Contacts of the strand formed by residues 540 - 546 (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 TYR 540 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531D PRO* 4.2 20.4 - - + -
532D PRO 5.1 1.6 + - - -
533D HIS 3.9 5.2 + - - -
534D PHE* 3.6 30.9 - + - -
535D ASP* 3.2 45.5 + - - +
538D LYS* 4.0 15.5 - - + +
539D LYS* 1.3 76.8 - - - +
541D PRO* 1.3 67.9 - - + +
542D LEU 3.8 0.3 + - - -
572D ASN* 3.6 27.6 - - + -
574D ILE* 3.6 20.4 - - + -
618D PHE* 2.8 18.9 + - + +
619D VAL* 3.4 6.6 - - - +
620D ASP* 2.7 29.1 + - - -
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Residues in contact with PRO 541 (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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539D LYS 4.3 0.4 - - - +
540D TYR* 1.3 87.0 - - + +
542D LEU* 1.3 59.3 + - - +
572D ASN* 3.6 20.6 - - + +
573D ILE* 4.2 7.2 - - + -
574D ILE* 2.9 29.6 + - - +
623D ARG* 3.4 51.4 - - + +
763D PHE* 3.6 31.9 - - + -
765D LEU* 5.1 4.9 - - + -
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Residues in contact with LEU 542 (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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528D MET* 4.8 2.0 - - + -
540D TYR 3.8 0.4 + - - -
541D PRO* 1.3 75.0 - - - +
543D LEU* 1.3 58.0 + - - +
544D LEU* 4.8 4.9 - - + +
574D ILE* 3.4 34.5 - - + +
576D ALA* 3.8 19.3 - - + -
610D ALA* 4.9 5.4 - - + -
613D PHE* 3.7 35.0 - - + -
619D VAL* 4.0 29.6 - - + -
623D ARG 3.0 9.6 + - - +
624D ILE* 3.3 21.6 - - + -
625D ALA 2.7 31.7 + - - +
763D PHE* 3.5 5.9 - - - -
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Residues in contact with LEU 543 (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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542D LEU* 1.3 75.4 - - - +
544D LEU* 1.3 62.9 + - - +
545D ASP 3.4 2.6 + - - -
563D TRP* 4.1 9.2 - - + -
567D LEU* 3.5 31.4 - - + -
573D ILE* 4.0 12.5 - - + +
574D ILE 2.7 12.3 + - - +
575D VAL* 3.2 12.6 - - + +
576D ALA 2.9 25.6 + - - -
625D ALA* 3.4 26.0 - - + -
626D ILE* 3.7 5.4 - - - +
627D TRP* 3.7 37.9 - - + +
759D ILE* 4.4 15.0 - - + -
763D PHE* 4.7 4.3 - - + -
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Residues in contact with LEU 544 (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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542D LEU* 4.1 6.0 - - + +
543D LEU* 1.3 71.1 - - - +
545D ASP* 1.3 62.5 + - - +
546D VAL* 3.6 13.5 - - + -
576D ALA* 3.3 22.2 - - + +
577D SER* 4.4 5.8 - - - +
578D PHE* 4.9 2.0 - - + +
606D GLN* 3.5 46.0 - - + +
609D ALA* 5.3 0.2 - - + -
610D ALA* 4.7 4.7 - - + +
613D PHE* 4.1 23.3 - - + -
625D ALA 2.7 17.9 + - - +
626D ILE* 3.3 10.2 - - + +
627D TRP 3.0 26.1 + - - +
647D PHE* 3.7 21.3 - - + -
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Residues in contact with ASP 545 (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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543D LEU 3.4 2.6 + - - -
544D LEU* 1.3 69.8 - - - +
546D VAL* 1.3 68.5 + - - +
554D LYS* 3.5 30.9 + - - +
562D ASN* 6.0 0.2 + - - -
564D ALA* 5.2 5.4 - - - +
575D VAL* 3.8 18.1 - - + +
576D ALA 2.7 13.1 + - - +
577D SER* 3.2 32.4 + - - +
578D PHE 4.6 1.4 + - - -
627D TRP* 3.5 41.2 + - - +
628D GLY* 4.9 1.0 - - - -
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Residues in contact with VAL 546 (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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544D LEU* 3.4 22.2 - - + +
545D ASP* 1.3 85.1 + - - +
547D TYR* 1.3 62.5 + - - +
554D LYS* 4.8 4.1 - - - -
606D GLN* 3.2 32.5 - - - +
626D ILE* 3.7 15.3 - - + -
627D TRP 3.0 8.3 + - - +
628D GLY* 3.4 9.2 - - - -
629D TRP 4.2 1.7 + - - -
632D GLY* 3.3 22.7 - - - +
635D VAL* 4.4 7.9 - - + -
636D THR* 3.2 29.8 - - - +
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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