Contacts of the strand formed by residues 382 - 388 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347D GLU* 5.6 1.4 + - - -
353D TRP 5.0 0.6 + - - -
355D GLY* 3.3 41.6 + - - +
356D ARG* 3.8 36.2 - - - +
360D SER* 6.0 0.2 + - - -
374D ILE* 3.8 21.4 + - + -
375D ILE* 3.5 13.4 - - - +
376D SER* 4.2 15.6 + - - +
381D TYR* 1.3 70.5 - - - +
383D HIS* 1.3 61.0 + - - +
403D GLU* 3.1 30.6 + - - +
404D VAL 3.0 23.0 + - - -
588D ASP* 2.9 34.4 + - - -
591D MET* 3.2 24.3 - - - +
592D HIS* 4.0 5.3 + - - -
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Residues in contact with HIS 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D ILE* 3.2 5.9 - - - -
375D ILE 3.0 32.0 + - - +
377D ASN* 3.3 16.6 - - - -
381D TYR* 3.3 23.8 + - - +
382D ARG* 1.3 74.1 + - - +
384D ILE* 1.3 66.4 + - - +
385D CYS 3.8 0.3 + - - -
396D PHE* 4.1 12.9 - - + -
398D THR* 3.1 32.6 + - - +
399D LYS* 3.4 26.2 + - - -
400D GLY 3.0 16.7 + - - -
402D TRP* 2.9 42.3 + + - -
404D VAL* 4.1 8.0 - - - +
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Residues in contact with ILE 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D TYR* 3.9 27.1 - - + -
373D LYS 3.6 4.7 - - - +
374D ILE* 4.4 8.1 - - + -
383D HIS* 1.3 75.6 - - - +
385D CYS* 1.3 61.8 + - - +
396D PHE* 3.3 6.6 - - - +
397D ILE* 2.9 50.8 + - + +
398D THR* 3.2 10.6 + - + +
404D VAL* 4.0 20.2 - - + -
407D ILE* 4.1 11.9 - - + -
415D LEU* 3.7 26.7 - - + -
417D TYR* 3.8 28.0 - - + -
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Residues in contact with CYS 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D TYR* 3.4 6.2 - - - -
373D LYS 2.8 31.9 + - - +
375D ILE* 3.8 6.7 - - + -
383D HIS 3.8 0.2 + - - -
384D ILE* 1.3 76.9 - - - +
386D TYR* 1.3 58.8 - - - +
387D PHE* 3.6 13.3 - - + -
394D CYS* 2.0 49.4 - - - -
395D THR 3.3 21.5 - - - -
396D PHE* 3.5 24.2 - - + -
397D ILE* 5.1 0.2 - - - -
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Residues in contact with TYR 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D THR* 4.8 2.9 - - - +
370D SER* 3.0 37.3 + - - -
371D PHE 3.5 7.9 - - - -
372D TYR* 3.6 40.4 + + + -
385D CYS* 1.3 70.7 - - - +
387D PHE* 1.3 63.3 + - - +
388D GLN* 3.6 25.4 + - - +
393D ASP 4.7 0.3 - - - +
394D CYS* 3.1 16.8 - - - +
395D THR* 2.7 34.3 + - - +
397D ILE* 4.2 6.9 - - + +
439D TYR* 3.3 21.3 - - - -
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Residues in contact with PHE 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D HIS* 3.8 28.0 - + + -
346D ILE 6.1 1.8 - - - -
370D SER* 3.1 23.0 - - - -
371D PHE* 2.9 56.2 + + + +
373D LYS* 4.1 17.7 - - + -
375D ILE* 3.8 18.8 - - + -
385D CYS* 3.6 30.1 - - + -
386D TYR* 1.3 75.7 - - - +
388D GLN* 1.3 63.7 + - - +
391D LYS 5.3 0.7 - - - -
392D LYS 4.3 12.6 - - - -
393D ASP 5.2 0.7 - - - -
394D CYS* 3.4 29.8 - - + +
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Residues in contact with GLN 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D HIS* 3.1 9.2 + - - -
369D ASN 4.1 4.6 + - - +
370D SER* 3.8 9.1 - - - -
386D TYR* 3.6 37.4 + - - +
387D PHE* 1.3 77.8 - - - +
389D ILE* 1.3 68.8 + - - +
390D ASP* 3.0 3.5 + - + +
391D LYS* 3.0 56.0 + - + +
393D ASP 5.0 4.2 + - - +
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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