Contacts of the strand formed by residues 424 - 429 (chain A) in PDB entry 3WSZ
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 TYR 424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ASP* 2.3 37.2 + - + -
355A SER* 5.6 1.9 - - - -
360A PHE* 3.9 24.3 - + - -
414A PHE* 3.3 38.1 - + + -
415A HIS 3.3 6.1 - - - +
416A ARG* 3.6 40.5 + - + -
417A VAL* 4.6 1.3 - - - +
422A GLY* 3.7 27.8 - - - -
423A VAL* 1.3 78.0 - - - +
425A ILE* 1.3 70.3 + - - +
441A VAL 4.1 0.2 - - - +
442A ILE* 3.3 2.6 - - - +
443A THR* 3.2 40.8 + - + +
446A LYS* 4.0 18.1 - - + +
450A TRP* 4.6 0.9 - - - -
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Residues in contact with ILE 425 (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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414A PHE* 4.6 0.9 - - - -
415A HIS* 2.7 42.9 + - + +
417A VAL* 4.8 7.9 - - + -
424A TYR* 1.3 81.9 - - - +
426A ALA* 1.3 63.9 + - - +
440A SER* 5.0 5.6 - - - +
441A VAL 3.5 7.4 - - - +
442A ILE* 3.7 28.7 - - + -
453A LEU* 4.6 7.6 - - + -
477A LEU* 4.1 24.2 - - + -
479A GLN* 3.1 10.9 + - - +
494A ILE* 3.7 27.1 - - + -
504A ILE* 4.6 16.2 - - + -
530A TRP* 4.4 10.5 - - + -
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Residues in contact with ALA 426 (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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372A LEU* 6.2 0.2 - - + -
386A LEU* 4.7 4.3 - - + -
389A VAL* 4.3 12.8 - - + -
413A ASP 3.3 12.6 - - - +
414A PHE* 3.7 20.9 - - + -
425A ILE* 1.3 73.2 - - - +
427A THR* 1.3 64.8 + - - +
440A SER* 3.5 5.4 - - - -
441A VAL* 3.0 37.6 + - + +
450A TRP* 4.1 17.1 - - + -
479A GLN* 4.2 2.5 - - - +
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Residues in contact with THR 427 (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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389A VAL* 3.6 6.6 - - - +
390A LEU* 2.7 54.0 + - + +
413A ASP* 3.1 33.5 + - - +
426A ALA* 1.3 76.9 + - - +
428A LEU* 1.3 66.0 + - - +
438A MET* 4.1 14.6 - - + -
439A ARG 3.4 11.7 - - - +
440A SER* 4.2 2.4 + - - -
477A LEU 4.0 15.8 + - - +
479A GLN* 4.1 5.7 + - - +
482A SER* 4.9 3.4 + - - -
514A LEU* 4.9 4.5 - - + -
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Residues in contact with LEU 428 (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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386A LEU* 3.7 31.0 - - + -
387A GLU 3.2 18.2 - - - +
388A ASN* 3.2 20.0 - - + +
389A VAL* 3.9 5.6 - - + -
426A ALA* 5.9 0.2 - - + -
427A THR* 1.3 75.7 - - - +
429A ILE* 1.3 60.7 + - - +
437A ASN 3.5 1.0 - - - +
438A MET* 3.4 6.6 - - - -
439A ARG* 2.7 43.9 + - + +
441A VAL* 3.6 38.6 - - + -
452A PHE* 5.4 5.6 - - + -
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Residues in contact with ILE 429 (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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388A ASN* 3.1 39.7 + - - +
389A VAL 4.5 2.5 - - - +
390A LEU* 4.0 36.8 - - + +
428A LEU* 1.3 74.9 - - - +
430A ASN* 1.3 63.3 + - - +
431A GLY 4.0 17.0 - - - +
437A ASN* 3.2 43.3 - - + +
438A MET* 3.7 21.1 - - + -
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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