Contacts of the strand formed by residues 405 - 408 (chain A) in PDB entry 4XE4
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 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ALA 3.9 0.3 - - - +
371A LEU* 3.3 5.0 - - - +
372A TYR* 2.6 54.1 + - + +
403A ASP 3.7 0.2 + - - -
404A LEU* 1.3 76.5 + - - +
406A VAL* 1.3 65.6 + - - +
407A VAL* 4.2 7.4 - - + -
422A THR* 3.4 30.5 - - + -
423A LEU 3.7 4.2 + - - +
424A ALA* 5.9 0.2 - - - -
1B NAG 4.0 15.7 - - - +
2B NAG 3.5 34.3 + - - -
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 4.1 10.8 - - + -
370A ALA 3.2 11.9 - - - +
371A LEU* 4.4 9.9 - - + -
388A VAL* 4.7 4.9 - - + -
405A THR* 1.3 75.2 - - - +
407A VAL* 1.3 63.1 + - - +
408A LEU* 4.0 26.4 - - + +
421A GLN 3.7 0.9 - - - +
422A THR* 3.4 1.6 - - - +
423A LEU* 2.6 53.1 + - + +
424A ALA 4.7 4.3 - - - +
425A VAL* 5.0 6.3 - - + +
446A LEU* 5.5 4.3 - - + -
448A LEU* 3.3 32.1 - - + -
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE 4.3 0.7 - - - +
369A ALA* 3.7 3.1 - - - -
370A ALA* 2.9 35.7 + - - +
372A TYR* 3.6 28.0 - - + -
405A THR* 4.4 5.6 - - + -
406A VAL* 1.3 76.7 - - - +
408A LEU* 1.3 72.7 + - - +
410A GLN* 3.9 29.8 - - + +
420A CYS* 4.0 17.5 - - + -
421A GLN 3.3 8.7 - - - +
422A THR* 3.9 17.5 - - - +
486A TRP* 5.7 0.2 - - - -
1B NAG 4.0 14.6 - - + +
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Residues in contact with LEU 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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366A PRO 5.7 1.6 - - - +
367A TYR 5.3 0.7 - - - +
368A ILE 4.4 5.2 - - - +
369A ALA* 3.5 31.9 - - + -
382A LEU* 4.2 25.4 - - + -
388A VAL* 4.7 1.3 - - + -
406A VAL* 4.0 12.6 - - + +
407A VAL* 1.3 74.1 - - - +
409A GLY* 1.3 63.4 + - - +
410A GLN 3.3 3.4 + - - -
419A PRO 4.2 0.2 - - - +
420A CYS* 3.2 2.8 - - - -
421A GLN* 2.8 41.8 + - + +
423A LEU* 4.2 16.6 - - + -
448A LEU* 4.6 4.0 - - + -
457A ALA* 3.6 31.6 - - + -
463A VAL* 4.0 20.9 - - + -
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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