Contacts of the strand formed by residues 538 - 543 (chain C) in PDB entry 4PE5
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 538 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C THR* 5.7 1.8 - - + +
537C GLY* 1.3 74.4 - - - +
539C THR* 1.3 59.7 + - - +
688C SER* 5.2 2.7 - - - -
689C VAL* 3.7 38.1 - - + +
692C TYR* 4.8 7.2 - - + -
730C ILE* 4.9 1.3 - - + -
731C TRP 3.7 14.6 - - - +
732C ASP* 3.3 27.6 - - - +
752C LEU* 3.3 3.3 - - - +
753C PHE* 2.9 67.0 + - + +
754C PHE* 3.6 35.6 + - + -
756C SER* 6.0 0.4 - - - +
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Residues in contact with THR 539 (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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538C LEU* 1.3 74.9 - - - +
540C ILE* 1.3 78.4 + - - +
730C ILE* 3.5 5.4 - - - +
731C TRP 2.9 31.6 + - - +
733C SER* 3.4 31.0 - - - +
736C LEU* 3.3 22.5 - - + +
737C GLU* 5.1 2.7 - - + +
748C THR* 4.3 12.7 - - + -
749C THR* 3.9 10.0 + - - -
751C GLU 3.6 16.6 + - - -
752C LEU* 4.1 7.0 - - - -
753C PHE* 4.6 1.8 - - - -
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Residues in contact with ILE 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C THR* 1.3 85.7 + - - +
541C LEU* 1.3 62.5 + - - +
542C VAL* 4.2 6.1 - - + -
664C ILE* 4.1 8.7 - - + -
666C GLY* 3.5 35.4 - - - +
667C ILE* 3.9 4.7 - - - +
672C LEU* 3.8 19.3 - - + -
728C ALA* 3.6 30.3 - - + -
729C PHE 3.7 4.7 - - - +
730C ILE* 3.6 22.0 - - + -
736C LEU* 3.7 3.6 - - - -
748C THR* 3.2 4.2 - - - -
749C THR* 2.6 41.3 + - - -
751C GLU 5.8 1.3 - - - +
753C PHE* 4.4 8.5 - - + -
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Residues in contact with LEU 541 (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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540C ILE* 1.3 73.2 - - - +
542C VAL* 1.3 64.5 + - - +
718C ILE* 4.4 10.8 - - + -
721C VAL* 3.7 28.8 - - + +
728C ALA* 3.3 6.4 - - - -
729C PHE* 2.9 47.9 + - + +
736C LEU* 3.6 41.1 - - + +
739C GLU* 4.5 5.4 - - + -
746C LEU* 3.9 32.3 - - + -
747C VAL 3.7 19.1 - - - +
748C THR* 4.1 3.6 - - + +
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Residues in contact with VAL 542 (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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540C ILE* 4.2 9.6 - - + +
541C LEU* 1.3 81.9 - - - +
543C LYS* 1.3 76.3 + - + +
663C ARG* 6.4 1.1 - - - -
664C ILE* 4.0 30.5 - - + +
679C PHE* 6.0 0.9 - - + -
721C VAL* 4.3 3.6 - - - -
727C HIS 3.6 20.4 - - - +
728C ALA* 4.1 7.2 - - + -
746C LEU* 4.8 1.8 - - - -
747C VAL* 2.8 40.6 + - + +
748C THR 5.7 0.2 - - - -
749C THR* 5.1 4.3 - - - -
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Residues in contact with LYS 543 (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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542C VAL* 1.3 86.8 - - + +
544C LYS* 1.3 68.0 + - - +
545C GLU 3.9 0.2 + - - -
721C VAL* 3.3 32.4 - - + +
722C ARG* 5.3 2.2 - - - +
724C ASN* 4.7 15.9 - - - +
726C LEU 5.6 2.2 - - - +
727C HIS 5.0 0.4 + - - -
745C ASP 3.5 9.2 - - - +
746C LEU* 4.2 4.9 - - + -
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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