Contacts of the strand formed by residues 479 - 484 (chain D) in PDB entry 5Y7K
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 479 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LEU* 6.4 1.8 - - + -
450D ASN* 5.2 11.2 - - + +
453D ARG* 3.6 24.9 - - + +
454D CYS* 4.1 17.3 - - - -
457D TYR* 5.6 1.7 - - - +
470D LEU 3.6 2.6 - - - +
471D ARG* 3.8 0.5 - - - -
472D CYS* 2.8 46.0 + - + +
477D LEU 3.4 0.4 + - - -
478D PRO* 1.3 74.1 - - - +
480D TYR* 1.3 65.5 + - - +
481D THR* 4.1 15.4 + - + +
493D VAL* 3.7 24.2 - - + -
495D GLU 3.5 15.3 - - - +
496D ASP* 3.9 12.6 - - + -
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Residues in contact with TYR 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LYS 3.6 18.6 - - - -
57D LEU* 3.4 22.7 - - - +
58D TYR* 3.7 21.8 - - + -
469D GLN* 3.4 24.7 - - - +
470D LEU 3.5 2.2 - - - -
471D ARG* 3.1 56.1 + - + +
478D PRO* 4.2 18.1 - - + +
479D LEU* 1.3 76.2 - - - +
481D THR* 1.3 68.0 + - - +
493D VAL* 3.6 2.1 - - - +
494D LEU* 2.9 32.8 + - + -
495D GLU* 2.8 39.9 + - + +
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Residues in contact with THR 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LEU* 4.8 4.6 - - + +
457D TYR* 5.6 0.9 - - - -
469D GLN* 3.2 5.2 - - - +
470D LEU* 2.9 41.0 + - - +
479D LEU* 4.1 22.2 - - + -
480D TYR* 1.3 81.4 - - - +
482D LEU* 1.3 60.3 + - - +
483D HIS* 2.8 31.0 + - + -
490D GLY* 6.1 0.2 - - - -
492D ARG 3.5 11.9 - - - +
493D VAL* 4.2 14.8 - - + -
494D LEU* 4.3 6.0 - - - +
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Residues in contact with LEU 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 5.5 0.4 - - + -
62D TRP* 4.0 22.7 - - + -
68D TYR* 3.8 33.0 - - + +
81D ALA* 4.0 12.1 - - + -
467D TYR* 4.0 3.8 - - + -
468D TYR 3.5 13.0 - - - +
469D GLN* 4.9 2.9 - - + -
481D THR* 1.3 71.6 - - - +
483D HIS* 1.3 86.6 + - - +
490D GLY* 3.7 1.0 - - - -
491D LEU* 2.8 34.8 + - + +
492D ARG* 3.1 34.6 + - + +
494D LEU* 4.2 21.2 - - + +
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Residues in contact with HIS 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D LEU 5.6 0.4 - - - -
449D LEU* 4.1 24.7 - - + -
467D TYR* 3.2 25.8 - - - +
468D TYR* 3.0 55.2 + + + +
470D LEU* 3.4 13.8 - - + +
481D THR* 2.8 36.3 + - + -
482D LEU* 1.3 79.2 - - - +
484D SER* 1.3 63.2 + - - +
488D ASP 4.0 6.0 + - - -
489D LYS 3.3 22.0 + - - +
490D GLY* 3.4 17.7 + - - -
491D LEU* 3.9 4.5 - - - -
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Residues in contact with SER 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 4.0 5.2 + - - -
466D LYS 4.6 0.2 - - - -
467D TYR* 3.2 27.7 - - - -
468D TYR* 4.4 2.2 - - - -
483D HIS* 1.3 72.1 - - - +
485D SER* 1.3 52.3 + - - +
486D VAL* 3.1 13.9 + - - -
487D ASN* 4.5 4.0 - - - -
488D ASP* 2.7 36.8 + - - -
489D LYS* 3.3 18.9 + - - +
491D LEU* 3.3 19.9 - - - +
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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