Contacts of the strand formed by residues 384 - 389 (chain A) in PDB entry 2QY0
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 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A TYR* 3.6 5.3 - - - +
373A THR* 2.9 59.1 + - - +
374A THR* 3.5 17.2 + - - +
382A LYS 4.0 8.3 - - - +
383A ALA* 1.3 77.7 - - - +
385A ILE* 1.3 64.6 + - - +
386A GLN* 6.1 0.6 - - - +
409A VAL* 3.9 33.9 - - - +
410A TYR 3.5 3.6 - - - +
411A THR* 3.5 25.4 - - + -
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Residues in contact with ILE 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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362A PRO* 3.4 32.5 - - + -
370A PHE* 3.8 20.9 - - + -
371A ARG 3.4 7.2 - - - +
372A TYR* 3.6 37.9 - - + -
373A THR* 4.7 4.0 + - - -
384A ARG* 1.3 74.8 + - - +
386A GLN* 1.3 60.7 + - - +
387A TYR* 3.8 24.0 - - + +
409A VAL* 3.6 6.4 - - - +
410A TYR* 2.8 48.2 + - + +
418A TRP* 4.0 19.5 - - + -
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.2 3.6 - - - -
371A ARG* 2.8 62.3 + - + +
373A THR* 4.6 10.3 + - - +
384A ARG* 6.1 0.4 - - - +
385A ILE* 1.3 73.7 - - - +
387A TYR* 1.3 74.3 + - - +
388A TYR* 3.9 4.2 + - + -
406A GLU* 5.8 0.6 - - - +
407A GLN* 4.6 10.3 - - - +
408A GLY 3.4 15.4 - - - +
409A VAL* 4.5 18.0 - - + +
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Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PRO* 3.5 6.6 - - + +
363A ARG* 2.7 41.5 + - - -
364A ASN 4.9 0.2 - - - -
365A LEU* 3.4 37.5 - - + -
369A ASP 3.3 13.2 - - - -
370A PHE* 3.8 17.0 - + + -
385A ILE* 3.8 19.7 - - + -
386A GLN* 1.3 86.4 + - - +
388A TYR* 1.3 59.8 + - - +
396A MET* 3.7 11.0 - - + +
407A GLN* 5.8 0.9 + - - -
408A GLY* 2.9 15.0 + - - +
410A TYR* 3.5 38.8 - + - -
418A TRP* 5.9 1.9 - - + +
427A ILE* 4.0 15.0 - - + +
428A PRO* 3.8 18.2 - - + -
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Residues in contact with TYR 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 3.8 2.7 - - - +
368A GLY* 3.1 2.9 - - - -
369A ASP* 2.8 64.4 + - + +
370A PHE 3.8 21.5 + - - -
371A ARG* 3.2 47.7 + - + +
386A GLN* 3.9 6.5 - - + -
387A TYR* 1.3 74.0 - - - +
389A CYS* 1.3 75.8 - - - +
390A HIS* 4.8 10.5 - + - -
396A MET* 3.9 7.2 - - - -
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Residues in contact with CYS 389 (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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367A ASN 3.7 1.8 - - - +
388A TYR* 1.3 92.0 - - - +
390A HIS* 1.3 60.7 + - - +
391A GLU* 2.9 20.2 + - + +
394A TYR* 4.1 17.0 - - + +
395A LYS* 4.5 0.2 - - - -
396A MET* 3.7 35.9 - - - +
429A ARG 4.3 0.7 - - - -
430A CYS* 2.1 57.4 - - + -
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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