Contacts of the strand formed by residues 560 - 566 (chain A) in PDB entry 2FY2
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 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A PHE* 4.0 24.7 - + - -
428A LEU* 3.9 5.0 - - - +
429A HIS* 2.9 35.6 + + - -
535A PHE 4.9 0.3 - - - +
536A VAL 2.8 10.1 + - - +
537A LEU* 4.3 12.8 - - + -
538A SER* 3.3 24.9 + - - +
554A PRO* 3.7 13.2 - - - +
555A VAL 4.6 0.3 + - - -
559A GLY* 1.3 76.9 - - - -
561A GLY* 1.3 61.7 + - - +
562A ALA 4.1 0.7 - - - -
575A ILE* 4.0 15.3 - - + -
576A SER 3.1 7.4 - - - -
577A SER* 3.6 15.3 - - - -
584A THR* 3.3 11.5 - - + -
585A SER 2.9 50.4 + - - -
586A SER 4.1 0.4 - - - -
589A PHE* 3.5 25.6 - + + -
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Residues in contact with GLY 561 (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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538A SER 3.7 3.8 - - - -
552A TYR* 4.2 11.6 - - - +
553A GLY 4.2 8.7 - - - -
560A TYR* 1.3 75.4 - - - +
562A ALA* 1.3 59.6 + - - -
563A CYS 4.1 0.4 - - - -
574A CYS 3.1 3.0 - - - +
575A ILE* 3.0 8.8 - - - +
576A SER* 2.7 51.8 + - - -
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Residues in contact with ALA 562 (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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421A LEU* 4.5 19.1 - - + -
537A LEU* 4.2 10.3 - - + -
538A SER 3.0 10.1 + - - +
539A THR* 3.1 30.6 - - + -
540A SER 3.1 4.7 + - - +
552A TYR* 3.1 13.6 + - - -
560A TYR* 4.1 1.1 - - + -
561A GLY* 1.3 73.7 - - - +
563A CYS* 1.3 59.8 + - - +
564A TYR* 4.1 3.3 + - + -
573A PHE* 5.8 3.1 - - + -
574A CYS 3.4 3.8 - - - -
575A ILE* 4.7 4.7 - - + +
589A PHE* 4.6 10.5 - - + -
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Residues in contact with CYS 563 (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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540A SER* 3.3 11.2 - - - -
542A VAL* 3.5 36.3 - - - -
550A CYS* 3.3 30.4 - - - +
551A CYS* 4.3 4.3 - - - -
552A TYR* 3.5 23.1 - - + +
561A GLY 4.1 0.4 - - - -
562A ALA* 1.3 73.9 - - - +
564A TYR* 1.3 61.5 + - - +
572A LEU 3.9 0.3 - - - +
573A PHE* 3.8 1.5 - - - -
574A CYS* 2.9 40.6 + - + +
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Residues in contact with TYR 564 (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 ASP* 2.7 24.2 + - - -
417A ILE* 3.7 41.7 - - + -
418A GLN* 2.8 33.9 + - - +
421A LEU* 3.9 16.2 - - + -
437A GLU* 3.3 2.4 + - - -
540A SER 3.1 17.4 + - - -
541A GLN* 3.3 35.5 + - + +
542A VAL* 2.9 25.9 + - - +
562A ALA 4.2 6.5 - - - -
563A CYS* 1.3 77.7 - - - +
565A ASN* 1.3 62.4 + - - +
566A PRO* 4.2 2.5 - - + -
571A ILE* 4.2 3.1 - - + -
572A LEU 3.0 11.2 - - - +
573A PHE* 3.7 20.4 - + + -
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Residues in contact with ASN 565 (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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542A VAL 3.5 19.8 + - - +
543A PRO* 3.5 2.1 - - - +
544A THR* 2.7 37.3 + - - +
548A MET 3.4 12.7 + - - -
549A PHE* 4.5 5.8 - - + +
550A CYS 6.0 0.7 - - - +
564A TYR* 1.3 74.6 - - - +
566A PRO* 1.3 63.6 - - - +
567A GLN* 3.0 28.1 + - - +
571A ILE* 3.6 1.1 - - - -
572A LEU* 2.9 46.5 + - + +
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Residues in contact with PRO 566 (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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403A LYS* 3.4 31.1 + - + +
413A PRO* 5.1 5.2 - - + -
417A ILE* 3.9 23.3 - - + -
541A GLN* 3.6 39.5 - - + +
543A PRO* 4.3 10.2 - - + +
564A TYR* 3.9 4.0 - - + +
565A ASN* 1.3 93.8 - - - +
567A GLN* 1.3 63.6 + - - +
570A THR 3.8 4.0 - - - +
571A ILE* 4.0 8.5 - - + -
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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