Contacts of the strand formed by residues 569 - 580 (chain A) in PDB entry 4YZ9
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 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A ILE* 4.1 0.2 - - - -
566A VAL* 3.4 10.5 + - + -
567A GLY* 2.9 25.3 + - - +
568A LYS* 1.3 77.3 - - - +
570A SER* 1.3 67.5 + - - +
571A PHE* 5.0 2.9 - - + -
590A MET 3.7 4.7 - - - +
591A PHE* 4.0 18.2 - - + -
598A VAL* 3.9 35.2 - - + -
630A CYS* 3.8 20.0 - - - +
631A THR* 3.9 1.3 - - - -
632A GLU* 3.8 26.8 - - + +
639A TYR* 3.3 32.1 - - + +
641A ALA* 4.0 13.2 - - + +
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Residues in contact with SER 570 (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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563A VAL* 4.6 7.7 - - - +
564A VAL 3.2 14.4 - - - -
565A ILE* 4.1 18.4 - - - -
566A VAL 4.8 0.2 - - - +
567A GLY 5.1 0.4 - - - -
568A LYS 5.0 1.6 + - - -
569A ILE* 1.3 77.7 - - - +
571A PHE* 1.3 65.5 + - - +
589A GLY* 3.1 1.7 - - - -
590A MET* 2.8 49.4 + - - +
598A VAL* 3.9 3.6 - - - +
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Residues in contact with PHE 571 (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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563A VAL* 3.4 8.8 - - - +
564A VAL* 2.8 70.8 + - + +
566A VAL* 4.4 3.4 - - + -
569A ILE* 5.0 2.2 - - + -
570A SER* 1.3 80.4 - - - +
572A CYS* 1.3 61.2 + - - +
573A PRO* 4.1 15.9 - - + -
587A TYR* 3.6 38.1 - + + -
588A ARG 3.3 15.0 - - - +
589A GLY* 3.6 2.5 - - - -
598A VAL* 3.9 29.2 - - + -
600A ARG* 5.6 2.2 - - - -
639A TYR* 3.6 32.5 - + - -
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Residues in contact with CYS 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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562A SER 3.5 22.4 - - - +
563A VAL* 5.2 1.8 - - + -
571A PHE* 1.3 76.4 - - - +
573A PRO* 1.3 67.3 - - - +
574A LYS* 3.6 14.8 - - - -
575A ASP* 3.1 46.4 + - + +
587A TYR* 3.5 5.5 - - - +
588A ARG* 2.9 16.7 + - + +
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Residues in contact with PRO 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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562A SER* 3.9 25.4 - - - +
563A VAL 4.8 0.4 - - - -
564A VAL* 3.3 34.3 - - + -
571A PHE* 3.9 9.9 - - + +
572A CYS* 1.3 83.3 - - - +
574A LYS* 1.3 62.8 + - + +
575A ASP 3.3 1.4 + - - -
576A VAL* 4.7 1.7 + - - +
587A TYR* 3.6 27.4 - - + -
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Residues in contact with LYS 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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562A SER* 3.4 41.6 - - - +
572A CYS* 3.3 9.7 - - - -
573A PRO* 1.3 77.8 - - + +
575A ASP* 1.3 57.0 + - - +
576A VAL* 3.9 6.1 + - - +
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Residues in contact with ASP 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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572A CYS* 3.1 35.1 + - + +
573A PRO 3.2 0.8 - - - -
574A LYS* 1.3 76.9 - - - +
576A VAL* 1.3 64.2 + - - +
577A LEU* 3.8 10.7 - - - +
587A TYR* 3.3 19.1 - - - +
588A ARG* 3.3 38.7 + - + -
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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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573A PRO 5.1 1.8 - - - +
574A LYS 3.9 5.1 + - - +
575A ASP* 1.3 77.9 + - - +
577A LEU* 1.3 64.2 + - - +
578A GLY 3.9 4.7 - - - +
579A HIS* 3.2 34.1 - - + +
585A ILE* 3.6 20.2 - - + -
586A VAL 3.4 11.9 - - - +
587A TYR* 4.2 10.3 - - + -
715A CYS* 3.7 11.8 - - - +
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Residues in contact with LEU 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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575A ASP* 3.8 15.7 + - - +
576A VAL* 1.3 74.6 - - - +
578A GLY* 1.3 56.8 + - - +
586A VAL* 2.6 24.4 + - + +
588A ARG* 3.7 49.6 - - + +
597A ALA* 3.9 15.5 - - + -
644A LEU* 3.3 34.5 - - + -
713A GLY 4.3 0.7 - - - -
714A LEU* 3.3 22.3 - - + +
715A CYS* 3.1 28.9 + - - +
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Residues in contact with GLY 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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576A VAL* 3.5 2.4 - - - +
577A LEU* 1.3 81.4 - - - +
579A HIS* 1.3 73.1 + - - -
580A GLY 4.2 0.7 - - - -
585A ILE* 3.7 1.0 - - - -
586A VAL* 2.9 38.7 + - - +
712A PHE* 4.5 0.7 - - - -
713A GLY 3.0 18.2 - - - -
714A LEU 4.7 0.7 - - - -
715A CYS* 4.2 3.6 - - - -
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Residues in contact with HIS 579 (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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576A VAL* 3.2 33.9 - - + +
578A GLY* 1.3 73.3 - - - -
580A GLY* 1.3 57.8 + - - +
584A THR 3.7 12.1 - - - +
585A ILE* 4.1 15.9 - - + -
690A LYS* 5.7 2.6 + - - -
712A PHE* 4.9 1.1 - - - -
713A GLY* 3.9 6.8 + - - -
715A CYS* 3.9 25.9 - - - -
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Residues in contact with GLY 580 (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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578A GLY 4.4 0.2 + - - -
579A HIS* 1.3 74.1 - - - +
581A ALA* 1.3 72.8 + - - +
582A GLU 4.0 0.2 - - - -
583A GLY* 4.0 1.7 + - - -
584A THR* 3.1 27.3 + - - +
688A ASP* 4.5 4.0 - - - -
690A LYS* 6.1 2.0 - - - -
693A ASN* 5.5 0.7 - - - -
711A ASP* 4.3 13.0 - - - -
712A PHE* 4.2 14.8 - - - +
713A GLY 5.3 0.2 - - - -
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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