Contacts of the strand formed by residues 540 - 546 (chain A) in PDB entry 2G5T
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A PRO* 4.0 21.8 - - + -
532A PRO 4.9 1.1 + - - -
533A HIS 3.9 3.5 + - - -
534A PHE* 3.6 29.7 - + - -
535A ASP* 2.8 48.4 + - - +
538A LYS* 4.0 31.7 - - + +
539A LYS* 1.3 74.4 - - - +
541A PRO* 1.3 72.5 - - + +
542A LEU* 3.7 1.4 + - - +
572A ASN* 3.4 26.5 - - + +
574A ILE* 3.7 20.8 - - + +
618A PHE* 3.0 16.9 + - + +
619A VAL* 3.5 7.4 - - - +
620A ASP* 2.9 20.8 + - - -
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Residues in contact with PRO 541 (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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538A LYS* 5.4 2.5 - - - +
539A LYS 4.4 0.2 - - - +
540A TYR* 1.3 90.5 - - + +
542A LEU* 1.3 60.1 + - - +
571A GLU 5.3 1.3 - - - +
572A ASN 3.8 8.3 - - - +
573A ILE* 3.5 24.5 - - + +
574A ILE* 3.1 22.3 + - - +
620A ASP* 4.5 1.8 - - + -
623A ARG* 3.3 57.9 - - + +
763A PHE* 3.8 16.8 - - + -
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Residues in contact with LEU 542 (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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528A MET* 4.6 3.1 - - + -
540A TYR 3.7 1.3 + - - +
541A PRO* 1.3 74.2 - - - +
543A LEU* 1.3 69.6 + - - +
544A LEU* 3.9 13.0 - - + +
574A ILE* 3.3 30.5 - - + +
576A ALA* 4.1 15.3 - - + -
610A ALA* 5.5 2.7 - - + -
613A PHE* 4.0 30.5 - - + -
619A VAL* 4.0 26.1 - - + +
623A ARG 3.0 7.9 + - - -
624A ILE* 3.3 20.3 - - + -
625A ALA 2.8 30.7 + - - -
763A PHE* 3.6 4.9 - - - -
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Residues in contact with LEU 543 (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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542A LEU* 1.3 75.5 - - - +
544A LEU* 1.3 72.4 + - - +
545A ASP 3.6 0.7 + - - -
563A TRP* 4.3 5.8 - - + -
567A LEU* 3.7 28.0 - - + -
573A ILE* 4.1 13.8 - - + +
574A ILE 2.8 11.9 + - - +
575A VAL* 3.3 13.9 - - + +
576A ALA 2.9 25.1 + - - +
625A ALA* 3.6 26.7 - - + +
626A ILE* 3.7 7.6 - - - +
627A TRP* 3.5 38.8 - - + +
759A ILE* 4.5 13.2 - - + -
763A PHE* 4.7 4.0 - - + -
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Residues in contact with LEU 544 (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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542A LEU* 3.9 5.8 - - + +
543A LEU* 1.3 72.0 - - - +
545A ASP* 1.3 61.9 + - - +
546A VAL* 3.5 0.7 + - + -
576A ALA* 3.7 21.3 - - + +
577A SER* 4.4 3.4 - - - +
578A PHE* 4.9 1.1 - - + +
606A GLN* 3.5 56.5 - - + +
610A ALA* 4.3 2.9 - - + +
613A PHE* 4.1 25.1 - - + -
625A ALA 2.6 18.4 + - - +
626A ILE* 3.3 11.6 - - + +
627A TRP 2.9 30.0 + - - +
647A PHE* 3.8 20.6 - - + -
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Residues in contact with ASP 545 (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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543A LEU 3.6 1.8 + - - -
544A LEU* 1.3 71.0 - - - +
546A VAL* 1.3 66.8 + - - +
554A LYS* 2.9 30.7 + - - +
562A ASN* 6.0 0.3 + - - -
564A ALA* 5.1 5.9 - - - +
575A VAL* 4.0 20.0 - - + +
576A ALA 2.7 12.9 + - - +
577A SER* 3.0 32.2 + - - +
578A PHE 4.6 0.3 + - - -
606A GLN* 4.6 3.1 + - - -
627A TRP* 3.7 33.8 + - - +
628A GLY* 5.3 0.7 - - - -
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Residues in contact with VAL 546 (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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544A LEU 4.5 1.1 - - - +
545A ASP* 1.3 80.3 + - - +
547A TYR* 1.3 64.8 + - - +
548A ALA* 3.7 17.9 - - + +
554A LYS* 4.5 2.9 + - - +
578A PHE 5.7 0.7 - - - +
606A GLN* 3.5 34.1 - - + +
626A ILE* 3.8 17.5 - - + -
627A TRP 2.9 17.5 + - - +
628A GLY* 3.2 9.7 - - - -
629A TRP 4.1 1.2 + - - -
632A GLY* 3.1 22.0 - - - +
635A VAL* 3.8 10.3 - - + -
636A THR* 3.4 20.4 - - - +
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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