Contacts of the strand formed by residues 470 - 477 (chain A) in PDB entry 5CHG
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 GLN 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A GLU 3.8 0.7 - - - -
467A ASN* 2.8 40.2 + - - +
468A GLY 4.2 0.9 - - - +
469A GLN* 1.3 80.7 - - - +
471A GLN* 1.3 67.9 + - - +
492A ILE* 3.3 20.3 - - + +
493A VAL 3.1 6.1 - - - +
494A VAL* 3.4 33.0 - - + +
498A GLU* 3.5 15.0 + - - +
502A ALA* 4.4 0.4 - - - +
529A GLU* 2.8 42.3 + - - +
530A HIS* 3.3 25.5 + - + +
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Residues in contact with GLN 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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440A HIS* 5.4 2.4 + - - +
441A ARG* 5.9 1.4 - - - -
442A GLY 5.7 3.5 + - - +
444A PHE* 3.7 47.9 - - + +
465A GLU 3.4 13.7 - - - +
466A GLU* 4.0 21.6 + - + +
467A ASN* 4.7 1.1 - - - -
469A GLN 4.7 6.8 - - - +
470A GLN* 1.3 80.8 - - - +
472A LYS* 1.3 59.9 + - - +
491A ILE 3.9 0.2 - - - +
492A ILE* 3.2 8.4 - - - +
493A VAL* 2.9 40.7 + - + +
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Residues in contact with LYS 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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444A PHE* 3.6 7.2 - - - -
462A VAL 4.4 0.7 - - - +
464A GLN* 3.6 6.1 - - - -
465A GLU* 3.2 61.6 + - + +
467A ASN* 4.3 4.9 - - - +
471A GLN* 1.3 75.0 - - - +
473A TYR* 1.3 62.9 + - - +
474A LEU* 3.9 25.1 - - + -
490A ASP* 5.4 0.2 - - - -
491A ILE 3.3 7.9 - - - +
492A ILE* 4.5 8.1 - - + -
505A TYR* 3.2 26.4 + - + -
506A PHE* 3.5 31.7 - - + -
5P A 3.8 20.2 + - - -
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Residues in contact with TYR 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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444A PHE* 3.6 17.5 - - + -
448A LEU* 3.6 39.5 - - + -
452A ARG* 4.6 2.2 - - - -
457A LEU* 3.6 26.0 - - + +
459A ASP 3.5 10.9 + - - -
460A ASP* 2.4 37.8 + - + -
462A VAL 4.2 2.9 - - - -
463A SER* 4.1 14.8 - - - -
472A LYS* 1.3 74.7 - - - +
474A LEU* 1.3 76.6 + - - +
475A GLY* 3.5 19.0 - - - -
489A LEU* 4.2 7.0 - - + -
490A ASP* 3.3 1.6 - - - +
491A ILE* 2.7 47.0 + - + +
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Residues in contact with LEU 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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342A TRP* 4.1 23.8 - - + -
461A LEU* 2.2 40.3 + - + +
462A VAL* 3.4 30.5 + - + -
465A GLU* 5.4 3.1 - - - +
472A LYS* 3.9 26.5 - - + -
473A TYR* 1.3 89.6 - - - +
475A GLY* 1.3 57.5 + - - +
488A ARG* 4.1 10.8 - - - +
489A LEU 3.6 0.2 - - - -
490A ASP* 3.2 26.0 - - - +
4P T 4.9 2.5 - - + +
5P A 4.1 13.9 - - - +
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Residues in contact with GLY 475 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ASP 3.8 4.7 - - - -
461A LEU* 4.1 7.0 - - - -
473A TYR* 3.5 18.1 - - - -
474A LEU* 1.3 74.2 - - - +
476A VAL* 1.3 62.7 + - - +
488A ARG* 2.9 13.7 + - - +
489A LEU* 2.8 43.5 + - - -
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Residues in contact with VAL 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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375A ILE* 3.9 20.6 - - + -
379A HIS* 3.7 20.0 - - + -
383A PHE* 3.6 23.3 - - + -
457A LEU* 3.5 6.1 - - - +
458A THR* 2.7 48.2 + - - +
459A ASP* 3.0 18.2 + - + +
461A LEU* 4.4 10.3 - - + -
473A TYR* 4.2 1.0 + - - -
475A GLY* 1.3 78.1 - - - +
477A CYS* 1.3 56.3 + - - +
486A HIS* 3.7 15.5 - - + -
487A ARG 3.4 10.3 - - - +
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Residues in contact with CYS 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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395A ILE* 3.9 24.0 - - - -
456A PHE* 3.1 45.3 - - + +
457A LEU* 4.2 2.5 - - + -
458A THR* 4.4 2.2 - - - -
475A GLY 4.2 0.6 - - - -
476A VAL* 1.3 76.4 - - - +
478A ARG* 1.3 63.7 + - - +
486A HIS* 3.4 2.6 - - - -
487A ARG* 2.8 40.6 + - - -
488A ARG 5.3 0.2 - - - -
489A LEU* 3.8 27.3 - - + +
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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