Contacts of the strand formed by residues 543 - 548 (chain A) in PDB entry 5TFM
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 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A PHE* 4.0 7.6 - - + -
539A GLN* 3.5 14.6 + - - +
540A LYS* 3.3 67.9 + - + +
542A ALA* 1.3 77.1 - - - +
544A VAL* 1.3 70.3 + - - +
558A VAL* 3.8 13.9 - - + -
559A ARG 3.5 26.0 - - - -
560A LEU* 3.7 28.5 - - + -
561A ARG 3.7 12.1 + - - -
632A VAL* 3.8 15.3 - - + -
633A PRO 3.0 6.1 + - - +
634A VAL* 3.4 13.8 - - + -
635A THR* 3.1 23.7 + - - -
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Residues in contact with VAL 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 ALA* 5.8 1.3 - - + -
543A TYR* 1.3 84.3 - - - +
545A GLY* 1.3 68.9 + - - +
546A ALA* 5.6 2.2 - - + -
557A LEU 3.7 3.8 - - - +
558A VAL* 3.5 18.9 - - - +
634A VAL* 4.5 0.8 - - - +
635A THR* 3.3 22.9 - - + +
637A GLU* 6.3 1.6 - - + -
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Residues in contact with GLY 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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544A VAL* 1.3 81.1 - - - +
546A ALA* 1.3 62.6 + - - +
557A LEU* 3.4 20.0 - - - -
558A VAL* 4.0 5.8 - - - -
635A THR 2.9 7.2 + - - +
636A ILE* 3.3 13.0 - - - +
637A GLU* 3.0 22.5 + - - +
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Residues in contact with ALA 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 VAL* 5.6 2.5 - - + -
545A GLY* 1.3 76.2 - - - +
547A LEU* 1.3 67.6 + - - +
554A VAL* 5.8 0.3 - - - +
557A LEU* 4.0 10.6 + - - +
637A GLU* 3.2 20.0 - - + +
639A PHE* 3.4 28.5 - - + -
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Residues in contact with LEU 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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546A ALA* 1.3 77.9 - - - +
548A ARG* 1.3 73.2 + - - +
551A GLU* 4.5 10.3 - - + +
554A VAL* 3.9 20.4 - - + -
557A LEU* 3.9 12.6 - - + -
600A VAL* 3.8 26.7 - - + -
602A ARG 5.8 1.6 - - - +
603A PRO* 6.5 0.2 - - + -
604A LEU* 4.6 16.4 - - + +
636A ILE* 3.7 30.7 - - + -
637A GLU 3.1 4.9 + - - +
638A VAL* 3.2 15.9 - - + -
639A PHE* 2.9 31.8 + - - -
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Residues in contact with ARG 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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547A LEU* 1.3 86.4 - - - +
549A GLU* 1.3 72.3 + - + +
550A ASN 3.9 0.5 + - - -
551A GLU* 3.2 37.8 + - + +
604A LEU* 5.5 1.0 + - - +
638A VAL* 4.1 1.5 - - - +
639A PHE* 3.7 32.3 - - + +
640A ASP 5.4 3.8 - - - +
641A GLU* 3.3 23.1 - - - +
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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