Contacts of the strand formed by residues 540 - 546 (chain A) in PDB entry 5XOU
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 ARG 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A PRO* 3.9 33.7 + - - +
471A ALA* 3.4 19.7 - - + +
472A GLU* 3.4 12.8 + - - +
473A LEU 3.9 2.4 + - - -
538A PRO* 3.3 3.2 - - - +
539A SER* 1.3 84.6 + - - +
541A VAL* 1.3 73.5 + - - +
566A ILE* 4.5 0.4 - - - -
567A ALA* 3.1 34.0 - - + +
568A TYR 4.3 7.1 + - - +
569A ASP* 3.4 15.5 + - - +
625A ASP* 3.2 27.7 + - - -
626A THR* 3.4 17.3 + - - -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ALA* 3.7 3.8 - - - -
473A LEU* 3.3 40.6 - - + +
475A VAL* 5.6 0.2 - - + -
523A LEU* 5.3 2.0 - - + -
527A LEU* 4.2 5.6 - - + -
538A PRO* 4.0 11.7 - - + -
540A ARG* 1.3 80.1 - - - +
542A LEU* 1.3 61.4 + - - +
543A LEU* 3.9 17.4 + - + -
561A LEU* 3.6 31.9 - - + -
566A ILE* 4.1 7.6 - - + -
567A ALA 2.9 14.0 + - - +
568A TYR* 3.4 4.1 - - + -
569A ASP* 3.0 26.0 + - - +
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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
----------------------------------------------------------
471A ALA* 3.6 13.6 - - + +
473A LEU 2.8 11.4 + - - +
474A ALA* 3.3 5.5 - - + +
475A VAL* 2.7 32.7 + - - +
541A VAL* 1.3 71.7 - - - +
543A LEU* 1.3 60.7 + - - +
544A LEU* 3.8 24.2 - - + +
569A ASP* 3.9 7.2 - - + +
571A VAL* 4.0 10.5 - - + -
631A LEU* 3.8 27.6 - - + +
634A GLN* 3.7 34.8 - - + +
635A ILE* 4.1 15.9 - - + -
638A LEU* 4.0 14.4 - - + -
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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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475A VAL* 3.5 7.6 - - + -
477A PHE* 3.8 19.3 - - + -
523A LEU* 3.8 35.0 - - + -
541A VAL* 4.2 14.4 - - + -
542A LEU* 1.3 79.8 - - - +
544A LEU* 1.3 63.0 + - - +
554A PHE* 3.9 25.4 - - + -
558A LEU* 4.1 22.0 - - + -
561A LEU* 4.3 6.3 - - + -
568A TYR* 4.9 1.6 - - + -
569A ASP 2.8 17.6 + - - +
570A LEU* 3.6 13.1 - - + +
571A VAL 2.9 24.9 + - - -
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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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474A ALA* 5.0 2.0 - - + -
475A VAL 2.6 17.9 + - - +
476A GLY* 3.3 1.3 - - - -
477A PHE* 2.9 32.0 + - - -
542A LEU* 3.8 33.0 - - + +
543A LEU* 1.3 73.3 - - - +
545A ARG* 1.3 60.6 + - - +
570A LEU* 5.4 0.4 - - - -
571A VAL* 3.6 28.9 - - + +
573A VAL* 4.5 4.0 - - + -
635A ILE* 4.0 13.7 - - + -
638A LEU* 4.6 8.7 - - + -
653A PRO* 4.0 29.2 - - + -
655A PRO* 4.6 14.4 - - + -
656A LEU* 3.5 19.6 - - + +
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Residues in contact with ARG 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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477A PHE* 3.9 24.4 + - - -
478A ASP* 4.0 12.1 + - - +
479A ALA* 4.3 1.2 - - - +
512A GLU* 3.2 41.7 + - - +
514A ILE* 4.1 9.8 - - - +
543A LEU 4.1 1.0 + - - -
544A LEU* 1.3 74.3 - - - +
546A ASN* 1.3 80.2 + - - +
547A GLY 3.5 2.5 + - - +
548A ARG 3.8 13.8 + - - +
549A VAL* 3.5 33.0 - - + -
550A PRO* 4.0 6.7 - - - +
553A GLU* 2.8 37.8 + - - -
554A PHE* 4.2 9.2 - - + -
570A LEU* 5.0 1.8 - - + -
571A VAL 2.9 10.4 + - - +
573A VAL* 2.8 28.8 + - - +
656A LEU* 4.1 2.9 - - - -
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Residues in contact with ASN 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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477A PHE 3.1 15.9 + - - +
478A ASP* 3.5 34.7 + - - +
512A GLU* 4.3 4.0 - - - +
545A ARG* 1.3 88.5 + - - +
547A GLY* 1.3 67.0 + - - +
548A ARG 4.5 0.2 - - - +
573A VAL 3.8 5.2 - - - -
575A LYS* 3.4 26.2 + - - +
652A LEU* 3.9 27.0 - - - +
656A LEU* 3.8 16.3 + - + +
660A ASP* 4.4 6.9 - - - +
9D C 4.1 5.0 + - - +
10D T 4.1 3.9 + - - -
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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