Contacts of the strand formed by residues 503 - 506 (chain A) in PDB entry 4OE5
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 ASN 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A LEU* 3.1 9.8 + - - +
479A THR* 3.3 24.2 - - + +
480A GLY 3.1 25.5 + - - +
501A ALA* 3.7 1.6 - - - +
502A GLY* 1.3 80.2 - - - +
504A PHE* 1.3 60.5 + - - +
505A TYR* 3.8 25.0 + - + +
546B VAL* 3.4 30.3 + - - +
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Residues in contact with PHE 504 (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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320A PHE* 3.8 27.1 - + - -
480A GLY 3.7 11.4 - - - -
481A ALA 4.1 5.8 - - - -
482A VAL* 3.4 32.5 - - + -
493A ALA* 4.5 2.2 - - + -
494A THR* 3.8 39.5 - - + -
497A LEU* 3.9 18.8 - - + -
501A ALA* 4.3 11.2 - - + +
502A GLY 4.0 0.2 - - - -
503A ASN* 1.3 74.0 - - - +
505A TYR* 1.3 66.1 + - - +
506A ILE* 4.8 6.3 - - + -
545B GLN* 4.0 21.5 - - - +
546B VAL 2.8 12.2 + - - +
547B ILE* 3.2 17.8 - - + +
548B LYS* 2.8 26.5 + - - +
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Residues in contact with TYR 505 (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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479A THR* 5.4 0.7 - - - +
480A GLY 2.9 20.4 + - - +
481A ALA* 3.1 3.7 - - + +
482A VAL* 2.9 27.5 + - - +
503A ASN* 3.8 39.1 + - + +
504A PHE* 1.3 77.3 - - - +
506A ILE* 1.3 63.5 + - - +
507A ASN 4.0 0.2 - - - -
508A ASP* 3.4 30.1 - - + +
509A LYS 3.6 13.2 - - - -
510A SER* 3.4 22.0 + - - -
511A THR 4.4 1.2 - - - -
512A GLY* 3.6 28.7 + - - -
513A SER 5.1 0.4 - - - -
546B VAL 6.0 0.4 - - - -
548B LYS* 3.2 31.2 - - + +
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Residues in contact with ILE 506 (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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482A VAL* 3.5 8.3 - - + +
490A VAL* 3.7 39.5 - - + -
494A THR* 4.6 5.8 - - - +
504A PHE* 4.8 9.9 - - + -
505A TYR* 1.3 74.1 - - - +
507A ASN* 1.3 82.3 + - - +
508A ASP* 3.2 1.1 + - - +
547B ILE* 3.9 26.0 - - + -
548B LYS 2.7 10.9 + - - +
549B GLU* 3.8 42.0 - - + +
550B THR 3.1 22.0 + - - -
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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