Contacts of the helix formed by residues 454 - 469 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ASP* 4.4 15.8 - - - +
213B ASN* 5.2 1.4 + - - -
220B PRO* 5.8 1.5 - - - +
267B PRO* 4.8 1.9 - - - +
271B TYR* 4.4 15.7 + - - -
370B ALA* 5.2 3.2 - - - +
425B ALA* 3.9 3.1 - - - -
449B ALA* 3.3 32.0 - - + +
450B GLY* 3.5 3.5 - - - -
451B GLN* 2.7 45.9 + - - +
453B ASN* 1.3 79.9 + - - +
455B SER* 1.3 63.3 + - - +
456B TYR* 2.9 2.0 - - - +
457B SER* 2.9 27.3 + - - +
458B LEU* 3.4 3.6 + - - +
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B MET* 4.2 5.2 - - - -
397B ALA* 3.9 20.6 - - - +
398B GLY* 5.2 1.6 + - - -
425B ALA* 3.7 4.3 + - - +
451B GLN 3.7 1.8 + - - -
452B CYS* 2.9 22.5 + - - +
454B ASP* 1.3 75.9 - - - +
456B TYR* 1.3 61.0 + - - +
458B LEU* 3.0 15.4 + - - +
459B ALA* 3.0 22.2 + - - +
493B VAL* 3.7 31.2 - - - +
497B LEU* 5.4 5.8 - - - +
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 4.2 17.5 - - + -
206B MET* 3.6 32.7 - - + +
207B ALA* 3.5 36.6 - - + +
210B ASP* 3.6 40.8 - - + +
371B HIS* 4.4 4.0 - + - -
453B ASN 3.1 17.1 + - - +
454B ASP* 4.7 1.1 - - - -
455B SER* 1.3 76.9 - - - +
457B SER* 1.3 57.1 + - - +
459B ALA* 3.1 10.1 + - + +
460B VAL* 2.9 55.9 + - + +
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Residues in contact with SER 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP* 3.9 5.7 + - - -
370B ALA* 3.4 17.7 - - - +
371B HIS* 3.0 48.8 + - - +
449B ALA* 4.1 6.3 - - - -
454B ASP* 2.9 16.9 + - - +
456B TYR* 1.3 78.8 - - - +
458B LEU* 1.3 58.3 + - - +
460B VAL* 3.2 2.9 + - - +
461B ILE* 2.8 36.4 + - - +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PHE 5.0 0.7 - - - +
395B VAL* 4.1 22.4 - - + -
397B ALA* 3.9 27.8 - - + -
423B LEU* 4.0 28.2 - - + +
424B THR 4.0 19.5 - - - +
425B ALA* 4.2 3.4 - - + -
447B LEU 5.1 1.3 - - - +
449B ALA* 3.7 22.7 - - + +
454B ASP 3.4 8.9 + - - +
455B SER* 3.0 11.3 + - - +
457B SER* 1.3 76.5 - - - +
459B ALA* 1.3 57.0 + - - +
461B ILE* 3.4 15.5 + - + +
462B ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B MET* 5.6 2.9 - - + -
455B SER 3.0 11.6 + - - +
456B TYR* 3.4 15.9 - - + +
458B LEU* 1.3 74.3 - - - +
460B VAL* 1.3 60.6 + - + +
462B ALA* 3.3 6.8 + - - +
463B LEU* 2.9 39.1 + - + +
497B LEU* 4.6 13.4 - - + +
500B LEU* 3.9 27.6 - - + -
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B HIS* 3.6 28.9 - - + +
375B LEU* 5.1 11.7 - - + -
456B TYR* 2.9 53.1 + - + +
457B SER 3.2 7.2 + - - +
459B ALA* 1.3 75.0 - - + +
461B ILE* 1.3 58.0 + - - +
463B LEU* 3.4 9.5 + - + +
464B LYS* 2.9 28.6 + - + +
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Residues in contact with ILE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B PHE 4.1 9.4 - - - +
370B ALA 4.5 0.2 - - - -
371B HIS* 4.3 14.4 - - - -
374B VAL* 3.7 47.6 - - + -
375B LEU* 4.3 7.4 - - + -
381B VAL* 6.4 1.1 - - + -
393B PHE* 6.5 0.4 - - + -
