Contacts of the strand formed by residues 407 - 411 (chain A) in PDB entry 3A4R
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 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ARG* 3.2 31.9 - - + +
346A GLN* 5.8 7.6 - - + -
385A PHE 4.4 1.2 - - - +
386A PHE* 3.4 24.0 - - - -
387A ASP 4.8 1.7 + - - -
405A GLY 4.7 5.8 - - - +
406A ASP* 1.3 77.9 + - - +
408A ILE* 1.3 65.9 + - - +
409A GLU* 4.4 5.7 + - + -
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Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 4.9 8.3 - - + -
344A ARG 2.9 10.3 + - - +
345A VAL* 3.3 21.0 - - + +
346A GLN* 2.9 27.9 + - - +
364A LEU* 4.8 6.1 - - + -
367A LEU* 4.1 25.4 - - + -
384A PHE* 4.2 18.4 - - + -
385A PHE 3.5 12.1 - - - +
386A PHE* 3.8 28.0 - - + -
391A LEU* 4.4 11.0 - - + -
402A LEU* 4.4 11.4 - - + -
407A LEU* 1.3 81.5 - - - +
409A GLU* 1.3 70.6 + - - +
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Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A GLN* 3.5 11.4 - - + +
383A SER 3.7 1.4 - - - +
384A PHE* 3.4 2.3 - - - -
385A PHE* 2.8 46.7 + - + +
407A LEU* 4.2 6.5 - - + -
408A ILE* 1.3 74.5 - - - +
410A VAL* 1.3 61.8 + - - +
411A TRP* 3.2 32.4 + - + +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A VAL* 3.5 30.1 - - + -
346A GLN 2.9 13.7 + - - +
347A GLY* 3.4 23.3 - - - -
348A LYS* 3.7 8.0 + - - +
371A TYR* 3.9 21.8 - - + +
382A LEU* 3.9 31.4 - - + -
383A SER 3.4 6.1 - - - +
384A PHE* 3.6 23.3 - - + -
409A GLU* 1.3 78.7 - - - +
411A TRP* 1.3 67.2 + - - +
412A GLY 5.0 0.7 - - - +
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Residues in contact with TRP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LYS* 5.7 2.2 - - - +
381A LYS 4.3 0.2 - - - +
382A LEU* 3.4 7.1 - - - +
383A SER* 2.8 39.0 + - - +
385A PHE* 3.6 33.5 - + + -
409A GLU* 3.2 27.0 + - - +
410A VAL* 1.3 82.1 - - - +
412A GLY* 1.3 62.6 + - - +
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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