Contacts of the strand formed by residues 342 - 346 (chain E) in PDB entry 5FXY
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 342 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E ALA* 4.1 8.7 - - + -
335E SER 3.5 14.1 - - - +
336E SER* 4.0 6.1 - - - -
341E ARG* 1.3 72.1 - - - +
343E ASN* 1.3 71.1 + - - +
344E VAL* 3.9 8.8 + - + +
368E PHE 4.0 0.9 - - - +
369E ILE* 3.8 0.7 - - - -
370E HIS* 2.9 38.7 + - + +
377E ILE* 3.7 13.4 - - + +
380E PHE* 3.5 43.5 - - + -
390E ILE* 4.5 2.0 - - + -
392E SER* 4.2 14.4 - - - -
402E TRP* 3.6 29.2 - - + -
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Residues in contact with ASN 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E SER* 4.3 6.9 + - - -
316E HIS* 3.2 53.9 + - - +
334E ALA* 3.3 4.7 - - - +
335E SER* 2.9 33.5 + - - +
341E ARG* 4.3 5.4 - - - +
342E LEU* 1.3 73.8 - - - +
344E VAL* 1.3 61.3 + - - +
345E TRP* 3.9 15.3 - - - +
366E LEU* 3.7 19.0 - - + +
368E PHE 3.5 3.6 - - - -
369E ILE* 3.6 27.3 - - - +
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Residues in contact with VAL 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E ILE* 4.0 20.9 - - + -
333E LEU 3.7 9.0 - - - +
334E ALA* 4.2 4.7 - - + +
342E LEU* 3.9 17.0 - - + +
343E ASN* 1.3 76.2 - - - +
345E TRP* 1.3 59.0 + - - +
366E LEU* 3.6 3.9 - - - +
367E LEU* 2.8 35.6 + - + -
368E PHE* 2.8 23.6 + - + +
382E TRP* 4.0 9.0 - - + -
388E TRP* 4.4 2.9 - - + -
390E ILE* 4.4 3.6 - - + -
402E TRP* 4.2 10.1 - - + -
404E MET* 3.7 33.4 - - + -
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Residues in contact with TRP 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E VAL* 4.5 3.3 - - + +
313E PHE* 3.4 53.9 - + + +
314E GLU 3.7 24.9 - - - -
315E SER* 3.8 11.7 - - - -
316E HIS* 4.1 9.2 - + - -
331E THR 3.8 0.3 - - - +
332E ILE* 3.4 8.5 - - - +
333E LEU* 2.6 66.5 + - + +
334E ALA* 4.4 2.9 - - - -
335E SER* 2.9 27.2 + - - -
343E ASN* 3.9 27.6 - - + +
344E VAL* 1.3 77.4 - - - +
346E ASP* 1.3 60.2 + - - +
347E LEU 3.9 0.9 - - - -
363E PRO* 4.4 2.5 - - + -
365E GLU* 3.5 10.1 - - + -
366E LEU* 3.7 38.6 - - + -
367E LEU* 4.6 0.9 - - - -
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Residues in contact with ASP 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E THR* 3.4 8.8 + - - -
332E ILE* 3.3 23.3 - - + +
344E VAL 4.2 0.2 + - - -
345E TRP* 1.3 71.9 - - - +
347E LEU* 1.3 56.2 + - - +
348E SER* 2.7 21.5 + - - -
349E LYS* 3.1 41.6 + - + +
365E GLU* 2.7 29.1 + - - +
367E LEU* 4.1 18.1 - - + +
531F ARG* 3.2 22.5 + - - -
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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