423B LEU* 5.2 16.6 - - + -
457B SER 2.8 27.1 + - - +
458B LEU* 3.6 16.4 - - + +
460B VAL* 1.3 76.3 - - - +
462B ALA* 1.3 57.8 + - - +
464B LYS* 3.2 7.4 + - - +
465B LEU* 2.9 45.4 + - + +
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Residues in contact with ALA 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B LEU 3.0 17.6 + - - +
459B ALA* 3.3 8.0 + - - +
461B ILE* 1.3 76.3 - - - +
463B LEU* 1.3 59.2 + - + +
465B LEU* 3.2 2.8 + - - +
466B LYS* 2.9 25.1 + - - +
474B VAL* 4.1 15.7 - - + -
477B LEU* 3.1 14.4 - - - +
479B ILE* 3.9 24.5 - - + -
481B TYR* 4.3 9.0 - - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B ALA* 2.9 25.0 + - + +
460B VAL* 3.8 8.3 - - + +
462B ALA* 1.3 76.3 - - + +
464B LYS* 1.3 61.1 + - - +
466B LYS* 3.4 21.2 + - + +
467B GLU* 3.2 20.4 + - - +
474B VAL* 4.2 22.9 - - + -
500B LEU* 4.6 30.5 - - + +
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B LEU* 4.1 37.9 - - + +
378B ALA* 6.0 6.5 - - + -
460B VAL* 2.9 18.4 + - + +
461B ILE* 3.2 8.3 + - - +
463B LEU* 1.3 75.4 - - - +
465B LEU* 1.3 62.4 + - + +
467B GLU* 2.8 34.3 + - - +
468B VAL* 2.9 47.7 + - + +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B VAL* 4.7 13.2 - - + -
382B ILE* 4.6 15.7 - - + -
385B VAL* 5.7 1.6 - - + -
393B PHE* 4.0 31.2 - - + -
461B ILE* 2.9 34.9 + - + +
462B ALA* 3.7 7.2 - - - +
464B LYS* 1.3 75.4 - - + +
466B LYS* 1.3 66.3 + - - +
468B VAL* 4.2 5.6 - - + -
469B PHE* 3.0 50.0 + - + +
477B LEU* 3.9 16.4 - - + -
478B PRO* 6.4 0.7 - - + -
479B ILE* 5.0 8.1 - - + -
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B ALA 2.9 14.0 + - - +
463B LEU* 3.4 24.6 - - + +
465B LEU* 1.3 76.6 - - - +
467B GLU* 1.3 57.1 + - - +
469B PHE 3.6 0.5 + - - -
470B GLY* 3.1 6.4 + - - -
471B LEU* 2.9 54.2 + - + +
472B GLU* 3.5 29.1 + - - +
473B ASP* 3.8 1.5 - - - +
474B VAL* 3.7 25.8 - - + +
477B LEU* 3.7 15.8 - - + +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B LEU 3.2 9.0 + - - +
464B LYS* 2.8 43.6 + - - +
466B LYS* 1.3 77.7 - - - +
468B VAL* 1.3 67.5 + - - +
470B GLY* 3.1 13.9 + - - -
471B LEU 5.6 0.2 - - - -
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Residues in contact with VAL 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ALA* 6.2 0.2 - - + -
382B ILE* 3.7 44.9 - - + -
464B LYS* 2.9 43.9 + - + +
465B LEU* 3.2 9.4 + - + +
467B GLU* 1.3 77.9 - - - +
469B PHE* 1.3 74.4 + - + +
470B GLY 3.5 0.3 + - - -
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Residues in contact with PHE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ILE* 4.3 16.4 - - + -
385B VAL* 3.5 37.2 - - + -
386B LYS* 4.1 20.0 - - + -
465B LEU* 3.0 48.7 + - + +
468B VAL* 1.3 86.6 - - + +
470B GLY* 1.3 63.5 + - - +
471B LEU* 3.3 25.8 + - + +
477B LEU* 4.5 8.5 - - + -
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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