Contacts of the helix formed by residues 365 - 374 (chain A) in PDB entry 6X70
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 CYS 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A PHE 3.6 3.4 + - - -
364A ASP* 1.3 74.0 - - - +
366A PHE* 1.3 58.6 - - - +
368A ALA* 3.3 2.5 + - + -
369A THR* 2.9 37.5 + - - -
384A PHE* 3.9 20.2 - - - -
402A SER* 3.4 12.8 - - - +
403A CYS 3.2 24.2 - - - +
404A ASN* 4.0 11.2 - - - -
405A TYR* 4.1 17.3 - - - -
408A ARG* 3.3 19.9 - - - +
414A ASN* 6.1 0.2 - - - +
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Residues in contact with PHE 366 (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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328A LEU* 6.0 0.2 - - + -
363A PHE* 3.4 45.7 + + + -
364A ASP 3.7 6.1 - - - -
365A CYS* 1.3 72.6 - - - +
367A PHE* 1.3 94.5 + + + +
369A THR* 3.2 4.0 + - - -
370A VAL* 2.9 46.5 + - + +
402A SER* 3.7 2.0 + - - -
441A PHE* 3.4 26.2 - + + -
444A LYS* 4.3 3.8 - - + -
445A SER 4.8 2.5 - - - -
466A ILE* 3.8 30.7 - - + -
467A ASP* 3.1 36.1 - - + +
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Residues in contact with PHE 367 (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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324A ARG* 4.1 28.5 - - + -
328A LEU* 3.8 30.7 - - + -
331A TRP* 4.2 10.5 - + - -
365A CYS 3.6 0.2 - - - -
366A PHE* 1.3 104.0 - + - +
368A ALA* 1.3 59.0 + - - +
371A ALA* 2.7 34.0 + - - +
391A VAL* 3.8 8.3 - - + -
401A ALA* 3.9 25.4 - - + -
402A SER* 3.5 13.4 + - - -
436A TYR* 4.4 2.7 - + - -
438A PHE* 5.0 0.9 - + - -
441A PHE* 3.4 47.4 - + + -
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A CYS* 3.7 5.4 - - + +
366A PHE 3.2 0.8 - - - -
367A PHE* 1.3 77.8 - - - +
369A THR* 1.3 63.2 + - - +
371A ALA* 3.9 1.2 - - - +
372A TYR* 3.0 24.8 + - - +
384A PHE* 3.9 11.4 - - + -
389A ILE* 4.6 9.4 - - + -
391A VAL* 3.6 13.7 - - + -
402A SER* 3.2 23.5 + - - +
403A CYS* 4.1 1.6 - - - -
404A ASN 4.1 22.4 - - - +
434A LEU* 4.5 2.8 - - - +
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Residues in contact with THR 369 (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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363A PHE* 6.1 0.4 - - - -
364A ASP* 3.1 14.8 + - - +
365A CYS* 2.9 18.5 + - - -
366A PHE* 3.6 4.3 - - - -
368A ALA* 1.3 76.7 - - - +
370A VAL* 1.3 58.6 + - - +
372A TYR* 3.2 4.1 + - + +
373A LEU* 2.9 39.9 + - + +
384A PHE* 3.6 27.8 - - + -
503A GLY 4.4 2.7 - - - +
504A CYS* 3.9 33.7 - - + -
505A THR* 4.7 7.5 - - + +
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Residues in contact with VAL 370 (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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366A PHE* 2.9 42.8 + - + +
369A THR* 1.3 72.9 - - - +
371A ALA* 1.3 67.4 + - - +
373A LEU* 3.2 6.2 + - - +
374A CYS* 2.9 35.5 + - - +
437A THR* 3.9 6.3 - - - +
440A GLN 4.0 6.7 - - - +
441A PHE* 3.5 26.0 - - + -
444A LYS* 3.7 29.6 - - + -
504A CYS* 4.2 10.1 - - - -
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Residues in contact with ALA 371 (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 PHE 2.7 23.6 + - - +
368A ALA 3.9 1.6 - - - +
370A VAL* 1.3 73.0 - - - +
372A TYR* 1.3 57.9 + - - +
374A CYS 3.6 0.5 - - - -
375A ARG* 3.0 28.9 + - - +
391A VAL* 3.6 21.1 - - + -
434A LEU* 3.8 12.7 - - + +
435A PRO 3.8 19.2 - - - +
437A THR* 4.0 15.3 - - + +
441A PHE* 3.9 4.1 - - + -
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Residues in contact with TYR 372 (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 ALA 3.0 19.6 + - - +
369A THR* 3.6 3.8 - - + +
371A ALA* 1.3 76.6 - - - +
373A LEU* 1.3 80.8 + - + +
375A ARG* 2.8 69.1 + - - +
382A CYS* 2.8 45.9 + - - -
383A ASP* 3.7 2.8 - - - -
384A PHE* 3.5 47.1 + + + -
389A ILE* 4.0 7.2 - - + -
434A LEU* 3.7 9.9 - - + -
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Residues in contact with LEU 373 (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 THR* 2.9 23.9 + - + +
370A VAL* 3.2 4.9 + - - +
372A TYR* 1.3 91.5 - - + +
374A CYS* 1.3 64.8 + - - +
375A ARG* 3.8 5.7 + - - +
444A LYS* 5.1 5.2 - - - +
501A THR 4.6 1.6 - - - +
502A ASN 3.8 16.8 - - - +
503A GLY* 3.6 24.7 - - - +
504A CYS* 3.6 31.0 - - - -
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Residues in contact with CYS 374 (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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370A VAL* 2.9 26.5 + - - +
371A ALA 3.6 3.1 - - - +
373A LEU* 1.3 79.7 - - - +
375A ARG* 1.3 66.9 + - - +
376A SER* 3.7 0.9 + - - -
437A THR* 4.7 11.7 - - + +
440A GLN* 3.2 54.0 + - + +
444A LYS* 4.4 14.4 - - - -
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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