Contacts of the helix formed by residues 540 - 550 (chain A) in PDB entry 2CFZ
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 THR 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A ASP* 1.3 72.7 + - - +
541A GLY* 1.3 61.4 + - - +
543A LEU* 3.3 6.9 + - + +
544A PHE* 3.0 59.0 + - + -
567A LEU* 4.1 11.9 - - + -
570A ILE* 3.4 20.6 - - - +
572A GLU* 4.1 3.0 + - - -
574A TYR* 3.7 21.1 - - + -
602A ARG* 2.8 30.5 + - - +
605A LEU* 5.1 1.6 - - + -
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Residues in contact with GLY 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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539A ASP* 3.0 10.4 + - - -
540A THR* 1.3 76.8 - - - +
542A LEU* 1.4 55.7 + - - +
544A PHE* 3.2 5.0 + - - +
545A ASP* 2.8 36.7 + - - +
574A TYR* 3.3 15.7 + - - -
585A ASN* 3.5 18.7 + - - -
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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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205A ILE* 4.2 3.4 - - + -
206A LYS* 3.8 47.1 - - + +
209A VAL* 3.9 16.8 - - + -
210A LEU* 3.7 32.5 - - + -
538A MET* 3.9 18.8 - - + -
539A ASP* 3.2 25.3 + - + +
541A GLY* 1.4 71.1 - - - +
543A LEU* 1.3 63.0 + - - +
545A ASP* 3.2 14.7 + - + +
546A TYR* 2.8 27.0 + - - +
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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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535A LEU* 4.2 8.1 - - + -
538A MET* 3.7 23.2 - - + -
539A ASP 3.0 13.3 + - - +
540A THR* 3.4 11.0 - - + +
542A LEU* 1.3 76.7 - - - +
544A PHE* 1.3 62.6 + - + +
546A TYR* 3.1 14.2 + - + +
547A LEU* 3.0 42.2 + - + +
602A ARG* 3.9 30.3 - - - +
605A LEU* 4.3 13.9 - - + -
606A ASN* 4.4 0.2 - - - +
609A LEU* 3.7 32.8 - - + -
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Residues in contact with PHE 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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540A THR* 3.0 40.5 + - + -
541A GLY 3.5 1.8 - - - +
543A LEU* 1.3 75.1 - - + +
545A ASP* 1.3 60.1 - - - +
547A LEU* 3.3 23.9 + - + +
548A GLY* 3.0 24.1 + - - -
565A LEU* 2.8 35.7 - - + -
574A TYR* 3.5 34.5 - + + -
576A LEU* 3.9 22.7 - - + -
583A LEU* 4.3 11.4 - - + +
585A ASN* 3.2 25.4 + - + +
605A LEU* 4.5 14.4 - - + -
637A PHE* 6.4 1.1 - + - -
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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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206A LYS* 5.8 1.0 + - - -
210A LEU* 3.9 20.7 - - + +
541A GLY 2.8 18.7 + - - +
542A LEU* 3.2 21.0 - - + +
544A PHE* 1.3 75.1 - - - +
546A TYR* 1.3 62.2 + - - +
548A GLY* 3.1 3.9 + - - -
549A VAL* 3.1 23.9 + - - +
585A ASN* 3.0 19.5 + - - +
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Residues in contact with TYR 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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209A VAL* 3.7 42.4 - - + -
210A LEU* 3.7 13.6 - - - +
212A GLY 5.7 0.9 - - - -
213A ASN* 5.7 3.3 + - - +
538A MET* 5.9 2.2 - - + -
542A LEU 2.8 13.2 + - - +
543A LEU* 3.1 17.9 + - + +
545A ASP* 1.3 74.7 - - - +
547A LEU* 1.3 73.4 + - + +
549A VAL* 3.0 18.0 + - + +
550A ARG* 3.1 39.5 + - + +
643A PHE* 4.0 24.6 - + - -
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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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543A LEU* 3.0 25.9 + - + +
544A PHE* 3.3 27.8 + - + +
546A TYR* 1.3 82.4 - - + +
548A GLY* 1.3 61.6 + - - +
550A ARG* 3.0 34.0 + - - +
551A LEU 3.3 8.3 + - - -
583A LEU* 4.2 12.8 - - + -
605A LEU* 6.2 2.2 - - + -
609A LEU* 4.8 16.6 - - + -
636A LEU* 6.3 0.7 - - + -
637A PHE* 4.1 26.2 - - + -
640A LEU* 3.5 31.3 - - + +
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Residues in contact with GLY 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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544A PHE 3.0 14.4 + - - -
545A ASP* 3.1 5.1 + - - -
547A LEU* 1.3 74.6 - - - +
549A VAL* 1.3 61.3 + - - +
551A LEU* 3.2 21.9 + - - +
582A HIS* 6.1 2.6 - - - -
583A LEU* 3.9 30.7 + - - +
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Residues in contact with VAL 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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210A LEU* 3.8 42.4 - - + +
545A ASP 3.1 12.8 + - - +
546A TYR* 3.0 16.4 + - + +
548A GLY* 1.3 76.0 - - - +
550A ARG* 1.3 58.0 + - - +
551A LEU 3.4 4.0 + - - +
643A PHE* 3.7 27.2 - - + -
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Residues in contact with ARG 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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546A TYR* 3.1 48.4 + - + +
547A LEU* 3.0 31.0 + - - +
549A VAL* 1.3 76.2 - - - +
551A LEU* 1.3 61.5 + - - +
552A ASP* 4.3 0.2 - - - -
609A LEU* 5.4 6.7 - - - +
640A LEU* 4.0 28.9 + - + +
641A GLY* 2.6 60.3 + - - +
642A ASP* 3.4 22.9 + - - +
643A PHE* 4.2 16.6 - - + -
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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