Contacts of the strand formed by residues 421 - 426 (chain A) in PDB entry 1UD8
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 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A THR* 4.0 21.1 - - + +
387A ALA* 4.1 4.9 - - + +
391A TYR* 3.9 6.5 - - + -
392A ALA* 3.5 41.7 - - + +
408A TRP* 4.8 3.8 - - + +
409A THR* 3.3 4.5 - - - -
410A ARG* 2.8 49.0 + - + +
420A GLY* 1.3 76.3 - - - +
422A ALA* 1.3 64.4 + - - +
423A THR* 3.8 21.5 - - - +
446A TRP* 3.5 8.7 - - - -
476A VAL* 4.1 9.2 - - + -
477A TYR 3.3 6.3 - - - +
478A VAL* 3.5 14.4 - - + -
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Residues in contact with ALA 422 (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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408A TRP 3.5 5.4 - - - -
409A THR* 3.6 17.9 - - + -
421A LEU* 1.3 77.0 - - - +
423A THR* 1.3 63.0 + - - +
435A MET* 3.9 4.0 - - + -
446A TRP* 3.8 4.7 - - + -
467A PHE* 3.6 37.0 - - + -
476A VAL* 3.5 1.9 - - - -
477A TYR* 3.0 37.9 + - - +
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Residues in contact with THR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ALA* 4.6 2.0 - - + -
353A THR* 3.1 23.8 + - - +
407A GLY* 3.0 4.0 - - - -
408A TRP* 2.8 73.4 + - + +
421A LEU* 3.8 6.9 - - - +
422A ALA* 1.3 72.3 - - - +
424A ILE* 1.3 62.2 + - - +
425A MET* 3.9 18.6 - - + -
435A MET* 3.6 4.7 - - - +
474A VAL* 4.1 8.3 - - + -
475A SER 3.6 8.7 - - - +
476A VAL* 3.8 11.4 - - + +
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Residues in contact with ILE 424 (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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405A VAL* 3.3 28.9 - - + -
406A VAL 3.8 8.5 - - - +
407A GLY* 4.9 0.7 - - - -
423A THR* 1.3 76.1 - - - +
425A MET* 1.3 67.2 + - - +
433A LYS* 3.9 24.5 - - + -
435A MET* 4.8 4.3 - - + -
467A PHE* 4.1 21.8 - - + +
468A PHE 3.4 9.9 - - - +
469A THR* 3.6 17.4 + - + -
474A VAL* 3.4 1.5 - - - +
475A SER* 2.8 35.5 + - - +
477A TYR* 3.3 35.4 - - + -
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Residues in contact with MET 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 3.6 27.6 - - + -
346A LEU* 3.8 33.2 - - + +
349A ALA* 4.3 1.1 - - + -
350A THR* 3.9 3.8 - - - +
405A VAL* 3.2 6.1 - - - +
406A VAL* 3.0 46.7 + - + +
408A TRP* 3.5 31.9 - - + -
423A THR* 3.9 6.3 - - + -
424A ILE* 1.3 80.3 - - - +
426A SER* 1.3 62.1 + - - +
469A THR* 3.6 7.9 - - - -
473A SER 3.3 15.0 - - - +
474A VAL* 3.6 22.9 - - + -
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Residues in contact with SER 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.0 5.6 - - - +
404A ASP* 3.2 18.0 - - - +
405A VAL* 3.6 14.5 - - - +
425A MET* 1.3 79.6 - - - +
427A ASN* 1.3 60.1 + - - +
428A GLY 2.9 25.8 + - - -
429A PRO 3.0 13.1 + - - -
430A GLY* 4.0 2.5 - - - -
469A THR* 3.9 2.0 + - - -
470A ASN 4.0 11.9 - - - -
472A GLY* 2.9 24.9 + - - -
473A SER 3.0 10.4 + - - +
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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