Contacts of the helix formed by residues 543 - 547 (chain C) in PDB entry 4OIP
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 ASN 543 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C LEU* 3.3 33.4 - - - +
405C ARG* 3.2 27.8 - - - +
442C GLU* 3.3 12.6 - - - +
541C SER* 3.2 1.0 + - - -
542C VAL* 1.3 78.4 + - - +
544C THR* 1.3 62.6 + - - +
546C LEU* 3.0 13.9 + - - +
547C ILE* 4.0 0.5 - - - +
562C SER* 3.2 28.4 + - - +
565C GLN* 2.9 24.7 + - - +
566C THR* 3.2 25.5 + - - +
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Residues in contact with THR 544 (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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439C CYS* 3.4 10.0 - - - -
441C VAL* 3.7 21.9 - - + +
442C GLU* 4.0 0.7 - - - +
540C PHE* 3.6 34.3 - - + -
541C SER* 2.8 25.6 + - - -
543C ASN* 1.3 77.3 - - - +
545C ASN* 1.3 59.2 + - - +
546C LEU 3.0 4.7 + - - -
547C ILE* 3.1 22.4 + - + +
550C LEU* 3.8 22.3 - - + +
562C SER* 3.1 16.0 + - - -
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Residues in contact with ASN 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ALA* 4.0 6.6 - - - +
537C LYS* 3.1 34.3 + - + +
540C PHE* 2.7 30.5 + - - +
541C SER 2.5 31.3 + - - +
542C VAL* 3.6 8.4 - - - +
543C ASN 3.2 0.4 - - - -
544C THR* 1.3 75.7 - - - +
546C LEU* 1.3 50.7 + - - +
547C ILE 3.3 2.2 - - - -
581C THR* 2.7 34.1 + - - +
583C LEU* 3.6 20.9 - - + +
905C ILE* 3.4 22.1 - - + +
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Residues in contact with LEU 546 (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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401C LEU* 3.6 37.0 - - + -
542C VAL 3.4 14.4 - - - +
543C ASN 3.0 11.1 + - - +
545C ASN* 1.3 76.9 - - - +
547C ILE* 1.3 60.4 + - - +
548C PRO* 3.2 12.0 - - - +
565C GLN* 3.3 14.8 - - - +
581C THR* 3.6 16.6 - - - +
583C LEU* 4.0 22.4 - - + -
584C GLU* 4.0 21.0 - - + +
587C VAL* 4.3 9.0 - - + -
666C LEU* 3.7 18.2 - - + -
842C ARG* 3.2 18.9 + - - -
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Residues in contact with ILE 547 (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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543C ASN 4.0 0.4 - - - +
544C THR* 3.1 20.9 + - + +
545C ASN 3.3 0.8 - - - -
546C LEU* 1.3 80.0 - - - +
548C PRO* 1.3 74.9 - - + +
550C LEU* 3.4 25.2 - - + +
553C ASP* 3.9 7.9 - - - +
558C ALA* 3.6 27.6 - - + +
562C SER* 3.8 11.4 - - - +
565C GLN* 4.0 12.6 - - - +
581C THR* 3.6 2.5 - - - -
842C ARG* 3.2 31.0 - - + +
843C HIS* 3.8 12.6 - - - +
905C ILE* 3.3 21.0 - - - +
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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