 3.9 30.3 - - + -
492A ILE 3.3 7.0 - - - +
493A LYS* 3.9 32.1 - - + +
386C TYR* 3.0 60.0 + - + -
418C ASN* 4.2 8.2 - - - +
421C LEU* 4.2 18.2 - - + -
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Residues in contact with TRP 356 (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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354A PHE* 3.6 17.6 - + + -
355A ILE* 1.3 71.2 - - - +
357A LYS* 1.3 73.6 + - - +
358A ILE* 3.6 26.6 + - + +
376A ILE* 3.4 35.0 - - + -
377A PHE 3.6 7.4 - - - -
378A SER* 3.3 35.7 - - - -
379A PRO* 3.9 18.3 - - + +
392A LEU* 4.0 21.1 - - + -
394A ILE* 3.6 30.7 - - + -
409A LEU* 5.3 1.1 - - + -
490A ILE 3.7 0.3 - - - +
491A PHE* 3.5 2.9 - - - -
492A ILE* 2.7 49.7 + - + +
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Residues in contact with LYS 357 (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 ILE* 3.9 4.4 + - + +
356A TRP* 1.3 80.7 + - - +
358A ILE* 1.3 62.8 + - - +
359A SER* 3.8 21.5 + - - +
489A ALA* 4.4 12.6 - - + -
490A ILE 3.6 6.7 - - - +
491A PHE* 3.6 33.1 - - + -
416C GLY 5.3 0.6 + - - -
417C PRO* 2.9 39.8 + - + +
418C ASN* 5.0 3.6 - - - +
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Residues in contact with ILE 358 (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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356A TRP* 3.7 53.6 - - + +
357A LYS* 1.3 73.3 - - - +
359A SER* 1.3 68.3 + - - +
361A PHE* 4.4 6.7 + - + +
364A LYS* 4.0 20.2 - - + +
376A ILE* 5.0 7.6 - - + -
394A ILE* 4.1 17.0 - - + -
396A LEU* 5.0 9.2 - - + -
488A ASP 4.2 0.2 - - - +
489A ALA* 3.2 6.1 - - - -
490A ILE* 2.9 58.3 + - + +
492A ILE* 4.3 2.9 - - + -
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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