Contacts of the helix formed by residues 451 - 460 (chain A) in PDB entry 1P9W
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 ASP 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A LEU 4.5 5.9 - - - +
450A VAL* 1.3 75.4 - - - +
452A ASP* 1.3 65.3 + - - +
453A ALA* 3.7 3.5 + - - -
454A LEU* 3.0 26.0 + - - +
455A GLN* 3.0 29.9 + - - +
470A HIS* 3.2 22.9 + - - -
474A THR* 5.7 4.9 - - - +
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Residues in contact with ASP 452 (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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451A ASP* 1.3 75.3 - - - +
453A ALA* 1.3 63.6 + - - +
455A GLN* 3.2 26.4 + - - +
456A GLU* 3.3 12.0 + - - +
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Residues in contact with ALA 453 (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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451A ASP* 3.4 3.4 + - - +
452A ASP* 1.3 78.8 - - - +
454A LEU* 1.3 62.6 + - - +
456A GLU* 3.3 11.1 - - - +
457A LEU* 3.2 26.0 + - + +
470A HIS* 3.5 28.7 - - + +
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Residues in contact with LEU 454 (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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448A LEU* 4.1 9.0 - - + -
449A LEU 3.8 19.1 - - - +
450A VAL* 4.0 18.6 - - + -
451A ASP* 3.0 22.4 + - - +
453A ALA* 1.3 74.4 - - - +
455A GLN* 1.3 61.8 + - - +
457A LEU* 3.1 13.9 + - + +
458A ILE* 2.8 41.5 + - + +
467A MSE 3.6 33.2 - - + -
470A HIS* 4.1 8.0 + - + -
471A ILE* 3.6 30.5 - - + -
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Residues in contact with GLN 455 (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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378A PHE* 5.8 2.6 - - - -
381A SER* 3.1 43.8 + - - +
382A SER* 4.3 8.4 - - - +
450A VAL* 3.6 18.9 - - + +
451A ASP* 3.0 21.0 + - - +
452A ASP* 3.2 17.0 + - - +
454A LEU* 1.3 75.0 - - - +
456A GLU* 1.3 52.3 + - - +
458A ILE* 3.2 2.5 + - - -
459A HIS* 2.8 38.0 + - - +
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Residues in contact with GLU 456 (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 ASP 3.3 8.1 + - - +
453A ALA* 3.3 13.5 - - - +
455A GLN* 1.3 76.6 - - - +
457A LEU* 1.3 59.8 + - + +
459A HIS* 3.9 5.3 - - - +
460A SER* 2.8 45.5 + - - -
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Residues in contact with LEU 457 (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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453A ALA* 3.2 14.8 + - + +
454A LEU* 3.1 13.7 + - + +
456A GLU* 1.3 77.6 - - + +
458A ILE* 1.3 66.5 + - - +
460A SER* 4.0 3.8 - - - +
461A GLU* 3.3 2.1 + - - -
462A ALA* 3.2 47.2 + - + +
463A GLY 4.8 0.7 + - - -
466A ALA* 3.8 20.0 - - + +
467A MSE 4.1 21.0 - - + +
470A HIS* 3.7 34.1 - - + +
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Residues in contact with ILE 458 (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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367A VAL* 4.1 31.9 - - + +
377A PRO* 3.9 9.3 - - + +
380A ILE* 3.8 17.7 - - + -
381A SER* 3.6 36.3 - - - +
384A LEU* 4.5 12.6 - - + -
450A VAL* 4.6 9.2 - - + -
454A LEU* 2.8 42.0 + - + +
455A GLN* 4.5 1.6 - - - -
457A LEU* 1.3 69.2 - - - +
459A HIS* 1.3 69.0 + - - +
461A GLU* 3.0 19.1 + - - +
467A MSE 4.2 15.0 - - - -
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Residues in contact with HIS 459 (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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377A PRO* 3.8 19.2 - - + +
378A PHE* 3.4 51.8 - + + +
381A SER* 3.9 8.5 - - - +
455A GLN 2.8 18.3 + - - +
456A GLU* 3.9 5.6 - - - +
458A ILE* 1.3 78.5 - - - +
460A SER* 1.3 60.2 + - - +
461A GLU* 3.3 4.2 + - - +
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Residues in contact with SER 460 (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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456A GLU* 2.8 34.8 + - - -
457A LEU* 3.7 7.1 + - - +
459A HIS* 1.3 72.8 - - - +
461A GLU* 1.3 69.6 + - - +
462A ALA* 3.7 13.3 + - - +
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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