Contacts of the helix formed by residues 449 - 461 (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 ALA 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A VAL* 3.6 10.5 - - - +
448A GLY* 1.3 71.2 - - - -
450A GLU* 1.3 60.3 + - + +
452A LEU* 3.3 2.0 + - - +
453A LEU* 2.8 36.5 + - + +
475A LEU* 3.5 29.1 - - + +
479A GLU* 3.7 19.9 + - - +
482A ASN* 4.0 10.3 - - - +
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Residues in contact with GLU 450 (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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448A GLY 3.4 0.6 - - - -
449A ALA* 1.3 81.1 - - + +
451A ARG* 1.3 56.2 - - - +
453A LEU* 3.4 21.6 + - - +
454A GLU* 2.9 30.0 + - - +
457A ARG* 4.4 12.8 + - - -
482A ASN* 5.3 2.4 + - - -
484A ALA* 5.3 2.4 - - - +
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Residues in contact with ARG 451 (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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446A MET 3.4 15.3 - - - +
447A GLY* 3.5 24.4 + - - +
448A GLY 3.4 2.3 + - - +
449A ALA 3.3 0.4 - - - -
450A GLU* 1.3 73.4 - - - +
452A LEU* 1.3 66.4 + - - +
454A GLU* 2.8 48.2 + - - +
455A GLN* 3.1 64.8 + - - +
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Residues in contact with LEU 452 (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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443A VAL* 3.8 35.2 - - + +
446A MET* 3.9 32.9 + - + -
448A GLY 3.1 10.7 + - - +
449A ALA* 3.5 9.0 - - - +
451A ARG* 1.3 75.8 - - - +
453A LEU* 1.3 61.6 + - - +
454A GLU 3.2 0.2 + - - -
455A GLN* 3.3 12.3 + - - +
456A ALA* 2.8 33.2 + - + +
471A VAL* 4.4 16.4 - - + +
472A VAL* 4.3 21.3 - - + -
474A ARG* 5.2 1.6 - - + -
475A LEU* 4.0 23.8 - - + +
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Residues in contact with LEU 453 (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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449A ALA 2.8 22.8 + - - +
450A GLU* 3.7 26.7 - - - +
452A LEU* 1.3 74.5 - - + +
454A GLU* 1.3 53.9 + - - +
456A ALA* 3.2 3.2 + - - +
457A ARG* 2.8 60.0 + - - +
472A VAL* 4.9 3.8 - - + -
475A LEU* 3.6 23.6 - - + -
482A ASN* 4.3 7.4 - - - +
484A ALA* 3.9 25.8 - - + +
485A ALA* 3.9 19.1 - - + +
488A LEU* 4.1 19.3 - - + -
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Residues in contact with GLU 454 (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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450A GLU 2.9 14.3 + - - +
451A ARG* 2.8 46.8 + - - +
452A LEU 3.2 0.2 - - - -
453A LEU* 1.3 78.6 - - - +
455A GLN* 1.3 62.3 + - - +
457A ARG* 3.6 11.6 + - - +
458A ALA* 3.3 17.8 + - - +
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Residues in contact with GLN 455 (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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446A MET* 3.5 28.3 + - - +
451A ARG* 3.1 50.9 + - - +
452A LEU* 3.8 6.2 - - - +
454A GLU* 1.3 73.8 - - - +
456A ALA* 1.3 61.2 + - - +
458A ALA* 3.3 8.1 + - - +
459A SER* 3.0 30.9 + - - -
462A ARG* 4.6 1.0 + - - -
467A TRP* 6.2 0.2 - - - -
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Residues in contact with ALA 456 (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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452A LEU* 2.8 22.1 + - + +
453A LEU* 3.7 4.3 - - - +
455A GLN* 1.3 74.5 - - - +
457A ARG* 1.3 60.2 + - - +
459A SER* 3.1 8.8 + - - -
460A TYR* 2.7 29.6 + - - +
467A TRP* 5.6 1.3 - - - +
468A VAL* 3.8 6.6 - - + +
471A VAL* 4.5 10.8 - - + -
472A VAL* 3.5 31.6 - - + -
488A LEU* 3.8 8.1 - - + -
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Residues in contact with ARG 457 (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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450A GLU* 4.4 10.3 + - - -
453A LEU* 2.8 51.5 + - - +
454A GLU* 3.8 10.0 - - - +
456A ALA* 1.3 73.2 - - - +
458A ALA* 1.3 55.4 + - - +
460A TYR* 3.3 10.5 + - - +
461A ALA* 2.9 27.7 + - - +
484A ALA* 3.9 30.9 + - - +
488A LEU* 3.8 20.9 - - + +
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Residues in contact with ALA 458 (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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454A GLU 3.3 10.1 + - - +
455A GLN* 3.3 11.5 + - - +
456A ALA 3.2 0.6 - - - -
457A ARG* 1.3 73.7 - - - +
459A SER* 1.3 65.1 + - - +
461A ALA* 3.3 9.0 + - - +
462A ARG* 3.2 43.4 + - - +
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Residues in contact with SER 459 (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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455A GLN* 3.0 14.2 + - - +
456A ALA* 3.5 7.9 - - - -
458A ALA* 1.3 73.6 - - - +
460A TYR* 1.3 65.9 + - - +
462A ARG* 3.0 34.8 + - - +
464A GLU* 3.2 27.2 + - - +
467A TRP* 3.7 33.2 + - - -
468A VAL* 3.9 7.4 - - - -
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Residues in contact with TYR 460 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.8 1.9 - - - +
27A SER* 5.2 4.9 - - - -
29A PHE* 5.0 0.7 - - - -
456A ALA 2.7 20.5 + - - +
457A ARG* 3.4 10.3 - - - +
458A ALA 3.3 0.2 - - - -
459A SER* 1.3 74.0 - - - +
461A ALA* 1.3 60.9 + - - +
463A GLY* 2.9 20.5 + - - +
464A GLU 4.7 0.4 - - - +
465A TYR* 3.6 34.6 + + - -
468A VAL* 3.6 11.3 - - + +
488A LEU* 3.8 21.1 - - + -
491A ASP* 3.8 18.8 - - + +
492A ALA* 3.7 31.6 - - + -
495A GLN* 3.6 23.6 + - - +
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Residues in contact with ALA 461 (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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29A PHE* 3.2 19.0 - - - -
457A ARG 2.9 14.1 + - - +
458A ALA* 3.6 12.6 - - - +
459A SER 3.2 0.2 - - - -
460A TYR* 1.3 80.5 - - + +
462A ARG* 1.3 58.2 + - + +
463A GLY 3.3 1.1 - - - -
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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