Contacts of the helix formed by residues 473 - 482 (chain A) in PDB entry 1BPO
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 THR 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A ASP* 3.2 10.8 + - - -
472A PRO* 1.3 75.8 - - - +
474A LEU* 1.3 63.3 + - - +
476A LEU* 3.6 6.6 - - + +
477A SER* 3.4 21.5 + - - -
150C GLY 3.8 19.7 - - - +
152C GLN* 4.8 4.7 - - + +
170C ILE 3.8 6.5 - - - +
171C SER* 3.3 35.4 - - - -
172C ALA* 2.9 28.2 + - - +
173C GLN* 5.0 0.3 + - - -
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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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445A LYS* 4.5 4.3 - - + -
448A LEU* 3.9 20.0 - - + -
449A GLU* 3.3 41.3 - - + +
452A LEU* 3.9 23.8 - - + -
467A VAL* 3.8 8.7 - - + -
471A ASP* 3.4 38.9 + - + +
472A PRO 3.1 0.6 - - - -
473A THR* 1.3 81.4 - - - +
475A ALA* 1.3 60.3 + - - +
477A SER* 3.7 6.1 + - - +
478A VAL* 2.9 33.1 + - - +
150C GLY* 5.4 7.0 - - - +
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Residues in contact with ALA 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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464A GLY 3.9 7.9 - - - +
467A VAL* 4.2 3.6 - - - -
468A LYS* 3.4 42.6 - - + +
471A ASP 3.5 2.9 + - - +
472A PRO* 3.1 8.7 + - + +
474A LEU* 1.3 77.2 - - - +
476A LEU* 1.3 59.4 + - - +
477A SER 3.2 0.2 - - - -
478A VAL* 3.8 6.6 - - - +
479A TYR* 2.7 47.7 + - + +
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PRO 2.8 15.1 + - - +
473A THR* 3.6 7.4 - - + +
475A ALA* 1.3 79.2 - - - +
477A SER* 1.3 53.1 + - - +
479A TYR* 3.5 9.2 - - - +
480A LEU* 2.7 37.9 + - + +
152C GLN* 4.1 15.5 - - + -
170C ILE* 3.2 30.7 - - + +
171C SER* 4.1 2.2 - - - -
172C ALA* 3.6 27.1 - - + +
177C VAL* 3.1 35.4 - - + -
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 3.7 17.0 - - - +
473A THR 3.4 13.3 + - - -
474A LEU* 3.7 6.9 + - - +
475A ALA 3.2 0.2 - - - -
476A LEU* 1.3 78.8 - - - +
478A VAL* 1.3 56.6 + - - +
479A TYR 3.3 0.2 - - - -
480A LEU* 3.5 9.1 - - - +
481A ARG* 2.8 40.6 + - - +
152C GLN* 3.0 32.8 + - - +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.7 6.7 - - + -
452A LEU* 3.8 21.5 - - + -
459A CYS* 3.1 32.2 - - + +
460A SER 4.0 2.9 - - - +
463A LEU* 4.2 10.1 - - + -
464A GLY* 3.7 28.7 - - - +
467A VAL* 4.7 12.3 - - + -
474A LEU 2.9 22.9 + - - +
475A ALA* 3.4 6.7 + - - +
477A SER* 1.3 77.0 + - - +
479A TYR* 1.3 56.5 + - - +
481A ARG* 3.3 0.6 + - - +
482A ALA* 2.7 30.5 + - - +
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Residues in contact with TYR 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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460A SER 4.3 0.7 - - - -
461A GLU* 3.0 41.1 - - + -
464A GLY* 3.5 13.9 - - - -
465A ASP* 2.2 37.7 + - - -
468A LYS* 3.9 19.8 - - + +
475A ALA* 2.7 39.3 + - + +
476A LEU* 3.5 7.9 - - - +
478A VAL* 1.3 69.1 - - - +
480A LEU* 1.3 54.8 + - - +
482A ALA* 3.0 2.4 + - - +
483A ASN* 2.4 40.5 + - - -
484A VAL* 4.3 24.2 - - + -
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Residues in contact with LEU 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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476A LEU* 2.7 26.3 + - + +
477A SER* 3.5 6.3 - - - +
479A TYR* 1.3 73.2 - - - +
481A ARG* 1.3 64.8 + - + +
483A ASN* 3.1 14.9 + - - +
484A VAL 5.6 0.4 - - - +
27C PHE* 3.4 65.4 - - + +
28C SER 5.0 1.2 + - - -
152C GLN* 3.6 32.5 - - + +
154C ILE* 5.1 4.3 - - + -
170C ILE* 5.6 2.2 - - + -
278C LYS* 6.1 2.5 - - - +
304C PHE* 6.4 0.4 - - + -
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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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452A LEU* 2.7 58.4 + - - +
453A LYS* 3.9 6.1 + - - +
455A ASP* 3.3 24.7 + - - +
457A LEU 4.8 7.5 + - - +
459A CYS* 3.5 21.8 - - - +
477A SER* 2.8 33.0 + - - +
478A VAL 3.5 5.2 - - - +
479A TYR 3.1 0.2 - - - -
480A LEU* 1.3 78.1 - - + +
482A ALA* 1.3 60.8 + - - +
483A ASN* 3.2 4.3 + - - +
27C PHE* 6.0 1.6 - - + -
28C SER* 3.5 32.7 + - - +
152C GLN* 5.5 2.9 + - - +
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Residues in contact with ALA 482 (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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429A LYS* 4.9 10.3 + - - +
459A CYS* 3.3 9.4 - - - +
460A SER* 3.1 47.6 - - - +
461A GLU* 4.1 2.0 - - - +
478A VAL 2.7 14.9 + - - +
479A TYR* 4.0 2.9 - - - +
481A ARG* 1.3 70.3 - - - +
483A ASN* 1.3 76.5 + - - +
484A VAL* 5.0 2.2 - - + +
23C ALA 5.4 1.4 - - - +
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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