Contacts of the strand formed by residues 571 - 578 (chain A) in PDB entry 4Y5U
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LEU* 3.9 6.7 - - + -
529A LEU* 4.0 12.6 - - + -
538A ILE* 4.2 17.5 - - + -
561A LEU* 3.7 36.6 - - + -
562A ARG 3.5 15.5 - - - +
563A PHE* 3.8 23.1 - - + -
570A GLY* 1.3 70.8 - - - -
572A THR* 1.3 61.8 + - - +
591A PRO* 3.9 0.2 - - - -
592A PHE* 2.7 56.4 + - + +
597A LEU* 4.2 22.7 - - + -
602A LEU* 4.2 8.7 - - + -
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Residues in contact with THR 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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560A LEU 3.8 0.2 - - - +
561A LEU* 3.5 8.0 - - - +
562A ARG* 2.9 65.7 + - + +
564A SER* 4.2 12.8 - - - +
571A ILE* 1.3 76.0 - - - +
573A ILE* 1.3 68.6 + - - +
574A ALA 4.0 0.3 + - - -
588A ASN* 4.6 1.9 + - - +
589A ILE 2.5 29.0 + - - -
590A GLN 4.5 1.3 - - - -
591A PRO* 3.8 10.8 - - - -
592A PHE* 5.2 0.4 - - - -
602A LEU* 6.3 0.2 - - - -
641B PTR 3.8 14.1 - - - +
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Residues in contact with ILE 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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559A PHE* 4.1 20.0 - - + -
560A LEU 3.5 7.6 - - - +
561A LEU* 3.8 15.3 - - + -
572A THR* 1.3 82.2 + - - +
574A ALA* 1.3 70.7 + - - +
575A HIS* 4.6 0.2 - - + -
588A ASN* 3.5 1.0 - - - -
589A ILE* 2.9 57.3 + - + +
590A GLN 5.0 0.6 + - - -
592A PHE* 4.1 29.6 - - + -
602A LEU* 5.0 0.4 - - + -
605A ARG* 5.8 0.4 - - + -
606A ILE* 4.4 19.3 - - + +
609A LEU* 4.7 6.3 - - + -
612A LEU* 4.3 17.3 - - + -
648A MET* 5.0 1.8 - - + -
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Residues in contact with ALA 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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547A VAL* 3.6 23.8 - - + -
551A LEU* 3.9 2.5 - - + -
559A PHE* 3.3 2.6 - - - +
560A LEU* 3.0 42.4 + - + -
562A ARG* 4.8 5.4 - - - -
572A THR 4.0 0.8 + - - -
573A ILE* 1.3 73.7 - - - +
575A HIS* 1.3 66.3 + - - +
586A ILE* 4.9 1.1 - - + -
587A GLU 3.5 5.6 - - - -
588A ASN* 3.3 23.3 - - - +
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Residues in contact with HIS 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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551A LEU* 3.8 8.2 - - - +
557A GLY* 5.3 1.6 - - - -
558A THR 3.4 14.1 - - - +
559A PHE* 3.5 11.7 - - + -
573A ILE* 4.6 0.7 - - + -
574A ALA* 1.3 79.3 - - - +
576A VAL* 1.3 67.6 + - - +
577A ILE* 4.0 10.0 + - + +
585A GLN 3.8 0.3 - - - +
586A ILE* 3.4 5.6 - - - +
587A GLU* 2.6 88.0 + - + +
589A ILE* 3.9 21.5 - - + +
611A GLN* 3.8 27.7 + - + +
612A LEU* 3.7 16.8 - - + +
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Residues in contact with VAL 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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551A LEU* 3.5 31.6 - - + +
554A GLU* 4.0 11.9 - - + +
555A PRO 3.2 23.8 - - - +
556A ASP* 3.8 0.6 - - - -
557A GLY* 2.9 28.6 + - - -
558A THR* 2.9 26.0 + - - +
575A HIS* 1.3 76.0 + - - +
577A ILE* 1.3 67.7 + - - +
578A ARG* 4.4 9.4 - - + +
584A PRO* 4.4 12.6 - - + -
585A GLN 3.8 5.2 - - - +
586A ILE* 3.7 13.7 - - + -
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Residues in contact with ILE 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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556A ASP* 3.2 14.6 - - - +
575A HIS* 4.1 20.0 - - + +
576A VAL* 1.3 77.4 - - - +
578A ARG* 1.3 65.4 + - - +
579A GLY* 4.4 2.6 + - - +
583A SER 3.8 2.1 - - - +
584A PRO* 3.7 1.0 - - - +
585A GLN* 3.1 46.8 + - + +
587A GLU* 4.6 10.5 - - + +
611A GLN* 3.5 26.0 - - - +
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Residues in contact with ARG 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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552A LEU 3.1 22.8 + - - -
553A ASN* 3.8 5.7 + - - +
554A GLU 2.6 31.1 + - - -
555A PRO* 5.1 3.2 - - - +
556A ASP* 2.5 36.0 + - + +
576A VAL* 4.2 4.7 - - + +
577A ILE* 1.3 76.4 - - - +
579A GLY* 1.3 64.4 + - - +
582A GLY* 3.6 32.9 + - - -
583A SER 3.8 7.6 - - - -
584A PRO* 3.3 33.1 - - + +
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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