Contacts of the helix formed by residues 474 - 479 (chain C) in PDB entry 5ZR1
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 474 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C TYR* 4.1 12.3 - - + +
327C SER* 3.4 28.9 - - - +
331C GLN* 5.1 2.2 - - - +
470C ASN* 5.3 2.8 - - + +
472C SER* 3.8 6.0 + - - +
473C GLY* 1.3 75.9 - - - +
475C LEU* 1.3 68.1 + - + +
476C THR 3.4 0.7 - - - -
477C GLN* 3.3 1.9 + - + -
478C SER* 2.9 42.3 + - - +
403F GLY* 3.3 32.8 - - - +
404F SER 3.4 12.3 - - - +
405F MET* 3.8 25.6 - - + +
407F GLN* 3.4 16.6 - - + +
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Residues in contact with LEU 475 (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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298C PHE* 3.9 27.4 - - + -
301C PHE* 3.6 28.0 - - + -
320C MET* 3.9 20.4 - - + +
323C TYR* 4.2 18.6 - - + +
324C SER* 4.2 17.9 - - - +
327C SER* 5.4 2.7 - - - -
469C ASP 5.3 4.3 - - - +
470C ASN* 4.6 18.3 - - + +
474C LEU* 1.3 91.0 - - + +
476C THR* 1.3 56.9 + - - +
477C GLN 3.2 0.4 - - - -
478C SER 4.6 0.2 - - - +
479C ILE* 3.1 39.7 + - + +
480C PHE* 3.4 8.8 + - - -
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Residues in contact with THR 476 (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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301C PHE* 3.7 25.7 - - + -
305C LYS* 4.5 8.5 + - - -
470C ASN* 5.8 2.9 - - + +
473C GLY* 4.1 22.7 - - - +
475C LEU* 1.3 75.7 - - - +
477C GLN* 1.3 57.8 + - + +
480C PHE* 2.9 28.3 + - - +
481C PRO* 3.7 3.3 - - - +
482C SER 4.6 1.7 + - - -
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Residues in contact with GLN 477 (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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317B TYR* 3.4 8.1 + - - -
477B PHE 3.9 6.9 - - - +
479B ASP* 5.0 1.2 - - - +
473C GLY 3.3 20.7 + - - +
474C LEU* 3.3 5.1 + - - +
475C LEU 3.2 0.4 - - - -
476C THR* 1.3 80.6 + - - +
478C SER* 1.3 60.9 + - - +
481C PRO* 3.3 19.4 - - - +
482C SER 6.0 0.2 - - - -
486C ASN* 3.1 34.5 + - - +
400F ARG* 4.1 22.9 + - - +
401F LYS* 4.5 13.9 + - - +
403F GLY* 4.5 13.9 - - - -
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Residues in contact with SER 478 (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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476B VAL* 3.7 12.7 - - - +
477B PHE* 2.8 45.4 + - - +
478B HIS* 4.9 1.6 + - - -
323C TYR* 2.9 36.7 + - - -
474C LEU* 2.9 25.6 + - - +
477C GLN* 1.3 78.2 - - - +
479C ILE* 1.3 60.7 + - - +
481C PRO* 4.5 0.2 - - - -
403F GLY* 4.1 8.3 + - - -
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Residues in contact with ILE 479 (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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312B PHE* 6.4 0.4 - - + -
475B PHE 5.1 2.2 - - - -
476B VAL* 5.3 4.0 - - + -
477B PHE* 3.7 14.7 - - - -
316C LEU* 4.8 1.3 - - + -
319C LYS* 3.8 44.1 + - + +
320C MET* 4.4 14.1 - - + -
323C TYR* 3.7 44.0 - - + -
475C LEU* 3.1 20.4 + - + +
478C SER* 1.3 79.8 - - - +
480C PHE* 1.3 87.9 + - + +
481C PRO* 3.4 7.9 - - - +
418E ILE* 3.8 3.8 - - - +
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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