Contacts of the strand formed by residues 518 - 524 (chain B) in PDB entry 1EX0
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 VAL 518 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517B ASN* 1.3 94.9 + - + +
519B ASP* 1.3 70.0 + - - +
539B PHE* 4.9 1.3 - - + -
540B ARG 3.2 11.9 - - - +
541B ASN* 4.2 6.5 - - - -
547B TYR* 3.8 17.7 - - + -
549B ILE* 4.3 1.8 - - + -
577B LEU* 3.8 21.5 - - + -
612B ILE* 3.1 28.7 - - + +
619B LEU* 3.3 40.2 - - + +
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ASN 5.5 0.7 + - - +
518B VAL* 1.3 81.3 - - - +
520B MET* 1.3 68.6 + - - +
521B ASP* 5.9 0.3 - - - +
539B PHE* 3.5 3.1 - - - -
540B ARG* 2.7 80.4 + - - +
542B ASN* 4.0 9.4 + - - -
619B LEU* 4.2 5.8 - - + -
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Residues in contact with MET 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ASP* 1.3 84.1 - - - +
521B ASP* 1.3 79.4 + - - +
522B PHE* 4.3 0.2 - - - -
537B ILE* 3.8 15.0 - - + -
538B THR 3.2 12.8 - - - +
539B PHE* 3.9 12.8 - - + -
608B VAL* 3.3 48.5 - - + +
609B THR* 4.7 1.8 - - - +
610B ALA* 5.2 1.6 - - + -
619B LEU* 4.1 24.7 - - + +
620B ALA 3.9 13.1 - - - +
621B LYS* 3.7 36.8 + - + +
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Residues in contact with ASP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ASP* 5.9 0.4 - - - +
520B MET* 1.3 83.8 - - - +
522B PHE* 1.3 66.1 + - - +
537B ILE* 3.6 1.2 - - - -
538B THR* 2.7 40.1 + - - +
621B LYS* 3.0 25.7 + - - +
623B LYS* 2.9 30.7 + - - -
1331B PO4 5.1 1.0 + - - -
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Residues in contact with PHE 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B MET* 4.3 0.4 - - - -
521B ASP* 1.3 85.1 + - - +
523B GLU* 1.3 64.4 + - - +
524B VAL* 3.8 9.9 - - + -
535B LEU* 3.9 20.9 - - + -
536B SER 3.3 13.0 - - - +
537B ILE* 3.7 14.6 - - + -
538B THR* 4.5 0.4 - - - +
606B PHE* 3.6 34.5 - - + -
608B VAL* 3.6 28.7 - - + -
621B LYS* 3.6 37.9 - - + -
623B LYS* 2.9 58.0 + - + -
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Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B PHE* 1.3 76.2 - - - +
524B VAL* 1.3 73.0 + - - +
525B GLU* 4.3 1.6 + - - +
535B LEU* 3.3 3.1 - - - +
536B SER* 2.9 39.7 + - - +
623B LYS* 5.1 2.2 - - - -
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASN* 6.1 0.9 - - - +
522B PHE* 3.8 27.1 - - + -
523B GLU* 1.3 87.9 - - - +
525B GLU* 1.3 69.5 + - - +
526B ASN* 3.7 7.8 + - - +
533B PHE* 3.5 32.3 - - + -
534B LYS 3.7 4.5 - - - +
535B LEU* 4.2 8.1 - - + +
606B PHE* 3.9 22.4 - - + -
623B LYS* 4.0 16.7 - - + +
624B SER 5.7 0.9 - - - +
625B THR* 4.4 11.2 - - - -
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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