Contacts of the strand formed by residues 476 - 481 (chain A) in PDB entry 1PMS
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 ARG 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A THR* 4.1 4.3 - - - -
467A LEU 3.0 25.1 + - - +
468A THR* 5.6 3.1 - - - +
469A ARG* 4.0 39.6 - - - +
474A HIS* 3.7 17.2 + - - +
475A GLU* 1.3 85.2 - - - +
477A HIS* 1.3 69.4 + - - +
478A ILE* 3.0 2.8 - - - +
487A CYS* 3.3 20.9 - - - -
488A CYS 3.2 14.4 - - - +
489A LYS* 3.3 23.8 - - + +
508A LYS* 4.1 28.1 - - - +
509A GLU* 4.4 15.8 + - - +
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Residues in contact with HIS 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 GLY 4.0 13.5 - - - -
466A THR* 3.9 17.5 - - + +
476A ARG* 1.3 76.1 - - - +
478A ILE* 1.3 59.5 + - - +
479A PHE* 3.9 25.8 - + + -
487A CYS* 3.2 7.6 - - - -
488A CYS* 3.0 41.2 + - + +
489A LYS* 4.6 7.1 + - - +
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Residues in contact with ILE 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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465A GLY 3.3 19.7 + - - -
467A LEU* 3.0 47.3 - - + +
468A THR* 5.5 1.8 - - - +
476A ARG* 3.0 5.2 - - + +
477A HIS* 1.3 84.8 - - - +
479A PHE* 1.3 85.6 + - - +
485A MET* 3.4 20.2 - - + -
486A ILE 3.3 11.9 - - - +
487A CYS* 3.9 17.9 - - + -
543A PHE* 6.3 0.2 - - + -
554A TRP* 2.8 44.6 - - + -
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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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443A GLN* 4.0 24.9 - - + -
461A PHE* 4.9 0.4 - - + -
463A MET 3.7 3.6 - - - -
464A GLU* 2.6 43.3 - - + +
465A GLY 4.8 3.4 - - - -
477A HIS* 3.9 28.3 - + + -
478A ILE* 1.3 97.8 - - - +
480A LEU* 1.3 61.9 + - - +
481A PHE* 3.5 12.6 - - + -
486A ILE* 2.9 58.9 + - + +
487A CYS 4.7 0.9 - - - -
488A CYS* 4.0 23.6 - - + -
554A TRP* 3.7 2.5 - - - -
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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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461A PHE* 3.0 5.4 - - - +
462A ILE* 2.6 56.4 + - + -
463A MET* 3.2 15.8 + - + -
479A PHE* 1.3 71.9 - - - +
481A PHE* 1.3 53.1 + - - +
482A ASP* 3.2 4.9 - - - +
483A GLY 4.8 2.9 - - - +
484A LEU 3.3 12.8 - - - +
485A MET* 3.3 31.9 - - + -
513A MET* 4.6 2.0 - - + -
554A TRP* 3.3 18.3 - - + +
557A ALA* 3.4 24.9 - - + +
558A LEU* 3.5 32.1 - - + -
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Residues in contact with PHE 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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439A MET* 4.8 4.0 - - + -
442A ILE* 3.0 32.5 - - + -
443A GLN* 5.4 4.3 - - + -
458A CYS 3.2 26.6 - - - +
459A ASN* 3.2 14.1 + - - -
461A PHE* 2.8 40.6 - + - -
479A PHE* 3.4 12.1 - - + -
480A LEU* 1.3 74.7 - - - +
482A ASP* 1.3 69.1 + - - +
483A GLY* 2.5 18.7 + - - -
484A LEU* 3.0 33.7 + - + -
486A ILE* 3.0 44.2 - - + -
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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