Contacts of the strand formed by residues 471 - 479 (chain A) in PDB entry 4Y05
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 HIS 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A GLU* 3.1 7.6 - - - +
404A ILE* 2.8 58.6 + - + +
470A SER* 1.3 73.2 - - - +
472A ALA* 1.3 60.6 + - - +
473A CYS* 4.2 0.7 - - + -
491A VAL* 4.5 11.4 - - + -
492A ASP 3.5 5.4 - - - +
493A LEU* 3.6 19.1 - - + +
494A ALA* 3.0 39.4 + - + -
516A ILE* 4.9 5.7 - - + +
519A SER* 2.8 34.8 + - - -
520A LEU* 4.4 10.3 - - + -
544A LEU* 4.1 17.9 - - + -
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Residues in contact with ALA 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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374A TYR* 3.9 9.1 + - - +
401A PHE* 4.2 19.3 - - + -
402A PHE 3.5 5.8 - - - +
403A GLU* 4.2 8.1 - - + +
412A LEU* 4.8 3.8 - - + -
456A ARG* 5.6 5.2 - - + -
470A SER* 4.1 0.4 + - - +
471A HIS* 1.3 73.7 - - - +
473A CYS* 1.3 59.0 + - - +
474A PHE 4.2 0.2 - - - -
490A LEU 3.8 1.0 - - - +
491A VAL* 3.3 6.7 - - - +
492A ASP* 2.9 44.2 + - + +
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Residues in contact with CYS 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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400A THR 4.0 0.3 - - - +
401A PHE* 3.3 5.8 - - - -
402A PHE* 2.8 72.7 + - + -
404A ILE* 5.6 1.8 - - + -
471A HIS* 5.7 0.7 - - + -
472A ALA* 1.3 72.2 - - - +
474A PHE* 1.3 61.7 + - - +
475A GLN* 3.8 20.2 - - - -
489A SER* 4.0 11.7 - - - -
490A LEU 3.5 2.7 - - - -
491A VAL* 3.8 23.3 - - + -
544A LEU* 5.5 5.2 - - + -
547A VAL* 5.5 0.2 - - - -
548A LEU* 4.2 7.4 - - - -
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Residues in contact with PHE 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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374A TYR* 3.6 45.1 - + + -
378A SER* 3.6 9.9 - - - -
399A VAL* 3.3 28.0 - - + -
400A THR 3.4 13.2 - - - -
401A PHE* 3.7 20.4 - + + -
445A VAL* 3.5 28.5 - - + -
448A MET* 5.7 0.7 - - + -
449A ILE* 4.1 15.7 - - + -
472A ALA 4.2 0.6 - - - -
473A CYS* 1.3 73.0 - - - +
475A GLN* 1.3 58.3 + - - +
476A ILE* 3.6 31.6 - - + -
489A SER* 3.6 0.7 - - - -
490A LEU* 2.7 42.8 + - + +
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Residues in contact with GLN 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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399A VAL* 3.3 12.6 - - - +
400A THR* 2.8 56.3 + - - +
402A PHE* 3.6 18.5 - - + -
434A LEU* 4.3 4.7 - - - +
473A CYS* 3.8 11.4 - - - -
474A PHE* 1.3 78.3 - - - +
476A ILE* 1.3 62.4 + - - +
477A ILE* 4.1 14.8 + - + +
487A LYS* 4.1 22.0 + - + +
488A PHE 3.2 6.1 - - - +
489A SER* 3.2 23.7 + - - +
547A VAL* 4.8 5.1 + - - +
548A LEU* 4.0 15.0 - - - +
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Residues in contact with ILE 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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336A ILE* 4.2 8.9 - - + +
377A ALA* 4.0 21.8 - - + -
378A SER* 4.0 11.4 - - - +
381A VAL* 3.9 35.0 - - + -
397A VAL* 3.9 24.0 - - + -
398A TYR 3.7 2.7 - - - -
399A VAL* 4.6 3.1 - - + -
474A PHE* 3.6 32.3 - - + -
475A GLN* 1.3 71.2 - - - +
477A ILE* 1.3 65.3 + - - +
478A LEU* 4.3 0.8 + - + -
486A GLY 4.2 0.2 - - - +
487A LYS* 3.3 3.8 - - - +
488A PHE* 2.7 47.4 + - + +
490A LEU* 4.3 7.9 - - + -
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Residues in contact with ILE 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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396A GLU 3.8 0.3 - - - +
397A VAL* 3.6 4.3 - - - -
398A TYR* 2.9 42.9 + - + +
400A THR* 4.1 16.2 - - + -
436A GLU* 3.5 33.4 - - + +
475A GLN* 4.3 12.8 - - + +
476A ILE* 1.3 77.4 - - - +
478A LEU* 1.3 63.7 - - - +
479A ARG* 3.9 19.2 + - + +
484A MET* 3.0 36.3 - - + -
486A GLY 3.6 2.7 - - - -
487A LYS* 3.8 22.7 - - + +
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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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336A ILE* 3.5 46.2 - - + +
337A PHE* 3.8 33.0 - - + -
381A VAL* 4.0 13.2 - - + -
385A LYS* 5.3 0.7 - - + -
395A LEU* 4.4 11.7 - - + -
396A GLU 3.6 3.6 - - - +
397A VAL* 3.8 29.2 - - + -
476A ILE* 4.2 0.6 - - + -
477A ILE* 1.3 74.1 - - - +
479A ARG* 1.3 56.7 + - - +
484A MET* 3.7 2.4 - - - +
485A HIS* 2.7 40.4 + - + -
486A GLY 2.7 21.8 + - - +
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Residues in contact with ARG 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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395A LEU* 3.4 5.2 - - - -
396A GLU* 2.9 37.2 + - - +
398A TYR* 3.8 34.1 - - + -
436A GLU* 2.9 37.3 + - - -
477A ILE* 4.0 5.5 - - + +
478A LEU* 1.3 77.4 - - - +
480A ALA* 1.3 61.5 + - - +
482A GLY* 2.9 38.1 + - - +
483A ARG 3.2 7.2 - - - +
484A MET* 3.3 27.5 - - - +
703A SO4 2.9 38.8 + - - -
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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