Contacts of the helix formed by residues 452 - 457 (chain C) in PDB entry 2CEA
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 452 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C GLU* 3.2 16.4 - - - +
444C SER* 3.8 23.3 - - - +
446C ILE 5.7 2.2 - - - +
449C GLY 3.7 4.5 + - - +
450C TYR 3.4 1.0 - - - +
451C LYS* 1.3 87.5 - - - +
453C LEU* 1.3 61.0 + - - +
454C GLY* 3.9 4.7 - - - +
455C TYR* 3.6 27.2 + - + +
456C THR* 3.1 19.2 + - - -
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Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C GLU* 2.5 18.3 + - - +
427C HIS* 3.5 11.7 - - + +
428C ALA* 3.2 45.3 - - + +
431C SER* 4.1 1.8 - - - +
438C GLU* 5.2 0.7 - - + +
439C PRO 4.9 3.1 - - - +
440C VAL* 3.8 36.3 - - + -
441C HIS 5.4 0.9 - - - +
442C ARG 3.5 14.8 + - - +
443C ILE* 3.8 2.0 - - + -
451C LYS 3.5 1.0 + - - -
452C ALA* 1.3 70.0 - - - +
454C GLY* 1.3 64.6 + - - +
455C TYR 3.2 0.4 - - - -
456C THR* 3.9 15.9 - - + -
457C LEU* 2.9 48.6 + - + +
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Residues in contact with GLY 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C HIS* 5.6 0.4 - - - -
424C GLU* 3.1 12.1 + - - -
427C HIS* 3.4 27.3 + - - -
452C ALA* 3.2 4.6 - - - +
453C LEU* 1.3 76.1 - - - +
455C TYR* 1.3 59.0 + - - +
457C LEU* 4.1 3.2 - - - +
458C HIS* 3.0 28.1 + - - -
500C ASP* 4.3 2.9 - - - +
1607C ZN 4.1 5.6 - - - -
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Residues in contact with TYR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C PRO* 5.8 2.9 - - + -
310C ASP* 5.3 0.4 - - - +
446C ILE 5.7 0.4 - - - -
447C PRO 4.2 5.4 + - - -
448C ARG* 3.3 31.0 - - + +
449C GLY 3.1 27.4 - - - -
450C TYR* 3.7 47.6 - + + +
452C ALA* 3.6 20.6 + - + +
453C LEU 3.2 0.2 - - - -
454C GLY* 1.3 76.2 - - - +
456C THR* 1.3 55.8 + - - +
457C LEU 3.2 0.2 - - - -
458C HIS* 2.6 39.4 + - - +
459C LEU* 3.4 8.7 + - + +
499C ASN* 6.1 0.9 - - - -
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Residues in contact with THR 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C GLU* 5.7 5.6 - - + -
439C PRO 5.6 4.9 - - - +
442C ARG* 5.3 2.8 + - - +
450C TYR 4.9 3.8 + - - -
451C LYS* 4.2 5.5 + - - -
452C ALA 3.1 14.3 + - - -
453C LEU* 3.1 25.8 + - + +
455C TYR* 1.3 77.5 - - - +
457C LEU* 1.3 58.9 + - + +
459C LEU* 2.7 50.1 + - + +
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C HIS* 3.8 23.1 - - + +
431C SER* 4.2 9.6 - - - +
438C GLU* 4.7 25.1 - - + -
453C LEU* 2.9 38.6 + - + +
454C GLY 4.1 3.1 - - - +
455C TYR 3.1 0.2 + - - -
456C THR* 1.3 77.7 - - + +
458C HIS* 1.3 59.0 + - - +
459C LEU 3.3 6.0 + - - +
475C LYS* 4.3 17.1 - - + +
478C ALA* 3.7 43.3 - - + +
479C LEU* 3.6 24.4 - - + +
503C ARG* 5.5 0.3 - - - +
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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
------------------------------------------------------------
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