Contacts of the strand formed by residues 341 - 347 (chain A) in PDB entry 4Y05
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 LYS 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A THR* 3.8 2.8 - - - +
339A GLY 4.7 7.3 + - - -
340A GLY* 1.3 80.6 + - - +
342A ALA* 1.3 62.0 + - - +
484A MET* 4.5 24.1 - - - +
485A HIS 5.1 1.4 + - - -
486A GLY* 4.9 2.8 - - - -
487A LYS* 3.5 19.3 - - + +
550A ASP* 3.2 42.4 - - - +
551A SER* 4.0 18.2 - - - +
553A ILE 5.2 0.4 - - - +
556A ASN* 3.3 7.9 + - - +
557A SER* 3.3 19.9 - - - +
558A ARG 3.0 25.2 + - - +
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Residues in contact with ALA 342 (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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332A LEU* 3.8 35.9 - - + +
335A THR* 4.5 4.3 - - + -
336A ILE* 3.9 5.4 - - + +
341A LYS* 1.3 76.3 - - - +
343A THR* 1.3 65.7 + - - +
487A LYS 2.9 7.3 + - - +
488A PHE* 3.3 22.8 - - + -
489A SER* 2.9 22.9 + - - -
551A SER* 4.5 2.0 + - - -
558A ARG 3.3 6.7 - - - +
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Residues in contact with THR 343 (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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332A LEU* 3.5 5.9 - - - +
342A ALA* 1.3 78.7 - - - +
344A CYS* 1.3 61.6 + - - +
345A PHE* 3.5 23.6 - - + -
488A PHE* 3.8 2.9 - - - -
489A SER* 3.2 19.7 - - - +
548A LEU* 4.8 6.3 - - + -
551A SER* 3.5 31.5 + - - +
552A PHE* 4.7 6.4 - - + -
558A ARG 3.1 5.5 + - - -
559A THR* 2.7 32.5 + - - -
560A CYS 2.9 24.1 + - - -
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Residues in contact with CYS 344 (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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329A ALA* 4.2 18.6 - - - -
343A THR* 1.3 76.1 - - - +
345A PHE* 1.3 59.4 + - - +
358A MET* 4.2 14.4 - - - +
373A ILE* 4.7 0.9 - - - -
488A PHE* 3.8 20.6 - - + -
489A SER 2.9 6.7 + - - +
490A LEU* 3.3 9.2 - - + -
491A VAL* 2.8 32.6 + - - +
560A CYS* 3.3 17.9 - - + -
562A ILE* 4.0 26.5 - - - -
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Residues in contact with PHE 345 (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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343A THR* 3.5 22.0 - - - -
344A CYS* 1.3 75.9 - - - +
346A ALA* 1.3 56.8 + - - +
358A MET* 4.9 1.1 - - - -
491A VAL* 3.3 31.9 - - + -
493A LEU* 4.0 15.7 - - + -
523A LEU* 3.6 39.0 - - + -
527A ILE* 4.3 13.9 - - + -
544A LEU* 4.9 1.6 - - + -
548A LEU* 3.8 26.9 - - + -
552A PHE* 4.2 6.3 - + - -
559A THR* 3.5 20.2 - - - -
560A CYS 3.0 16.5 + - - +
561A MET* 3.4 12.1 - - + +
562A ILE* 2.8 34.3 + - - +
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Residues in contact with ALA 346 (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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345A PHE* 1.3 73.0 - - - +
347A TYR* 1.3 57.1 + - - +
354A LYS* 3.6 29.1 - - + +
357A THR* 5.0 2.7 - - - -
358A MET* 3.8 30.7 - - + -
491A VAL 2.9 7.9 + - - +
492A ASP* 4.6 0.9 - - - -
493A LEU* 3.2 29.4 + - - +
562A ILE* 3.4 10.8 - - + +
564A THR* 4.9 4.5 - - + -
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Residues in contact with TYR 347 (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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346A ALA* 1.3 73.7 - - - +
348A GLY* 1.3 59.8 + - - +
354A LYS* 3.9 3.1 - - - +
493A LEU* 3.8 23.3 - - + -
494A ALA 5.6 0.7 - - - -
496A ASN* 3.0 35.4 + - + +
520A LEU* 3.9 26.9 - - + +
561A MET* 4.0 18.2 - - + -
562A ILE 3.0 7.8 + - - +
563A ALA* 3.2 11.0 - - + -
564A THR* 2.8 30.8 + - - -
577A ASN 4.7 0.5 + - - -
578A THR* 3.9 20.9 - - + -
581A TYR* 3.1 63.4 - + - +
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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