Contacts of the strand formed by residues 468 - 481 (chain A) in PDB entry 5IZL
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 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A PHE 3.9 18.2 + - - +
370A SER* 4.1 14.8 + - - +
371A GLN 3.5 26.6 + - - +
372A GLU* 3.4 23.6 + - + +
373A TYR* 2.7 35.6 + - - +
465A PRO 5.6 0.7 - - - +
466A ARG 3.6 10.0 + - - +
467A LEU* 1.3 72.1 - - - +
469A VAL* 1.3 56.7 + - - +
470A TYR* 3.9 1.4 + - - -
582A LYS* 4.6 10.1 - - + +
585A VAL* 4.5 15.7 - - + -
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Residues in contact with VAL 469 (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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349A MET* 3.7 27.1 - - + -
351A PHE* 3.9 21.1 - - + -
373A TYR* 3.4 24.7 - - + +
375A PHE* 4.0 25.4 - - + -
467A LEU* 2.9 23.5 + - + +
468A LYS* 1.3 71.4 - - - +
470A TYR* 1.3 55.2 + - - +
582A LYS* 3.3 5.6 - - - +
583A ARG* 2.7 43.1 + - + +
584A TYR* 4.4 6.6 + - + -
585A VAL 5.2 0.2 + - - -
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Residues in contact with TYR 470 (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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354A ALA* 4.6 4.0 - - + +
355A PRO* 3.9 24.9 - - - +
372A GLU* 3.5 38.6 - - + -
373A TYR 3.2 16.0 + - - -
374A LEU* 3.5 24.5 - - + +
375A PHE* 3.1 23.6 + - - -
468A LYS 4.4 0.7 - - - -
469A VAL* 1.3 73.0 - - - +
471A LYS* 1.3 66.1 + - - +
472A LEU* 4.4 9.3 - - + +
580A THR* 3.8 30.1 - - + -
581A PHE 3.3 10.8 - - - +
582A LYS* 3.6 26.2 - - + +
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Residues in contact with LYS 471 (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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374A LEU* 5.3 0.2 - - - -
375A PHE* 4.0 25.9 - - + +
469A VAL* 4.4 0.6 + - - +
470A TYR* 1.3 75.5 - - - +
472A LEU* 1.3 60.5 + - - +
473A LYS* 3.7 15.4 + - - -
580A THR* 3.4 4.9 - - - -
581A PHE* 2.6 54.9 + - + +
583A ARG* 4.9 2.4 - - + +
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Residues in contact with LEU 472 (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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355A PRO* 6.4 1.6 - - + -
374A LEU* 4.3 27.4 - - + +
470A TYR* 4.0 6.4 + - + +
471A LYS* 1.3 72.5 - - - +
473A LYS* 1.3 67.1 + - - +
474A HIS* 4.1 3.8 + - + +
578A SER* 6.4 1.6 - - - -
579A LEU 4.1 5.8 - - - +
580A THR* 3.6 27.4 - - + -
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Residues in contact with LYS 473 (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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471A LYS* 3.7 16.1 + - + +
472A LEU* 1.3 80.3 - - - +
474A HIS* 1.3 63.9 + - - +
475A LYS* 6.2 1.3 - - + -
577A LEU 4.4 0.4 - - - -
578A SER* 3.7 3.6 - - - -
579A LEU* 2.9 62.6 + - + +
581A PHE* 4.4 17.9 - - + -
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Residues in contact with HIS 474 (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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472A LEU* 4.1 5.1 + - + +
473A LYS* 1.3 78.3 - - - +
475A LYS* 1.3 60.7 + - - +
476A HIS* 3.5 28.8 + + - -
576A VAL* 3.2 27.0 - - + +
577A LEU 3.2 5.7 + - - -
578A SER* 3.1 24.1 + - - -
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Residues in contact with LYS 475 (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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473A LYS* 4.2 1.3 - - + -
474A HIS* 1.3 73.5 - - - +
476A HIS* 1.3 71.8 + - - +
493A LEU* 4.7 23.1 - - + +
576A VAL* 3.3 2.8 - - - +
577A LEU* 3.1 38.1 + - + +
579A LEU* 6.4 2.2 - - + -
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Residues in contact with HIS 476 (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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474A HIS* 3.5 38.5 + + - -
475A LYS* 1.3 83.1 + - - +
477A GLY* 1.3 59.3 + - - +
492A SER 3.9 2.1 - - - +
493A LEU* 3.3 18.9 - - - +
574A HIS* 6.4 0.7 - - + -
575A VAL 3.6 4.3 - - - +
576A VAL* 3.2 24.5 - - + +
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Residues in contact with GLY 477 (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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476A HIS* 1.3 75.3 - - - +
478A LEU* 1.3 57.8 + - - -
492A SER 3.7 6.5 - - - -
493A LEU* 3.5 18.8 - - - +
574A HIS* 3.4 10.4 - - - +
575A VAL* 2.9 42.3 + - - +
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Residues in contact with LEU 478 (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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477A GLY* 1.3 74.5 - - - -
479A VAL* 1.3 71.4 + - - +
490A GLY* 3.5 1.9 - - - -
491A ARG 2.9 34.8 + - - +
492A SER* 4.4 9.1 + - - -
572A SER* 6.1 5.8 - - - -
574A HIS* 4.6 6.1 - - - +
575A VAL* 4.2 5.3 - - - +
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Residues in contact with VAL 479 (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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478A LEU* 1.3 84.2 - - - +
480A GLU* 1.3 67.1 + - - +
481A ARG 3.6 17.7 - - - +
488A VAL* 3.7 21.1 - - + -
490A GLY* 3.6 7.4 - - - -
491A ARG 5.0 0.2 - - - -
510A LEU* 3.8 13.0 - - + -
572A SER* 4.4 17.7 + - - +
573A GLN* 3.6 25.0 + - + +
574A HIS* 5.0 0.2 - - - +
575A VAL* 3.6 22.0 - - + -
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Residues in contact with GLU 480 (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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479A VAL* 1.3 80.9 - - - +
481A ARG* 1.3 71.3 + - + +
489A ILE 3.2 13.4 + - - +
490A GLY* 3.7 4.8 - - - -
491A ARG* 5.4 3.6 - - + +
543A ILE 5.7 0.9 - - - +
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Residues in contact with ARG 481 (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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479A VAL* 3.6 12.6 - - - +
480A GLU* 1.3 87.3 - - + +
482A ALA* 1.3 68.6 - - - +
483A MET* 6.4 1.3 - - - +
488A VAL* 4.2 1.0 - - - +
489A ILE* 3.3 34.7 + - + +
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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