Contacts of the helix formed by residues 429 - 434 (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 THR 429 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 3.6 28.5 - - + -
425E VAL* 3.4 23.6 - - + +
426E GLU* 2.4 28.8 + - - +
428E LEU* 1.3 74.6 - - - +
430E ALA* 1.3 52.5 + - - +
431E LEU 3.5 0.2 - - - -
432E LEU* 3.4 17.2 - - + +
433E GLU* 2.6 29.1 - - - +
543E LEU* 4.8 4.9 - - + +
547E ARG* 3.9 28.7 + - - -
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Residues in contact with ALA 430 (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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426E GLU 3.0 3.2 + - - +
427E ALA* 3.0 17.9 + - - +
429E THR* 1.3 76.1 - - - +
431E LEU* 1.3 57.0 + - - +
432E LEU 2.9 10.4 + - - -
433E GLU* 3.0 23.3 - - - +
434E VAL* 3.1 15.8 - - - +
495E GLY* 3.4 29.6 - - - +
498E LEU* 4.2 5.4 - - + -
502E LEU* 3.5 19.1 - - + -
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Residues in contact with LEU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E ALA* 3.1 13.9 - - + +
428E LEU* 3.5 3.3 + - - +
430E ALA* 1.3 74.4 - - - +
432E LEU* 1.3 60.2 + - - +
434E VAL 3.2 9.6 - - - +
435E GLY* 5.5 1.8 - - - -
476E ASN* 2.3 46.4 + - - +
479E LEU* 4.0 17.5 - - + +
480E SER* 3.5 31.4 - - - +
483E ALA* 3.4 32.5 - - + -
491E LEU* 5.0 3.6 - - + +
492E LEU* 5.3 3.6 - - + +
494E ARG* 5.3 2.5 - - + -
495E GLY* 3.6 31.9 - - - +
498E LEU* 4.7 5.4 - - + -
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Residues in contact with LEU 432 (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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34E LEU* 3.5 35.9 - - + +
36E ILE* 4.6 12.6 - - + -
39E LEU* 5.4 7.2 - - + -
428E LEU 3.2 17.3 - - - +
429E THR* 3.4 22.4 - - + +
430E ALA 2.9 0.4 - - - -
431E LEU* 1.3 84.8 - - - +
433E GLU* 1.3 67.2 + - - +
473E TRP* 3.9 30.3 - - - +
476E ASN* 4.7 2.2 + - - +
477E PHE* 4.9 12.3 - - + -
480E SER* 4.3 15.9 - - - +
541E ASN* 4.8 2.9 - - - +
543E LEU* 3.4 25.6 - - + -
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Residues in contact with GLU 433 (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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429E THR 2.6 22.3 - - - +
430E ALA 3.0 15.3 - - - +
432E LEU* 1.3 70.3 - - - +
434E VAL* 1.3 61.4 + - + +
472E ARG* 4.0 21.5 + - - -
473E TRP* 4.7 5.0 + - - +
476E ASN* 4.8 0.4 - - - -
502E LEU* 3.1 41.5 - - + +
538E LEU* 4.7 19.6 - - + +
541E ASN* 3.2 40.3 + - + +
544E THR* 3.7 11.4 - - + +
547E ARG* 3.7 5.9 + - - -
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Residues in contact with VAL 434 (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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430E ALA 3.1 15.9 - - - +
431E LEU* 3.2 15.8 - - - +
432E LEU 3.5 1.2 - - - -
433E GLU* 1.3 82.5 - - + +
435E GLY* 1.3 62.1 + - - +
436E ASN* 3.5 5.6 - - - +
472E ARG* 4.9 4.0 - - - +
476E ASN* 2.3 26.8 + - - +
498E LEU* 3.9 24.5 - - + -
501E ASP* 5.4 6.5 - - - +
502E LEU* 3.8 24.7 - - + -
538E LEU* 5.4 12.6 - - + -
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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