Contacts of the strand formed by residues 531 - 538 (chain B) 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 GLU 531 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B PRO* 5.4 0.2 - - - +
529B PHE 4.3 0.6 - - - -
530B ILE* 1.3 79.4 - - - +
532B THR* 1.3 61.7 + - - +
734B ALA* 4.6 4.0 - - - +
760B THR 3.7 5.8 - - - +
761B GLY* 4.1 1.3 - - - -
535C TYR* 3.9 35.4 - - + -
755C ARG* 6.2 3.8 - - + -
756C SER 5.9 0.4 - - - +
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Residues in contact with THR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B THR* 4.7 4.7 - - + +
530B ILE* 4.1 1.3 - - - +
531B GLU* 1.3 75.5 - - - +
533B GLY* 1.3 73.2 + - - +
732B ASP* 2.8 36.8 + - - +
733B ALA* 3.1 16.4 + - - -
734B ALA* 3.1 11.6 + - - -
756B VAL* 4.9 4.8 - - - +
759B SER* 3.9 4.2 - - - -
760B THR 2.8 27.0 + - - +
761B GLY* 3.6 20.0 - - - +
762B TYR* 3.7 22.7 - - + +
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Residues in contact with GLY 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B THR* 5.7 4.5 - - - -
532B THR* 1.3 90.9 + - - +
534B ILE* 1.3 62.2 + - - -
691B THR* 5.1 1.8 - - - -
732B ASP* 3.2 10.2 - - - +
733B ALA* 2.5 34.2 + - - +
756B VAL* 4.8 2.2 - - - -
757B PHE 4.1 1.1 - - - -
758B ALA 3.5 13.7 - - - -
760B THR* 4.3 5.4 - - - -
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Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B GLY* 1.3 69.9 - - - -
535B SER* 1.3 69.7 + - - +
690B SER 5.7 0.2 - - - -
691B THR* 3.8 28.7 - - + +
694B ASN* 3.8 30.3 - - + -
695B ILE* 4.9 4.9 - - + +
730B ILE* 3.6 29.4 - - + -
731B TYR 3.8 3.1 - - - +
756B VAL 3.4 0.3 - - - -
757B PHE* 2.7 56.6 + - + +
758B ALA* 4.0 15.9 - - + -
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Residues in contact with SER 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ILE* 1.3 81.4 + - - +
536B VAL* 1.3 62.0 + - - +
729B PHE 3.5 0.2 - - - +
730B ILE* 3.5 7.1 - - - -
731B TYR 2.9 33.9 + - - +
733B ALA* 3.3 22.0 - - - +
736B LEU* 3.4 10.2 - - - +
737B ASN* 5.5 1.3 + - - -
750B THR* 4.5 9.9 - - - -
755B LYS 3.4 12.8 + - - -
756B VAL* 3.3 20.1 - - - +
757B PHE 5.1 0.2 - - - +
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B SER* 1.3 74.6 - - - +
537B MET* 1.3 56.4 + - - +
538B VAL 4.1 1.1 - - - +
663B VAL* 5.1 8.7 - - + -
728B ALA* 4.9 10.5 - - + -
729B PHE 3.2 7.0 - - - +
730B ILE* 3.7 22.4 - - + -
736B LEU* 3.9 2.2 - - - -
750B THR* 3.3 4.7 + - - -
751B ILE* 2.6 50.4 + - + +
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Residues in contact with MET 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL* 1.3 75.4 - - - +
538B VAL* 1.3 64.7 + - - +
718B LEU* 6.2 2.5 - - + -
721B LEU* 3.6 27.1 - - + +
728B ALA* 4.3 0.8 - - - -
729B PHE* 3.3 17.1 + - + +
736B LEU* 3.8 28.0 - - + +
740B ALA* 6.2 1.1 - - + -
748B LEU* 4.5 5.7 - - + +
749B VAL 3.3 19.5 - - - +
750B THR* 4.3 2.2 - - - -
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL* 4.1 2.0 + - - +
537B MET* 1.3 77.9 - - - +
539B SER* 1.3 68.5 + - - +
661B ASP 4.7 13.9 - - - +
662B GLN* 6.3 0.4 - - - -
663B VAL* 6.1 3.1 - - + +
727B ASP 4.3 8.7 - - - +
728B ALA* 4.6 12.5 - - + +
748B LEU* 3.8 4.4 - - - +
749B VAL* 3.2 28.8 + - + +
750B THR 5.0 0.2 - - - -
751B ILE* 5.0 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
------------------------------------------------------------
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