Contacts of the helix formed by residues 454 - 469 (chain A) in PDB entry 1UPX
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 ASP 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASP* 4.4 15.6 - - - +
213A ASN* 5.3 1.6 + - - -
220A PRO* 5.8 2.0 - - - +
267A PRO* 4.8 1.7 - - - +
271A TYR* 4.4 15.2 + - - -
370A ALA* 5.2 2.5 - - - +
425A ALA* 4.0 3.1 - - - -
449A ALA* 3.3 31.8 - - - +
450A GLY* 3.5 3.9 - - - +
451A GLN* 2.8 40.5 + - - +
453A ASN* 1.3 84.4 + - - +
455A SER* 1.3 63.5 + - - +
456A TYR* 2.9 2.2 - - - +
457A SER* 2.9 27.8 + - - +
458A LEU* 3.4 3.1 + - - +
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Residues in contact with SER 455 (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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206A MET* 4.6 2.5 - - - -
397A ALA* 4.1 12.6 - - - +
398A GLY* 5.2 1.6 + - - -
425A ALA* 3.8 10.2 + - - +
451A GLN 3.7 1.6 + - - -
452A CYS* 2.8 22.9 + - - +
453A ASN 4.6 0.2 - - - -
454A ASP* 1.3 77.6 - - - +
456A TYR* 1.3 60.3 + - - +
458A LEU* 3.0 25.1 + - - +
459A ALA* 3.0 13.7 + - - +
493A VAL* 3.6 30.8 - - - +
497A LEU* 5.3 6.4 - - - +
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Residues in contact with TYR 456 (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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203A VAL* 4.1 20.9 - - + -
206A MET* 3.8 24.3 - - + +
207A ALA* 3.5 36.2 - - + +
210A ASP* 3.7 39.3 - - + +
371A HIS* 4.4 5.6 - + - -
453A ASN 3.1 17.7 + - - +
454A ASP* 2.9 1.1 - - - -
455A SER* 1.3 76.9 - - - +
457A SER* 1.3 58.2 + - - +
459A ALA* 3.1 12.1 + - + +
460A VAL* 2.9 51.2 + - + +
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Residues in contact with SER 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 4.0 4.7 + - - -
370A ALA* 3.5 18.1 - - - +
371A HIS* 2.9 49.5 + - - +
449A ALA* 4.2 5.6 - - - -
454A ASP* 2.9 16.8 + - - +
456A TYR* 1.3 78.4 - - - +
458A LEU* 1.3 57.4 + - - +
460A VAL* 3.2 2.9 + - - +
461A ILE* 2.8 35.5 + - - +
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Residues in contact with LEU 458 (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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369A PHE 5.0 0.9 - - - +
395A VAL* 4.2 21.3 - - + -
397A ALA* 4.0 28.0 - - + -
423A LEU* 4.0 28.1 - - + +
424A THR 4.0 18.6 - - - +
425A ALA* 4.2 4.9 - - + -
447A LEU 5.1 1.1 - - - +
449A ALA* 3.7 22.0 - - + +
454A ASP 4.0 9.0 - - - +
455A SER* 3.0 11.5 + - - +
457A SER* 1.3 75.4 - - - +
459A ALA* 1.3 57.9 + - - +
461A ILE* 3.4 15.8 + - + +
462A ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 459 (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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455A SER 3.0 11.2 + - - +
456A TYR* 3.4 14.6 - - + +
458A LEU* 1.3 74.1 - - - +
460A VAL* 1.3 59.3 + - + +
462A ALA* 3.3 6.8 + - - +
463A LEU* 2.9 37.4 + - + +
497A LEU* 4.5 14.7 - - + +
500A LEU* 3.8 28.9 - - + -
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Residues in contact with VAL 460 (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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371A HIS* 3.7 26.7 - - + +
375A LEU* 4.7 14.1 - - + -
456A TYR* 2.9 53.5 + - + +
457A SER* 3.6 7.9 - - - +
459A ALA* 1.3 75.2 - - + +
461A ILE* 1.3 58.5 + - - +
463A LEU* 3.4 9.2 + - + +
464A LYS* 2.9 27.5 + - - +
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Residues in contact with ILE 461 (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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369A PHE 4.1 9.2 - - - +
371A HIS* 4.3 9.0 - - - -
374A VAL* 3.6 49.6 - - + -
375A LEU* 4.1 12.3 - - + -
381A VAL* 6.4 0.7 - - + -
393A PHE* 6.6 0.2 - - + -
423A LEU* 5.3 15.3 - - + -
457A SER* 2.8 27.1 + - - +
