Contacts of the strand formed by residues 486 - 490 (chain A) in PDB entry 5FZ9
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 TRP 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 5.5 2.9 - - - -
99A VAL* 4.6 22.7 - - + -
100A LYS 3.9 24.2 - - - -
427A ALA* 4.3 9.9 - - + -
428A ASP* 3.5 36.1 - - - -
429A ILE* 3.4 23.8 - - + +
481A GLY* 3.0 31.3 + - - -
484A LEU 3.7 13.2 - - - -
485A PRO* 1.3 73.0 - - - +
487A LEU* 1.3 62.4 + - - +
488A TYR* 3.6 35.2 - + + +
598A GLU* 3.3 7.1 - - - +
599A ALA 2.9 30.5 + - - +
1756A DMS 3.7 25.3 - - + +
1768A NUK 6.5 0.7 - - + -
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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
----------------------------------------------------------
427A ALA* 3.4 3.1 - - - -
428A ASP 2.8 30.0 + - - +
429A ILE 4.6 0.7 - - - +
430A ALA* 3.9 16.6 - - + +
434A PHE* 3.6 29.2 - - + +
435A GLY 3.3 26.9 - - - +
436A SER* 4.2 1.8 - - - -
485A PRO* 5.0 0.7 - - + +
486A TRP* 1.3 75.1 - - - +
488A TYR* 1.3 61.7 + - - +
596A PHE* 4.1 19.5 - - + -
597A ALA 3.6 2.2 - - - +
598A GLU* 3.6 41.1 - - + +
1761A EDO 3.0 26.8 + - - +
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Residues in contact with TYR 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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426A GLY 3.3 4.5 - - - +
427A ALA* 3.7 26.9 - - + -
486A TRP* 3.6 34.6 - + + +
487A LEU* 1.3 73.2 - - - +
489A VAL* 1.3 63.6 + - - +
490A GLY 3.9 1.3 + - - -
509A ASN* 4.6 6.3 - - - -
517A LYS* 4.9 1.0 + - - +
595A ASN* 4.5 0.9 - - - +
596A PHE* 3.4 5.2 - - - -
597A ALA* 2.8 51.0 + - + +
599A ALA* 3.9 16.2 - - + -
1756A DMS 2.4 33.3 + - - +
1768A NUK 3.4 68.5 - - + +
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 4.0 25.8 - - + -
379A LEU* 4.1 11.7 - - + -
382A PHE* 3.7 28.7 - - + -
425A TYR* 3.5 10.2 - - - +
426A GLY 3.0 28.9 + - - +
434A PHE* 4.4 3.6 - - + -
488A TYR* 1.3 73.5 - - - +
490A GLY* 1.3 58.7 + - - +
594A PHE* 3.9 16.6 - - + -
595A ASN 3.5 5.4 - - - +
596A PHE* 4.0 20.4 - - + -
1761A EDO 3.4 18.2 - - - +
1768A NUK 5.4 1.1 - - - -
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Residues in contact with GLY 490 (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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382A PHE* 3.6 4.2 - - - -
425A TYR* 4.9 0.4 - - - -
488A TYR 3.9 2.2 + - - -
489A VAL* 1.3 74.1 - - - +
491A MET* 1.3 59.8 + - - +
494A SER* 3.7 3.4 - - - -
591A ASN* 3.7 17.5 - - - -
593A GLY 3.8 3.1 - - - -
594A PHE* 3.3 13.5 - - - -
595A ASN* 3.0 43.8 + - - -
1768A NUK 4.9 1.5 + - - -
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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