Contacts of the strand formed by residues 571 - 578 (chain A) in PDB entry 2FY5
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 ILE 571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A LYS* 4.7 1.1 - - - -
398A PHE* 2.9 48.9 + - + +
401A TYR* 3.8 12.1 - - + +
402A GLY* 4.1 4.7 - - - -
406A ILE* 4.4 15.9 - - + -
417A ILE* 4.1 33.9 - - + -
564A TYR* 4.5 4.0 - - + -
565A ASN 3.7 3.8 - - - +
566A PRO* 4.3 11.7 - - + -
570A THR* 1.3 81.6 - - - +
572A LEU* 1.3 66.6 + - - +
573A PHE* 3.4 31.4 - - + -
597A LEU* 4.3 13.0 - - + -
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Residues in contact with LEU 572 (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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282A ASP* 5.5 3.6 - - - +
395A VAL* 3.8 21.8 - - + -
396A TYR 3.5 7.0 - - - +
397A LYS* 3.5 31.8 - - + +
548A MET 5.3 1.3 - - - +
549A PHE* 3.5 42.4 - - + -
563A CYS 3.7 0.9 - - - +
564A TYR* 3.0 8.8 - - - +
565A ASN* 2.9 48.0 + - + +
570A THR* 4.3 1.8 + - - +
571A ILE* 1.3 72.3 - - - +
573A PHE* 1.3 61.5 + - - +
574A CYS* 4.7 4.0 - - - -
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Residues in contact with PHE 573 (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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394A ILE 3.7 1.4 - - - +
395A VAL* 3.6 2.3 - - - +
396A TYR* 2.5 57.6 + + + +
398A PHE* 4.3 2.2 - - + -
417A ILE* 3.8 25.8 - - + -
420A ALA* 5.5 1.1 - - + -
421A LEU* 3.9 24.7 - - + -
562A ALA* 5.6 3.6 - - + -
563A CYS 3.9 0.7 - - - -
564A TYR* 3.9 15.5 - + + -
571A ILE* 3.4 37.5 - - + -
572A LEU* 1.3 72.8 - - - +
574A CYS* 1.3 61.7 + - - +
575A ILE* 3.8 19.9 + - + +
593A VAL* 3.6 31.0 - - + -
597A LEU* 3.8 19.7 - - + -
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Residues in contact with CYS 574 (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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393A PHE* 4.1 9.2 - - + -
394A ILE 3.7 4.3 - - - -
395A VAL* 4.5 9.9 - - - -
549A PHE* 3.7 31.0 - - - -
550A CYS 3.3 24.9 - - - +
551A CYS* 3.8 17.2 - - + -
552A TYR 5.7 0.3 + - - +
561A GLY 3.2 5.9 - - - +
562A ALA* 3.3 1.7 - - - -
563A CYS* 2.8 42.3 + - + +
572A LEU* 4.7 4.0 - - - -
573A PHE* 1.3 75.5 - - - +
575A ILE* 1.3 58.7 + - - +
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Residues in contact with ILE 575 (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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393A PHE* 3.5 6.2 - - - -
394A ILE* 3.0 41.3 + - + +
396A TYR* 5.0 0.9 - - + -
560A TYR* 4.2 9.0 - - + -
561A GLY 3.2 5.8 - - - +
562A ALA* 4.6 6.7 - - + -
573A PHE* 4.1 24.0 - - + +
574A CYS* 1.3 77.6 - - - +
576A SER* 1.3 63.0 + - - +
586A SER* 3.7 23.5 + - - +
589A PHE* 3.6 39.5 - - + -
590A ALA* 3.7 29.2 - - + -
593A VAL* 4.5 5.6 - - + -
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Residues in contact with SER 576 (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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391A LEU* 4.2 6.5 - - - -
392A ASP 3.4 6.1 - - - -
393A PHE* 3.8 14.4 - - - -
552A TYR 2.8 27.6 + - - -
553A GLY* 3.3 7.7 - - - -
554A PRO* 3.3 16.5 - - - +
560A TYR* 3.1 9.5 - - - +
561A GLY* 2.7 40.7 + - - -
575A ILE* 1.3 75.7 - - - +
577A SER* 1.3 61.2 + - - +
586A SER* 3.6 2.2 - - - -
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Residues in contact with SER 577 (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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390A ASN 3.9 0.7 - - - +
391A LEU* 3.9 3.1 - - - +
392A ASP* 2.9 40.3 + - - +
554A PRO* 3.4 11.6 - - - +
559A GLY 3.6 4.3 - - - -
560A TYR* 3.6 17.9 - - - -
576A SER* 1.3 77.1 - - - +
578A PHE* 1.3 68.4 + - - +
584A THR* 3.6 17.8 + - - -
585A SER 4.1 1.2 + - - -
586A SER* 2.8 24.2 + - - -
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Residues in contact with PHE 578 (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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94A VAL* 4.2 18.4 - - + -
95A ASN* 4.0 20.2 - - - -
387A ILE* 5.9 2.9 - - + -
390A ASN* 3.3 37.5 - - + +
391A LEU* 4.7 2.5 - - + -
392A ASP* 4.6 2.2 - - - -
554A PRO* 3.5 36.3 - - + -
556A VAL 3.7 21.3 - - - -
557A PRO* 3.6 30.7 + - + +
559A GLY 4.5 1.8 + - - -
577A SER* 1.3 79.6 + - - +
579A HIS* 1.3 62.0 + - - +
580A SER* 3.0 8.8 + - - +
581A CYS* 3.1 12.3 + - - +
584A THR* 3.4 16.4 + - - +
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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