458A LEU* 3.6 17.0 - - + +
460A VAL* 1.3 73.5 - - - +
462A ALA* 1.3 65.8 + - - +
464A LYS* 3.2 7.2 + - - +
465A LEU* 3.0 41.3 + - + +
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Residues in contact with ALA 462 (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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458A LEU 2.9 17.4 + - - +
459A ALA* 3.7 7.4 - - - +
461A ILE* 1.3 77.7 - - - +
463A LEU* 1.3 57.4 + - + +
465A LEU* 3.3 2.9 + - - -
466A LYS* 2.9 24.1 + - - +
474A VAL* 4.2 15.3 - - + -
477A LEU* 3.1 15.3 - - - +
479A ILE* 4.1 23.1 - - + -
481A TYR* 4.4 8.1 - - + +
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Residues in contact with LEU 463 (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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459A ALA* 2.9 24.1 + - + +
460A VAL* 3.8 9.0 - - + +
462A ALA* 1.3 73.4 - - + +
464A LYS* 1.3 64.7 + - - +
466A LYS* 3.4 19.5 + - + +
467A GLU* 3.1 22.3 + - - +
474A VAL* 4.3 20.6 - - + -
500A LEU* 4.5 32.3 - - + +
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Residues in contact with LYS 464 (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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375A LEU* 4.0 39.0 - - + -
378A ALA* 5.0 15.0 - - + -
460A VAL* 2.9 15.7 + - + +
461A ILE 3.4 8.1 - - - +
463A LEU* 1.3 72.9 - - - +
465A LEU* 1.3 65.6 + - + +
467A GLU* 3.1 24.3 + - - +
468A VAL* 2.9 54.4 + - + +
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Residues in contact with LEU 465 (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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378A ALA* 5.4 4.0 - - + +
381A VAL* 4.5 14.6 - - + -
382A ILE* 4.0 28.9 - - + +
385A VAL* 5.9 0.9 - - + -
393A PHE* 4.4 27.8 - - + -
461A ILE* 3.0 33.6 + - + +
462A ALA* 3.3 10.1 + - - +
464A LYS* 1.3 76.7 - - + +
466A LYS* 1.3 66.2 + - - +
468A VAL* 4.5 2.5 - - - +
469A PHE* 3.0 41.5 + - + +
477A LEU* 3.8 16.6 - - + -
478A PRO* 6.4 0.7 - - + -
479A ILE* 5.0 7.0 - - + -
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Residues in contact with LYS 466 (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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462A ALA 2.9 14.0 + - - +
463A LEU* 3.5 23.8 - - + +
465A LEU* 1.3 77.3 - - - +
467A GLU* 1.3 61.6 + - - +
469A PHE 3.8 0.3 - - - -
470A GLY 3.1 2.9 + - - -
471A LEU* 2.8 61.9 + - + +
472A GLU* 3.5 25.9 + - - +
474A VAL* 3.8 29.8 - - + +
477A LEU* 3.8 16.7 - - + +
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Residues in contact with GLU 467 (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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463A LEU 3.1 13.4 + - - +
464A LYS* 3.1 29.9 + - - +
466A LYS* 1.3 77.2 - - - +
468A VAL* 1.3 66.6 + - - +
470A GLY* 3.1 14.2 + - - -
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Residues in contact with VAL 468 (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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382A ILE* 3.4 45.3 - - + -
386A LYS* 6.1 1.8 - - - +
464A LYS* 2.9 49.6 + - + +
465A LEU* 4.1 4.7 - - - +
467A GLU* 1.3 77.3 - - + +
469A PHE* 1.3 62.4 + - + +
470A GLY 3.2 1.1 + - - -
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Residues in contact with PHE 469 (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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382A ILE* 3.9 20.6 - - + -
385A VAL* 3.8 35.7 - - + -
386A LYS* 4.0 32.5 - - + -
465A LEU* 3.0 45.4 + - + +
468A VAL* 1.3 80.0 - - + +
470A GLY* 1.3 62.9 + - - +
471A LEU* 3.3 25.8 + - + +
477A LEU* 4.0 15.7 - - + -
478A PRO* 5.6 2.5 - - + -
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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