Contacts of the helix formed by residues 473 - 481 (chain A) in PDB entry 5D3O
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 PHE 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A MET* 3.4 11.4 - - + +
471A TYR 2.8 2.4 + - - -
472A ASP* 1.3 76.8 - - - +
474A SER* 1.3 59.5 + - - +
475A GLY 3.3 2.9 + - - -
476A GLN* 3.2 36.2 + - + -
477A PHE* 2.9 46.2 + + + +
480A HIS* 5.8 0.4 - + - -
511A ASP* 6.0 2.0 - - - -
513A MET* 3.6 25.5 - - + -
515A ASN* 3.7 18.6 - - - +
520A ILE* 4.4 11.9 - - + -
524A HIS* 4.0 28.5 - + - -
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Residues in contact with SER 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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466A HIS 4.3 3.1 - - - +
467A SER 3.4 27.8 - - - -
468A CYS* 3.6 4.9 - - - -
469A GLY 3.5 5.7 + - - -
470A MET* 3.0 29.1 + - - -
471A TYR 2.7 22.1 + - - -
472A ASP 3.4 1.8 - - - -
473A PHE* 1.3 78.4 - - - +
475A GLY* 1.3 54.5 + - - +
477A PHE* 3.6 1.8 - - - +
478A ALA* 2.8 37.5 + - - +
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Residues in contact with GLY 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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472A ASP 5.0 1.6 + - - -
473A PHE 3.3 0.2 - - - -
474A SER* 1.3 75.9 - - - +
476A GLN* 1.3 65.2 + - - +
478A ALA* 4.0 4.3 - - - +
479A PHE* 3.1 24.9 + - - +
316B LYS 4.8 1.2 - - - +
317B GLU* 3.9 31.4 + - - +
318B PRO* 6.1 1.3 - - - -
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Residues in contact with GLN 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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472A ASP 5.9 0.4 - - - +
473A PHE* 3.2 39.4 + - + -
474A SER 3.4 0.2 - - - -
475A GLY* 1.3 73.5 - - - +
477A PHE* 1.3 58.8 + - - +
479A PHE* 3.3 2.7 + - - +
480A HIS* 3.0 56.1 + - + +
316B LYS* 3.8 28.6 - - - +
317B GLU* 3.1 24.6 + - - +
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Residues in contact with PHE 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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465A MET 6.1 0.9 - - - -
466A HIS 5.6 2.9 - - - -
470A MET* 3.5 25.8 - - + -
473A PHE* 2.9 32.9 + + + +
474A SER 3.6 4.5 - - - +
476A GLN* 1.3 76.0 - - - +
478A ALA* 1.3 59.4 + - + +
481A VAL* 2.7 74.3 + - + +
483A LEU 3.2 26.2 - - - -
485A ALA* 3.8 22.9 - - + -
493A ILE* 5.7 0.9 - - + -
495A LEU* 4.6 3.6 - - + -
520A ILE* 4.1 23.1 - - + -
523A CYS* 4.1 19.3 - - + -
524A HIS* 5.0 3.4 - + - -
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Residues in contact with ALA 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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466A HIS* 3.5 44.2 - - + +
467A SER* 5.6 0.4 - - - -
474A SER 2.8 22.3 + - - +
475A GLY* 4.1 4.5 - - - +
477A PHE* 1.3 73.7 - - - +
479A PHE* 1.3 65.7 + - - +
482A GLY* 3.1 25.7 + - - +
483A LEU 5.3 0.7 - - - +
533A HIS* 3.7 4.0 + - - -
463B SER* 4.7 2.0 + - - -
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Residues in contact with PHE 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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475A GLY 3.1 18.8 + - - +
476A GLN* 3.6 4.3 - - - +
478A ALA* 1.3 76.3 - - - +
480A HIS* 1.3 83.7 + + + +
533A HIS* 2.8 26.0 + - - -
307B THR* 4.5 7.4 - - + -
311B HIS* 4.0 14.6 - - - -
316B LYS* 3.6 33.9 - - + +
459B ARG* 5.4 0.9 - - - -
460B ASN* 3.4 41.1 - - - +
463B SER* 3.9 16.5 + - - -
464B LEU* 3.8 38.8 - - + -
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Residues in contact with HIS 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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473A PHE* 5.8 0.7 - + - -
476A GLN* 3.0 41.9 + - + +
479A PHE* 1.3 95.4 - + - +
481A VAL* 1.3 60.5 + - - +
524A HIS* 3.6 30.3 - + + +
527A VAL* 4.0 9.5 - - - +
533A HIS* 3.8 7.5 - - - -
307B THR* 5.3 6.1 - - + -
316B LYS* 3.3 37.7 + - - -
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Residues in contact with VAL 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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477A PHE* 2.7 56.0 + - + +
480A HIS* 1.3 75.1 - - - +
482A GLY* 1.3 61.7 + - - +
483A LEU* 3.9 19.9 - - + +
495A LEU* 5.0 0.9 - - + -
523A CYS* 3.9 27.6 - - + +
524A HIS* 3.9 28.7 - - + +
527A VAL* 3.5 22.3 - - + +
533A HIS* 3.3 14.7 - - - -
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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