Contacts of the strand formed by residues 482 - 486 (chain A) in PDB entry 5FLZ
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 LEU 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A LEU* 6.2 2.5 - - + -
425A ILE* 3.2 35.9 - - + -
426A PHE* 3.6 27.6 - - + -
477A LEU 3.9 5.6 - - - +
478A MET* 3.2 31.5 + - + +
479A ARG* 2.9 27.0 + - - +
481A LEU* 1.4 86.9 - - + +
483A MET* 1.3 64.8 + - - +
562A PHE* 3.4 34.5 - - + -
563A ASP 3.7 2.5 - - - -
564A ILE* 4.0 16.4 - - + -
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Residues in contact with MET 483 (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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462A LEU* 4.8 10.3 - - + -
466A GLU* 4.2 21.1 - - - +
479A ARG* 5.7 2.5 - - - +
480A GLN 3.9 17.0 - - - +
481A LEU 4.2 2.0 - - - +
482A LEU* 1.3 79.6 - - - +
484A ILE* 1.3 62.7 + - - +
562A PHE* 3.7 6.3 - - - -
563A ASP* 2.7 55.0 + - - +
565A ASN* 3.9 31.2 - - - +
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Residues in contact with ILE 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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434A ASN* 6.1 2.7 - - - +
438A PHE* 3.9 28.3 - - + -
458A TYR* 3.0 23.9 + - - +
462A LEU* 3.3 43.8 - - + +
465A PHE* 6.5 0.7 - - + -
479A ARG* 6.2 1.1 - - - +
483A MET* 1.3 73.8 - - - +
485A GLN* 1.4 54.6 + - - +
560A LEU* 4.4 5.6 - - + -
561A LYS 3.1 18.2 - - - +
562A PHE* 3.8 26.9 - - + +
563A ASP* 3.2 5.8 - - - +
587A ARG* 4.4 14.4 - - - +
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Residues in contact with GLN 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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458A TYR* 3.0 13.5 + - - -
484A ILE* 1.4 70.2 - - - +
486A PHE* 1.3 70.6 + - - +
487A ASP* 3.4 25.1 + - - -
559A HIS 3.3 12.5 - - - +
560A LEU* 3.4 5.4 - - - -
561A LYS* 2.7 55.9 + - + +
563A ASP* 3.2 22.6 + - + +
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Residues in contact with PHE 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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445A GLU 5.4 0.9 - - - -
446A LEU* 5.5 3.4 - - + -
450A TYR* 3.4 50.2 - + - -
454A ASN* 3.8 26.5 - - + -
455A ASN* 3.8 24.4 + - - +
458A TYR* 3.8 27.6 - + + -
485A GLN* 1.3 86.4 + - - +
487A ASP* 1.3 71.1 + - - +
488A THR* 3.8 6.9 + - - +
556A ALA* 4.0 20.2 - - + -
559A HIS* 3.7 28.5 - - + -
560A LEU* 4.1 11.2 - - + -
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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