Contacts of the strand formed by residues 538 - 543 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A THR* 5.6 1.8 - - + +
537A GLY* 1.3 72.3 - - - +
539A THR* 1.3 59.2 + - - +
688A SER* 5.4 2.7 - - - -
689A VAL* 3.7 42.0 - - + +
692A TYR* 4.7 8.5 - - + -
730A ILE* 4.8 1.6 - - + -
731A TRP 3.5 9.0 - - - +
732A ASP* 3.3 26.9 - - - +
752A LEU* 3.3 2.5 - - - +
753A PHE* 3.0 69.6 + - + +
754A PHE* 3.5 38.3 + - + -
756A SER* 6.0 0.4 - - - +
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Residues in contact with THR 539 (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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537A GLY 3.8 0.4 + - - -
538A LEU* 1.3 74.8 - - - +
540A ILE* 1.3 79.4 + - - +
730A ILE* 3.5 4.9 - - - +
731A TRP 2.9 31.3 + - - +
733A SER* 3.5 30.3 - - - +
736A LEU* 3.3 23.1 - - + +
737A GLU* 5.0 3.6 - - + +
748A THR* 4.4 10.5 - - + -
749A THR* 4.0 10.0 + - - -
751A GLU 3.8 14.7 + - - -
752A LEU* 4.1 7.9 - - - -
753A PHE* 4.5 3.1 - - - -
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Residues in contact with ILE 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A THR* 1.3 87.2 + - - +
541A LEU* 1.3 62.8 + - - +
542A VAL* 5.7 1.8 - - + -
664A ILE* 5.1 6.7 - - + -
666A GLY* 3.4 35.4 - - - +
667A ILE* 4.0 5.2 - - - +
672A LEU* 4.1 11.4 - - + -
728A ALA* 3.6 30.1 - - + -
729A PHE 3.5 7.6 - - - +
730A ILE* 3.6 25.4 - - + -
736A LEU* 3.7 3.4 - - - -
748A THR* 3.3 5.2 - - - -
749A THR* 2.7 46.5 + - - -
751A GLU 5.9 1.1 - - - +
753A PHE* 4.4 7.2 - - + -
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Residues in contact with LEU 541 (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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540A ILE* 1.3 72.7 - - - +
542A VAL* 1.3 61.8 + - - +
718A ILE* 4.3 14.1 - - + -
721A VAL* 3.9 25.9 - - + +
728A ALA* 3.3 6.7 - - - -
729A PHE* 2.9 38.8 + - + +
736A LEU* 3.7 46.0 - - + +
739A GLU* 4.4 7.4 - - + -
746A LEU* 3.9 33.9 - - + +
747A VAL 3.6 23.8 - - - +
748A THR* 4.1 3.1 - - + +
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Residues in contact with VAL 542 (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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540A ILE* 4.1 2.6 + - + +
541A LEU* 1.3 75.2 - - - +
543A LYS* 1.3 66.8 + - - +
664A ILE* 5.6 10.5 - - + -
721A VAL* 4.2 5.2 - - - -
727A HIS 3.7 18.2 - - - +
728A ALA* 4.8 2.9 - - + -
746A LEU* 3.8 4.4 - - - -
747A VAL* 2.9 39.4 + - - +
748A THR 5.8 1.8 - - - -
749A THR* 5.9 2.9 - - - +
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Residues in contact with LYS 543 (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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542A VAL* 1.3 78.2 - - - +
544A LYS* 1.3 67.9 + - - +
545A GLU* 3.7 1.7 + - - -
721A VAL* 3.7 26.6 - - + +
722A ARG* 5.7 0.9 - - - +
724A ASN* 4.5 17.9 - - - +
726A LEU 5.7 2.2 - - - +
727A HIS 4.8 1.6 + - - -
745A ASP 3.6 8.5 - - - +
746A LEU* 4.5 4.5 - - + -
747A VAL* 5.5 0.2 - - - -
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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