Contacts of the helix formed by residues 452 - 463 (chain O) in PDB entry 1UW9
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 SER 452 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422O VAL* 3.9 20.7 - - - +
448O ALA 3.0 15.8 + - - -
449O CYS 3.4 9.8 + - - +
451O TRP* 1.3 92.4 - - - +
453O PRO* 1.3 58.9 - - - +
454O GLU* 3.7 9.3 + - - +
455O LEU* 3.1 26.7 + - - +
456O ALA 3.0 22.2 + - - -
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Residues in contact with PRO 453 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411O TRP* 3.5 18.3 - - + -
449O CYS 4.9 0.7 - - - +
451O TRP 3.5 11.2 - - - +
452O SER* 1.3 81.9 - - - +
454O GLU* 1.3 77.2 + - - +
456O ALA* 3.6 8.8 - - + +
457O ALA 3.0 19.2 + - - -
2T MET* 3.6 33.7 - - + -
135T ALA 6.0 1.3 - - - +
139T SER* 4.9 2.0 - - - +
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Residues in contact with GLU 454 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409O HIS* 2.9 23.7 + - - -
411O TRP* 3.8 19.0 - - + -
415O PRO* 3.6 40.6 - - + +
418O ALA* 4.3 3.1 - - + -
419O ALA* 3.5 11.4 - - - +
452O SER* 3.9 7.9 + - - +
453O PRO* 1.3 91.5 - - - +
455O LEU* 1.3 61.5 + - - +
457O ALA 3.5 0.2 + - - -
458O ALA 3.2 7.1 + - - -
2T MET* 4.0 2.4 - - - +
4T TRP* 3.7 26.9 - - + -
139T SER* 2.7 32.2 + - - -
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Residues in contact with LEU 455 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384O VAL* 3.6 31.9 - - + -
419O ALA* 3.7 16.9 - - - +
422O VAL* 3.8 14.8 - - + -
423O ALA* 4.1 12.3 - - + +
445O ILE* 3.9 15.5 - - + +
448O ALA* 3.5 32.5 - - + -
449O CYS* 3.9 10.8 - - - +
452O SER* 3.1 22.6 + - - +
454O GLU* 1.3 74.7 - - - +
456O ALA* 1.3 54.7 + - - +
458O ALA* 3.1 2.1 + - - +
459O CYS* 2.8 43.2 + - - -
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Residues in contact with ALA 456 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449O CYS* 3.7 30.0 - - + +
452O SER 3.0 14.3 + - - +
453O PRO* 3.6 12.1 - - + +
455O LEU* 1.3 76.5 - - - +
457O ALA* 1.3 56.2 + - - +
459O CYS* 3.3 2.9 + - - +
460O GLU* 3.0 33.1 + - - +
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Residues in contact with ALA 457 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409O HIS* 3.9 9.9 - - + -
410O PRO* 4.2 6.1 - - + -
411O TRP* 3.7 31.2 - - + +
453O PRO 3.0 16.8 + - - +
454O GLU 3.8 4.5 - - - +
456O ALA* 1.3 75.4 - - - +
458O ALA* 1.3 62.5 + - - +
460O GLU* 3.5 6.7 + - - +
461O VAL* 3.3 28.4 + - - +
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Residues in contact with ALA 458 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384O VAL* 3.9 18.6 - - + -
409O HIS* 3.7 19.2 + - + -
410O PRO* 5.1 0.4 - - - -
419O ALA* 3.8 12.8 - - + -
454O GLU 3.2 12.9 + - - +
455O LEU 3.1 8.6 + - - +
457O ALA* 1.3 74.3 - - - +
459O CYS* 1.3 66.0 + - - +
461O VAL* 3.3 4.1 + - - -
462O TRP* 3.3 41.8 + - + +
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Residues in contact with CYS 459 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384O VAL* 3.9 7.2 - - - -
385O TRP* 2.9 43.2 + - + +
445O ILE* 3.4 25.4 - - - -
449O CYS* 3.4 25.4 - - - -
455O LEU* 2.8 31.8 + - - +
456O ALA 3.3 5.4 + - - +
458O ALA* 1.3 72.0 - - - +
460O GLU* 1.3 56.9 + - - +
463O LYS* 3.0 20.5 + - - +
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Residues in contact with GLU 460 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456O ALA 3.0 18.4 + - - +
457O ALA* 3.8 7.9 - - - +
458O ALA 3.2 0.4 - - - -
459O CYS* 1.3 80.0 - - - +
461O VAL* 1.3 63.1 + - + +
462O TRP 3.5 0.2 + - - -
463O LYS* 3.8 30.2 + - - +
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Residues in contact with VAL 461 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408O GLY 4.8 0.4 - - - +
410O PRO* 3.8 24.7 - - + -
457O ALA 3.3 16.1 + - - +
458O ALA 3.3 5.6 + - - +
460O GLU* 1.3 78.2 - - + +
462O TRP* 1.3 82.7 + - + +
463O LYS 3.9 0.2 + - - -
464O GLU 5.3 0.7 + - - -
465O ILE* 4.6 4.5 - - - +
15V ALA* 4.2 11.2 - - + +
16V GLY* 3.7 34.5 - - - +
17V VAL 5.5 0.7 + - - -
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Residues in contact with TRP 462 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383O HIS* 3.4 42.2 - - + +
384O VAL* 4.6 4.9 - - + -
385O TRP* 3.9 3.4 - - + -
404O GLY 3.6 10.1 - - - -
405O GLY* 3.5 30.3 - - - -
408O GLY 3.5 21.1 - - - -
409O HIS* 3.7 22.9 - + - -
458O ALA* 3.3 42.4 + - + +
459O CYS 3.8 1.6 - - - -
461O VAL* 1.3 94.3 - - + +
463O LYS* 1.3 66.7 + - - +
464O GLU 3.3 2.9 - - - -
465O ILE* 3.1 22.7 + - + -
16V GLY* 5.0 0.2 - - - -
17V VAL* 4.3 3.8 - - + -
66V TRP* 3.4 29.6 - + - -
67V THR* 3.1 24.6 + - + -
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Residues in contact with LYS 463 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383O HIS* 5.6 0.3 - - - -
385O TRP* 3.5 26.2 - - + +
459O CYS 3.0 17.3 + - - +
460O GLU* 3.8 27.7 + - - +
461O VAL 3.5 2.2 - - - -
462O TRP* 1.3 77.6 - - - +
464O GLU* 1.3 83.9 + - + +
465O ILE 3.5 1.2 + - - +
466O LYS* 5.6 4.3 - - - +
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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