Contacts of the strand formed by residues 545 - 550 (chain A) in PDB entry 1M9S
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 545 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A ALA* 3.9 16.4 - - + -
481A ARG 3.7 3.4 - - - -
482A VAL* 3.9 19.1 - - + +
483A ARG* 3.7 13.2 - - - +
506A LEU* 4.2 3.6 - - + -
514A MET* 3.8 37.2 - - + -
516A ILE* 4.6 3.4 - - + -
528A TYR* 4.4 24.0 - - + -
530A PHE* 5.3 1.3 - - + -
540A VAL* 3.9 33.9 - - + -
541A ASP 4.2 1.3 - - - +
542A THR* 3.4 18.5 + - - +
543A ARG 3.3 3.5 - - - +
544A ALA* 1.3 85.6 - - - +
546A ASN* 1.3 63.3 + - - +
547A THR* 4.0 4.0 + - + +
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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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480A ALA* 3.2 2.8 - - - -
481A ARG* 2.9 36.8 + - - +
483A ARG* 3.9 21.5 - - + +
545A LEU* 1.3 76.8 - - - +
547A THR* 1.3 59.7 + - - +
548A PHE* 2.8 32.0 + - - +
604A GLU* 4.5 6.7 + - - -
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Residues in contact with THR 547 (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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478A ALA* 4.8 3.6 - - + -
479A TYR 3.2 11.9 - - - +
480A ALA* 3.6 15.3 - - + -
516A ILE* 4.7 4.7 - - + -
528A TYR* 3.4 37.2 + - + +
542A THR 5.5 2.7 - - - +
545A LEU* 4.0 3.3 - - + -
546A ASN* 1.3 72.3 + - - +
548A PHE* 1.3 60.3 + - - +
549A TYR* 3.0 16.4 + - - -
550A LYS* 5.2 8.0 - - - +
553A MET* 5.2 2.3 - - - +
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Residues in contact with PHE 548 (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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479A TYR* 3.1 32.0 + + + -
480A ALA 3.5 21.1 - - - -
481A ARG* 3.4 35.0 - - + -
513A ASN* 3.2 23.1 - - - -
546A ASN* 2.8 26.1 + - - +
547A THR* 1.3 71.2 - - - +
549A TYR* 1.3 64.8 + - + +
553A MET* 3.6 17.7 - - - +
577A VAL* 4.1 13.0 - - + -
603A ILE* 3.6 24.8 - - + +
604A GLU* 3.2 34.0 + - + +
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Residues in contact with TYR 549 (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 THR* 3.7 20.4 - - + +
478A ALA* 3.1 24.8 - - - +
479A TYR* 3.0 35.8 + + + +
547A THR* 3.0 4.1 - - - -
548A PHE* 1.3 95.8 - - + +
550A LYS* 1.3 78.2 + - - +
551A GLN* 3.8 7.3 - - - +
553A MET* 3.8 2.2 - - - -
554A GLU* 2.7 28.1 + - + -
575A VAL* 3.7 21.9 - - + +
576A PRO* 3.5 24.6 - - + +
577A VAL* 3.7 20.2 - - + -
603A ILE* 3.7 22.7 - - + -
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Residues in contact with LYS 550 (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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476A VAL* 4.2 22.9 - - - +
477A THR 3.3 21.8 - - - +
478A ALA* 3.5 13.2 - - + -
519A GLU* 5.0 5.7 + - - -
528A TYR* 3.4 22.7 + - - +
547A THR* 5.2 9.6 - - - +
549A TYR* 1.3 84.3 - - - +
551A GLN* 1.3 59.0 + - - +
552A SER* 3.8 20.9 - - - +
553A MET* 2.8 43.6 + - + +
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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