Contacts of the helix formed by residues 451 - 461 (chain A) in PDB entry 1OX4
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 VAL 451 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A VAL* 3.6 28.3 - - + -
405A PRO* 4.2 7.4 - - + -
436A TYR* 2.8 37.2 + - + +
438A CYS* 3.7 9.8 - - - -
450A GLY* 1.3 68.7 - - - -
452A TRP* 1.3 66.0 + - - +
454A LEU* 4.2 1.3 - - + -
455A THR* 2.9 43.2 + - + -
468A LEU* 4.3 4.9 - - + -
484A LEU* 4.2 6.7 - - + -
487A HIS* 3.6 22.9 - - + +
488A VAL* 4.1 15.3 - - + -
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Residues in contact with TRP 452 (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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419A LYS* 3.8 40.7 - - + +
450A GLY* 5.4 0.2 - - - -
451A VAL* 1.3 85.6 - - - +
453A GLU* 1.3 84.5 + - + +
455A THR* 3.3 6.9 + - - -
456A ARG* 3.0 66.0 - - - +
487A HIS* 3.4 37.9 + + + +
488A VAL* 6.2 0.4 - - - +
490A ASP* 3.8 29.4 - - + -
491A ALA* 3.5 30.5 - - + -
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TYR* 2.4 39.5 + - + +
417A LYS* 4.6 2.5 - - - +
418A ASN* 3.4 19.3 - - - +
419A LYS* 2.8 34.5 + - - +
449A LEU* 3.7 19.7 - - + -
450A GLY* 3.2 22.7 - - - +
452A TRP* 1.3 85.2 - - + +
454A LEU* 1.3 66.8 + - - +
456A ARG* 4.7 0.9 - - - +
457A ALA* 3.1 11.1 + - - +
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Residues in contact with LEU 454 (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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367A ALA* 3.4 16.6 - - + +
368A VAL* 3.8 15.3 - - + -
371A ALA* 3.4 25.8 - - + -
401A ILE* 5.2 2.5 - - + -
402A SER 5.7 0.7 - - - +
403A VAL* 3.8 30.5 - - + -
404A ASP 5.7 0.4 - - - +
438A CYS* 3.3 27.8 - - + -
449A LEU* 3.7 17.4 - - + +
450A GLY 2.9 17.4 + - - +
451A VAL 3.3 2.9 + - - +
453A GLU* 1.3 76.7 - - - +
455A THR* 1.3 63.7 + - - +
457A ALA* 3.3 1.9 + - - +
458A CYS* 3.0 34.3 + - - -
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Residues in contact with THR 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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401A ILE* 6.2 0.2 - - - -
403A VAL* 4.2 8.5 - - + -
451A VAL* 2.9 37.6 + - + +
452A TRP 3.3 4.9 + - - -
454A LEU* 1.3 76.5 - - + +
456A ARG* 1.3 59.5 + - - +
458A CYS* 3.3 3.0 + - - +
459A GLU* 2.9 31.9 + - - +
466A ILE* 4.0 30.3 - - + +
488A VAL* 3.9 17.5 - - + +
491A ALA* 3.8 9.4 - - - +
492A VAL* 3.4 21.1 - - - +
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Residues in contact with ARG 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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374A TYR* 5.4 0.6 + - - -
375A TYR* 4.3 5.3 + - - +
452A TRP* 3.0 62.1 + - - +
453A GLU* 4.1 2.9 - - - +
455A THR* 1.3 81.7 + - - +
457A ALA* 1.3 63.2 + - - +
459A GLU* 3.7 7.2 + - - +
460A ALA* 3.1 23.0 + - - +
490A ASP 4.7 1.8 + - - -
491A ALA* 2.7 48.9 + - + +
492A VAL* 3.9 5.2 - - + -
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Residues in contact with ALA 457 (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 ALA* 3.6 27.6 - - + -
374A TYR* 3.6 33.8 - - + -
375A TYR* 3.7 5.1 + - + +
453A GLU 3.1 18.7 + - - +
454A LEU 3.7 0.2 - - - +
456A ARG* 1.3 74.9 - - - +
458A CYS* 1.3 59.6 + - - +
460A ALA* 3.2 4.5 + - - +
461A LEU* 2.9 33.7 + - - +
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Residues in contact with CYS 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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367A ALA* 3.7 28.0 - - - -
371A ALA* 4.6 2.7 - - - -
387A ILE* 3.6 22.9 - - + +
401A ILE* 3.8 25.1 - - + -
454A LEU* 3.0 28.3 + - - +
455A THR* 3.8 5.6 - - - +
457A ALA* 1.3 74.6 - - - +
459A GLU* 1.3 65.2 + - - +
461A LEU* 3.2 11.2 + - - +
462A GLY 3.1 5.9 + - - -
463A ALA* 3.0 22.7 + - + +
466A ILE* 5.1 1.6 - - + -
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Residues in contact with GLU 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 THR 2.9 18.5 + - - +
456A ARG* 3.7 7.3 + - - +
458A CYS* 1.3 72.7 - - - +
460A ALA* 1.3 70.1 - - - +
462A GLY* 2.8 16.3 + - - -
463A ALA* 3.9 10.5 + - - +
491A ALA 4.5 2.3 - - - +
492A VAL* 3.6 15.5 - - + +
493A LYS* 2.8 41.1 + - - +
494A ILE* 3.2 34.4 + - + +
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Residues in contact with ALA 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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374A TYR* 3.7 28.9 - - + +
456A ARG 3.1 11.5 + - - +
457A ALA 3.4 8.7 - - - +
459A GLU* 1.3 81.8 - - - +
461A LEU* 1.3 63.1 + - - +
462A GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 3.8 39.0 - - + +
371A ALA 4.5 0.7 - - - +
374A TYR* 3.8 24.9 - - + -
381A GLY* 4.0 9.6 - - - -
385A SER* 4.3 6.5 - - - +
387A ILE* 3.5 17.9 - - + +
388A GLU* 3.4 47.2 - - + +
391A SER* 3.6 6.1 + - - -
392A LYS* 5.5 2.3 - - - -
457A ALA 2.9 23.5 + - - +
458A CYS* 3.5 12.6 - - - +
459A GLU 3.0 0.6 - - - -
460A ALA* 1.3 76.4 - - - +
462A GLY* 1.3 55.8 + - - +
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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