Contacts of the helix formed by residues 355 - 371 (chain A) in PDB entry 5D3O
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 ASN 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A VAL* 1.3 80.6 - - - +
356A ASN* 1.3 65.2 + - - +
357A ALA* 3.6 26.7 - - - +
358A GLU* 3.0 40.6 + - - +
359A LYS* 3.1 12.0 + - - +
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Residues in contact with ASN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASN* 1.3 70.6 - - - +
357A ALA* 1.3 66.7 + - - +
358A GLU 2.9 0.3 + - - -
359A LYS* 3.1 26.8 + - - +
360A PHE* 2.8 26.9 + - - +
414A GLY* 3.1 34.9 + - - +
415A ILE* 5.2 1.6 - - - +
417A ASP* 4.9 5.7 + - - +
418A PHE* 3.9 22.5 - - + +
421A GLN* 5.2 9.7 - - - +
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Residues in contact with ALA 357 (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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355A ASN* 3.5 16.3 - - - +
356A ASN* 1.3 78.4 - - - +
358A GLU* 1.3 58.2 + - + +
360A PHE* 3.6 5.8 - - - +
361A ASP* 2.9 37.0 + - - +
421A GLN* 5.7 1.1 - - - -
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Residues in contact with GLU 358 (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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351A LYS* 5.4 0.7 - - + -
354A VAL* 3.3 29.8 - - + +
355A ASN* 3.0 24.5 + - - +
356A ASN 3.0 0.6 - - - -
357A ALA* 1.3 80.0 - - + +
359A LYS* 1.3 56.0 + - - +
360A PHE 3.2 0.2 - - - -
361A ASP* 3.1 11.0 + - - +
362A TYR* 2.7 38.1 + - - +
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Residues in contact with LYS 359 (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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347A THR 5.7 0.2 + - - -
348A SER 5.5 2.6 + - - -
350A ILE* 3.8 9.3 + - + +
351A LYS* 2.9 44.2 - - + +
352A GLN* 4.3 6.0 - - - +
353A GLY 4.7 2.0 - - - +
354A VAL* 3.3 22.1 + - + +
355A ASN 3.1 11.3 + - - +
356A ASN* 3.1 28.4 + - - +
358A GLU* 1.3 72.5 - - - +
360A PHE* 1.3 58.2 + - - +
362A TYR* 3.0 9.9 + - - +
363A VAL* 2.9 31.2 + - - +
415A ILE* 4.2 19.0 - - - +
418A PHE* 3.6 29.2 - - + -
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Residues in contact with PHE 360 (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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356A ASN 2.8 19.8 + - - +
357A ALA* 3.6 6.5 - - - +
359A LYS* 1.3 70.0 - - - +
361A ASP* 1.3 76.9 + - - +
362A TYR 3.0 0.3 + - - -
363A VAL* 3.1 4.3 + - - +
364A MET* 2.9 58.3 + - + +
378A PHE* 3.5 30.1 - + + -
418A PHE* 3.7 16.2 - + + -
421A GLN* 3.5 54.1 - - + +
422A LEU* 4.3 4.3 - - + -
425A ILE* 4.2 11.7 - - + -
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Residues in contact with ASP 361 (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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357A ALA* 2.9 27.3 + - - +
358A GLU* 3.1 12.6 + - - +
360A PHE* 1.3 82.2 - - - +
362A TYR* 1.3 57.7 + - - +
364A MET* 3.3 6.0 + - - +
365A GLN* 2.9 35.3 + - - +
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Residues in contact with TYR 362 (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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300A ILE* 4.2 8.1 - - + -
304A ASP* 2.4 37.2 + - - -
350A ILE* 4.2 12.6 - - + -
351A LYS* 3.8 46.3 + - + -
358A GLU 2.7 14.5 + - - +
359A LYS* 3.2 13.5 - - - +
361A ASP* 1.3 78.4 - - - +
363A VAL* 1.3 64.9 + - - +
365A GLN* 3.2 27.5 - - + +
366A PHE* 3.2 33.0 + + - +
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Residues in contact with VAL 363 (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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293A VAL* 5.8 2.0 - - + -
297A LYS* 5.5 4.7 - - + -
300A ILE* 4.2 18.8 - - + -
350A ILE* 4.2 29.6 - - + -
359A LYS 2.9 15.5 + - - +
360A PHE* 3.8 5.2 - - - +
362A TYR* 1.3 76.0 - - + +
364A MET* 1.3 59.9 + - - +
366A PHE* 2.8 23.7 + - - +
