Contacts of the helix formed by residues 483 - 488 (chain A) in PDB entry 1PS9
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 TYR 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLN* 4.4 2.4 + - - -
414A ILE* 5.4 0.4 - - + -
465A ILE* 4.4 2.8 - - - +
467A PRO* 3.6 35.9 - - + +
482A SER* 1.3 76.3 - - - +
484A LEU* 1.3 80.0 + - + +
486A VAL* 4.5 2.0 - - - +
487A LEU* 2.8 40.7 + - + +
505A ILE* 3.6 32.1 - - + -
509A THR* 3.9 7.6 - - - +
621A VAL* 4.1 8.1 - - - -
622A ILE 3.2 27.0 + - - +
623A CYS* 3.9 21.5 - - - -
624A ALA 5.6 0.4 - - - -
625A GLY 4.5 9.6 - - - -
626A GLN* 3.3 24.4 + - - +
701A FAD 3.7 23.1 - - + -
703A NAP 5.2 0.7 - - - -
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Residues in contact with LEU 484 (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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411A GLN* 6.4 1.1 - - + -
414A ILE* 3.3 32.8 - - + -
467A PRO* 3.4 31.0 - - + -
482A SER* 3.1 8.2 - - - +
483A TYR* 1.3 97.9 - - + +
485A ASP* 1.3 62.9 + - - +
487A LEU* 5.0 0.2 - - - -
488A ARG* 2.8 63.3 + - + +
489A ASP* 3.0 9.5 + - - +
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Residues in contact with ASP 485 (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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480A VAL 5.2 0.3 - - - +
481A LEU* 3.7 19.0 - - + +
482A SER* 2.6 38.7 + - - +
484A LEU* 1.3 78.9 - - - +
486A VAL* 1.3 51.5 + - - +
488A ARG* 5.0 2.1 + - - -
489A ASP* 3.3 18.8 - - + +
490A LYS 3.3 5.7 + - - -
491A ALA* 2.7 39.1 + - + +
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Residues in contact with VAL 486 (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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481A LEU* 4.1 11.2 - - + -
482A SER 3.3 13.5 + - - +
483A TYR* 3.9 6.5 - - - +
484A LEU 3.2 0.4 - - - -
485A ASP* 1.3 78.3 - - - +
487A LEU* 1.3 72.3 + - + +
490A LYS* 3.4 22.7 - - - +
491A ALA* 4.2 5.7 - - - +
493A VAL* 3.8 22.9 - - + -
509A THR* 4.7 2.2 - - + -
512A TYR* 4.2 8.9 - - + -
513A LEU* 3.5 35.9 - - + -
621A VAL* 4.0 22.7 - - + -
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Residues in contact with LEU 487 (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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414A ILE* 3.7 18.1 - - + +
417A GLN* 4.0 8.2 - - + +
418A ILE* 3.9 10.5 - - + -
483A TYR* 2.8 30.6 + - + +
484A LEU* 5.0 0.2 - - - -
486A VAL* 1.3 78.2 - - + +
488A ARG* 1.3 57.8 + - - +
490A LYS* 2.9 30.2 + - - +
505A ILE* 5.1 0.2 - - + -
509A THR* 3.7 26.5 - - - +
512A TYR* 3.6 43.1 - - + -
701A FAD 3.4 32.5 - - + -
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Residues in contact with ARG 488 (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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405A HIS* 4.9 20.1 + - - -
414A ILE* 4.0 31.2 - - + -
417A GLN* 5.3 5.1 + - - +
484A LEU* 2.8 47.6 + - - +
485A ASP* 5.0 2.8 + - - -
487A LEU* 1.3 77.9 - - - +
489A ASP* 1.3 88.5 + - - +
490A LYS* 3.3 13.8 + - - +
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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