Contacts of the strand formed by residues 409 - 414 (chain E) in PDB entry 5U8T
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 PHE 409 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E TRP* 4.9 0.2 - - - -
274E ILE* 3.3 50.6 - - + +
288E TYR* 6.3 2.0 - + - -
292E TYR* 4.1 12.3 - + - -
295E LEU* 3.4 48.2 - - + -
296E GLN* 3.3 35.7 - - + -
299E VAL* 4.4 6.5 - - + -
318E LEU* 4.2 7.4 - - + -
319E ASN 4.1 4.0 - - - -
320E ILE* 3.5 16.6 - - + -
323E ASP* 3.4 5.0 + - - +
408E GLY* 1.3 79.5 - - - -
410E VAL* 1.3 67.0 + - - +
411E ARG 4.3 0.7 - - - -
420E SER* 3.5 0.7 - - - -
421E ALA* 2.9 25.9 + - - +
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Residues in contact with VAL 410 (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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271E TRP* 4.4 0.2 - - - -
318E LEU* 3.0 24.7 - - - +
319E ASN 3.1 20.7 + - - +
321E GLN* 4.3 22.4 - - + +
323E ASP* 3.4 13.9 - - - +
330E ARG* 4.6 6.7 - - - +
408E GLY 4.3 0.7 - - - +
409E PHE* 1.3 79.1 - - - +
411E ARG* 1.3 69.2 + - - +
412E THR* 4.0 4.8 - - + +
418E SER* 4.2 10.3 - - - -
419E ILE 3.4 25.8 - - - +
420E SER* 3.2 23.3 - - - +
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Residues in contact with ARG 411 (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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267E LEU 5.3 0.8 + - - -
268E SER* 4.9 9.3 - - - +
271E TRP* 3.4 68.9 - - + +
317E THR* 6.3 0.4 - - - -
318E LEU* 3.7 11.6 - - + +
410E VAL* 1.3 78.2 - - - +
412E THR* 1.3 71.5 + - - +
413E LEU* 4.8 14.7 - - - +
418E SER* 3.4 1.4 - - - -
419E ILE* 2.9 37.6 + - + +
424E PHE* 6.0 3.6 - - - -
486E ASP* 2.6 44.5 + - - +
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Residues in contact with THR 412 (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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316E LEU* 2.9 30.3 - - - +
317E THR 3.0 36.6 + - - +
318E LEU* 4.4 3.2 - - - +
319E ASN* 5.1 1.8 - - + +
410E VAL* 4.0 9.2 - - + +
411E ARG* 1.3 90.9 + - - +
413E LEU* 1.3 60.1 + - - +
414E GLY* 3.2 1.6 - - - -
418E SER* 3.3 24.9 - - - +
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Residues in contact with LEU 413 (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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415 ASP* 4.9 3.8 - - - +
313E PRO 5.1 1.6 - - - +
314E ASP* 6.2 0.4 - - - -
316E LEU* 3.0 33.7 - - + +
411E ARG* 4.3 14.1 - - - +
412E THR* 1.3 74.1 - - - +
414E GLY* 1.3 63.1 + - - +
415E TYR* 2.9 5.9 + - - +
416E ARG* 3.3 57.8 + - + +
417E GLY 2.9 10.0 + - - +
419E ILE* 5.8 4.1 - - + +
486E ASP* 5.1 10.3 - - + +
489E VAL* 3.7 19.1 - - + -
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Residues in contact with GLY 414 (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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705 GLY* 4.1 11.9 - - - -
311E LYS* 5.6 9.4 - - - -
316E LEU* 3.1 19.5 - - - +
412E THR* 3.2 2.2 - - - +
413E LEU* 1.3 74.8 - - - +
415E TYR* 1.3 57.7 + - - -
417E GLY* 2.4 37.6 + - - -
418E SER* 4.7 4.7 - - - -
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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