367A LEU* 2.8 34.0 + - + +
418A PHE* 4.4 11.4 - - + -
422A LEU* 3.9 26.0 - - + -
425A ILE* 4.5 1.3 - - + -
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Residues in contact with MET 364 (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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360A PHE* 2.9 55.1 + - + +
361A ASP* 3.6 6.3 - - - +
363A VAL* 1.3 76.0 - - - +
365A GLN* 1.3 56.2 + - - +
367A LEU* 3.3 7.3 + - - +
368A ASN* 2.9 43.5 + - - +
376A VAL* 3.5 40.8 - - + +
377A GLY 3.8 17.7 - - - +
378A PHE* 4.9 1.8 - - - -
425A ILE* 4.2 13.5 - - + -
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Residues in contact with GLN 365 (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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361A ASP* 2.9 17.2 + - - +
362A TYR* 3.2 22.9 - - + +
364A MET* 1.3 75.5 - - - +
366A PHE* 1.3 58.2 + - - +
368A ASN* 3.3 10.2 + - - +
369A LYS* 3.0 53.6 + - - +
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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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300A ILE* 3.7 32.3 - - + -
303A ASN* 3.2 24.5 - - - -
304A ASP* 3.7 10.3 - - - -
362A TYR* 3.4 38.4 - + - +
363A VAL* 2.8 11.1 + - - +
365A GLN* 1.3 76.4 - - - +
367A LEU* 1.3 58.8 + - - +
369A LYS* 3.4 16.0 - - + +
370A MET* 3.1 37.2 + - + +
452A VAL* 3.1 31.0 - - + -
453A LEU* 3.7 15.7 - - + -
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Residues in contact with LEU 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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289A LEU* 4.8 8.5 - - + -
293A VAL* 5.0 3.4 - - + -
296A LEU* 3.8 31.6 - - + -
300A ILE* 4.8 2.0 - - + -
363A VAL* 2.8 26.9 + - + +
364A MET* 3.7 7.9 - - - +
366A PHE* 1.3 74.5 - - - +
368A ASN* 1.3 58.7 + - - +
370A MET* 3.1 23.2 + - + +
371A ALA* 2.8 31.5 + - - +
376A VAL* 4.0 12.3 - - + -
425A ILE* 3.7 41.3 - - + -
435A MET* 3.5 15.3 - - + +
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Residues in contact with ASN 368 (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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364A MET* 2.9 38.2 + - - +
365A GLN* 3.4 11.7 - - - +
367A LEU* 1.3 77.2 - - - +
369A LYS* 1.3 60.1 + - - +
371A ALA* 3.3 3.2 + - - -
373A ASN* 2.7 51.3 + - - +
374A GLU 3.5 10.2 - - - +
376A VAL* 3.4 23.1 + - - +
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Residues in contact with LYS 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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365A GLN* 3.0 47.6 + - - +
366A PHE* 3.4 19.1 - - + +
368A ASN* 1.3 75.1 - - - +
370A MET* 1.3 63.4 + - - +
372A GLY* 3.1 15.1 + - - -
373A ASN* 5.0 6.5 - - - +
445A CYS* 3.9 4.9 - - - +
448A THR* 5.1 1.6 + - - +
450A GLU* 3.0 32.6 + - - +
451A ARG 5.7 0.2 - - - +
452A VAL* 3.9 26.2 - - + +
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Residues in contact with MET 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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296A LEU* 4.2 25.1 - - - +
300A ILE* 3.6 26.0 - - + -
366A PHE* 3.1 38.4 + - + +
367A LEU* 3.1 26.2 + - + +
369A LYS* 1.3 78.9 - - - +
371A ALA* 1.3 56.4 + - - +
372A GLY 3.2 2.9 + - - -
434A VAL* 3.6 2.9 - - - +
435A MET* 3.4 23.9 + - + +
438A THR* 2.9 30.1 + - + +
439A LEU* 6.3 0.7 - - - -
445A CYS* 4.0 0.5 - - - -
452A VAL* 3.5 17.9 - - + -
453A LEU* 4.1 21.5 - - + -
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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 LEU 2.8 15.9 + - - +
368A ASN 4.0 2.9 - - - +
369A LYS 3.2 0.6 - - - -
370A MET* 1.3 75.2 - - - +
372A GLY* 1.3 60.7 + - - +
373A ASN 3.0 4.1 + - - -
374A GLU* 3.2 36.1 + - - +
376A VAL* 4.3 1.3 - - + -
431A SER* 3.7 18.8 - - - +
434A VAL* 3.6 13.7 - - - +
435A MET* 3.6 23.6 - - + -
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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