Contacts of the strand formed by residues 382 - 388 (chain C) in PDB entry 5Y7K
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 ARG 382 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347C GLU* 5.2 2.6 + - - -
353C TRP 4.6 0.4 + - - -
355C GLY* 3.2 39.9 + - - +
356C ARG* 3.8 37.6 - - - +
374C ILE* 3.8 19.4 + - + -
375C ILE* 3.4 8.5 - - - +
376C SER* 3.8 27.2 - - - +
381C TYR* 1.3 72.0 - - - +
383C HIS* 1.3 64.0 + - - +
403C GLU* 3.4 26.5 + - - +
404C VAL 3.1 22.7 + - - -
588C ASP* 3.2 18.7 + - - +
591C MET* 3.1 30.5 - - - +
592C HIS* 4.0 7.3 + - - -
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Residues in contact with HIS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C LYS 3.7 0.2 - - - +
374C ILE* 3.2 5.7 - - - -
375C ILE 2.9 32.3 + - - +
377C ASN* 3.5 14.6 - - - -
381C TYR* 3.3 24.5 + - - +
382C ARG* 1.3 75.6 + - - +
384C ILE* 1.3 65.1 + - - +
385C CYS 3.7 0.5 + - - -
396C PHE* 4.1 13.5 - - + -
398C THR* 3.2 36.9 + - - +
399C LYS* 3.6 20.0 - - - -
400C GLY 3.0 15.9 + - - -
402C TRP* 2.8 49.4 + + - -
404C VAL* 4.1 5.3 - - - +
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Residues in contact with ILE 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 3.8 27.8 - - + -
373C LYS 3.5 4.5 - - - +
374C ILE* 4.3 2.2 - - + -
383C HIS* 1.3 75.8 - - - +
385C CYS* 1.3 61.6 + - - +
396C PHE* 3.4 5.5 - - - +
397C ILE* 3.0 47.4 + - + +
398C THR* 3.2 8.2 + - + +
404C VAL* 3.9 22.7 - - + -
407C ILE* 3.8 18.2 - - + -
415C LEU* 3.6 26.7 - - + -
417C TYR* 3.8 29.2 - - + -
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Residues in contact with CYS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 3.3 9.2 - - - -
373C LYS 2.8 27.6 + - - +
375C ILE* 3.7 18.2 - - + -
383C HIS 3.7 0.6 + - - -
384C ILE* 1.3 74.6 - - - +
386C TYR* 1.3 57.6 + - - +
387C PHE* 3.5 14.7 - - + -
394C CYS* 2.0 50.7 - - - -
395C THR 3.4 20.4 - - - -
396C PHE* 3.7 15.0 - - + -
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Residues in contact with TYR 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C THR* 4.8 3.6 - - + +
370C SER* 3.5 30.0 + - - -
371C PHE 4.0 2.5 - - - -
372C TYR* 3.4 44.4 + + + -
384C ILE 4.3 0.2 + - - -
385C CYS* 1.3 69.6 - - - +
387C PHE* 1.3 61.6 + - - +
388C GLN* 3.3 25.5 + - - +
393C ASP 4.8 0.3 - - - +
394C CYS* 3.2 6.0 - - - +
395C THR* 2.7 53.6 + - + +
397C ILE* 4.1 6.5 - - + +
436C LEU 6.0 0.9 - - - -
439C TYR* 3.1 21.1 - - - -
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Residues in contact with PHE 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C HIS* 3.7 31.4 - + + -
346C ILE 6.0 2.0 - - - -
370C SER* 3.2 24.8 + - - -
371C PHE* 2.8 52.8 + + + +
373C LYS* 3.5 26.9 - - + -
375C ILE* 3.9 13.5 - - + -
385C CYS* 3.5 30.5 - - + -
386C TYR* 1.3 77.5 - - - +
388C GLN* 1.3 63.1 + - - +
391C LYS 5.1 0.4 - - - -
392C LYS 4.5 9.0 - - - -
393C ASP 5.3 0.2 - - - -
394C CYS* 3.4 28.9 - - + +
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Residues in contact with GLN 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C HIS* 3.1 6.8 - - - -
369C ASN 3.8 4.1 - - - +
370C SER* 2.5 20.6 + - - -
386C TYR* 3.3 42.7 + - - +
387C PHE* 1.3 75.1 + - - +
389C ILE* 1.3 66.9 + - - +
390C ASP* 4.4 1.8 - - + +
391C LYS* 2.9 67.1 + - + +
393C ASP 5.0 2.6 + - - -
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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