Contacts of the strand formed by residues 405 - 413 (chain A) in PDB entry 3EPZ
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 HIS 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A MSE 4.2 10.0 - - + +
381A LEU* 4.0 17.5 - - + +
384A GLU* 2.5 40.7 + - - -
403A PRO* 3.8 15.1 + - + -
404A GLN* 1.3 74.8 - - - +
406A LYS* 1.3 59.2 + - - +
439A ALA* 4.5 6.7 - - + -
440A LYS 3.1 7.0 - - - +
441A PRO* 3.9 21.0 - - + +
442A ILE* 4.0 4.7 - - - -
484A ALA* 4.1 14.3 - - + +
485A GLU 2.9 19.7 + - - +
486A TYR* 3.3 19.3 - + + -
487A ILE* 2.7 36.6 + - - +
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Residues in contact with LYS 406 (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 HIS* 1.3 73.2 - - - +
407A LEU* 1.3 61.6 + - - +
408A THR 4.3 0.2 - - - -
438A SER 3.6 1.1 - - - +
439A ALA* 3.2 6.6 - - - +
440A LYS* 2.6 44.9 + - + +
442A ILE* 3.6 36.7 - - + +
447A PRO 6.3 0.7 - - - -
487A ILE* 3.4 6.7 - - + -
489A MSE 4.2 24.7 - - + -
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Residues in contact with LEU 407 (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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406A LYS* 1.3 75.5 - - - +
408A THR* 1.3 57.8 + - - +
410A PHE* 3.7 28.1 - - + -
435A PHE* 3.5 35.7 - - + -
436A SER 4.0 4.7 - - - +
437A GLY* 3.6 22.7 - - - +
438A SER 3.5 16.6 - - - +
439A ALA* 3.9 13.9 - - + -
458A LEU* 4.5 8.3 - - + -
486A TYR* 4.4 14.1 - - + -
487A ILE 2.7 13.8 + - - +
488A LEU* 3.5 16.8 - - + -
489A MSE 2.7 30.9 + - - +
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Residues in contact with THR 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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406A LYS* 6.3 0.2 - - - -
407A LEU* 1.3 73.5 - - - +
409A CYS* 1.3 76.3 + - + +
410A PHE 3.1 3.9 + - - -
437A GLY* 3.3 2.1 - - - -
438A SER* 3.0 50.1 + - - +
489A MSE 3.5 13.9 - - - +
490A ASP* 3.3 27.5 + - - +
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Residues in contact with CYS 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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408A THR* 1.3 83.3 + - + +
410A PHE* 1.3 59.3 + - - +
411A SER* 4.2 0.5 + - - -
436A SER* 4.1 1.0 + - - +
437A GLY* 3.7 9.2 - - - -
438A SER* 5.2 4.3 - - - +
490A ASP* 2.7 17.4 + - - +
491A PRO 4.0 2.0 - - - -
492A SER* 3.5 29.4 - - - +
493A PRO* 4.5 8.3 - - - -
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Residues in contact with PHE 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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407A LEU* 3.7 36.1 - - + -
408A THR 3.9 0.7 - - - +
409A CYS* 1.3 76.1 - - - +
411A SER* 1.3 66.1 + - - +
412A VAL* 4.6 5.4 - - + -
435A PHE* 6.0 0.4 - - + -
436A SER 3.0 13.5 - - - +
479A PHE* 6.3 0.2 - - + -
488A LEU* 3.6 32.3 - - + -
489A MSE 3.5 13.5 - - - -
490A ASP 3.2 32.6 + - - -
491A PRO* 3.7 11.2 - - + -
492A SER 2.9 18.4 + - - -
495A TYR* 3.5 32.5 - + - +
499A PHE* 3.6 33.4 - + - -
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Residues in contact with SER 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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368A GLY* 5.1 4.7 - - - -
369A GLN 5.2 4.1 + - - -
409A CYS 4.8 0.7 + - - -
410A PHE* 1.3 71.4 - - - +
412A VAL* 1.3 63.1 + - - +
413A TYR* 4.1 6.2 - - - -
419A LEU* 3.9 20.1 - - - +
435A PHE* 3.1 8.7 - - - +
436A SER* 3.0 42.3 + - - -
492A SER* 3.0 27.0 + - - -
494A GLU* 4.3 5.2 + - - -
495A TYR* 3.8 9.0 - - - +
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Residues in contact with VAL 412 (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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410A PHE* 4.6 5.6 - - + -
411A SER* 1.3 80.1 - - - +
413A TYR* 1.3 64.3 + - - +
419A LEU* 3.3 7.6 - - - +
420A CYS 2.9 30.7 + - - +
422A ILE* 4.1 8.3 - - + -
433A LEU* 3.9 24.7 - - + -
434A PHE 3.4 9.6 - - - +
435A PHE* 4.2 1.3 - - + -
461A ILE* 4.2 11.2 - - + -
479A PHE* 3.7 31.9 - - + -
495A TYR* 3.3 33.6 - - + +
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Residues in contact with TYR 413 (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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368A GLY* 4.6 11.2 - - - -
370A HIS* 6.0 0.3 - - - -
411A SER* 4.1 3.4 - - - -
412A VAL* 1.3 82.9 - - - +
414A CYS* 1.3 76.8 + - - +
415A LYS* 6.0 0.2 - - - -
417A GLY* 3.7 18.8 - - - +
418A HIS 3.0 25.1 - - - +
419A LEU* 4.0 10.5 - - + +
420A CYS* 4.1 2.9 - - - +
433A LEU* 3.4 9.1 - - - -
434A PHE* 2.7 52.0 + + + +
435A PHE* 3.8 14.1 + - - -
436A SER* 3.8 25.7 - - - -
456A LYS* 4.2 2.3 - - - +
457A ASN* 2.8 50.2 + - - -
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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