Contacts of the helix formed by residues 355 - 373 (chain A) in PDB entry 5OQN
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 THR 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ILE* 4.8 4.0 - - - +
353A ASP* 4.6 18.2 - - - +
354A PHE* 1.3 74.0 - - - +
356A VAL* 1.3 55.9 + - - +
357A GLU* 2.9 18.2 + - - +
358A ILE* 2.7 40.0 + - + +
359A ALA* 2.7 33.9 + - - +
421A ILE* 4.8 0.4 - - - -
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ASP* 6.0 0.2 - - - +
320A VAL* 4.5 7.8 - - + +
321A SER* 5.0 13.9 - - - +
354A PHE 4.0 0.8 + - - -
355A THR* 1.3 70.7 - - - +
357A GLU* 1.3 85.9 + - + +
359A ALA* 4.5 4.3 - - - -
360A PHE* 3.1 25.5 + - - +
417A THR* 4.1 38.4 - - + +
420A PHE* 3.6 36.7 - - + -
421A ILE* 4.7 3.3 - - + +
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Residues in contact with GLU 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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312A ILE* 3.8 15.7 - - + +
315A LEU* 3.5 50.7 - - + +
316A GLU* 3.7 33.9 - - + +
320A VAL* 4.8 4.8 + - + +
355A THR* 3.3 23.2 + - - +
356A VAL* 1.3 93.6 - - - +
358A ILE* 1.3 54.9 + - - +
360A PHE* 3.7 1.0 - - - +
361A LEU* 2.7 35.0 + - - +
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ILE* 3.9 23.8 - - + -
346A PHE* 3.7 14.1 - - + -
353A ASP* 4.0 15.5 - - - +
354A PHE* 3.2 29.8 - - + -
355A THR* 2.7 38.7 + - + +
357A GLU* 1.3 69.1 - - - +
359A ALA* 1.3 54.6 + - - +
361A LEU* 2.8 10.5 + - + +
362A PHE* 2.7 33.3 + - - +
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Residues in contact with ALA 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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354A PHE* 4.0 17.6 - - + -
355A THR 2.7 18.5 + - - +
356A VAL* 4.3 3.1 - - - +
358A ILE* 1.3 74.1 - - - +
360A PHE* 1.3 61.2 + - - +
362A PHE* 3.3 4.2 + - - +
363A ARG 3.2 15.8 + - - -
421A ILE* 3.8 42.8 - - + -
424A GLN* 3.3 19.4 - - + +
425A LEU* 4.5 2.4 - - + +
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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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315A LEU* 3.7 32.3 - - + -
320A VAL* 3.5 18.2 - - + -
326A CYS* 3.5 42.2 - - + -
327A VAL* 4.1 5.8 - - + -
330A ILE* 4.2 15.9 - - + -
356A VAL 3.1 21.0 + - - +
357A GLU 3.7 0.4 - - - +
359A ALA* 1.3 73.5 - - - +
361A LEU* 1.3 68.9 + - - +
363A ARG* 3.1 36.4 + - - -
364A ALA* 2.8 32.4 + - + +
424A GLN* 3.3 23.4 - - - +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 3.7 33.4 - - + -
312A ILE* 4.6 12.3 - - + -
315A LEU* 3.6 24.0 - - + -
330A ILE* 4.6 9.0 - - + -
334A PHE* 5.0 7.0 - - + -
344A ILE* 5.3 10.3 - - + -
346A PHE* 4.4 11.4 - - + -
357A GLU 2.7 16.4 + - - +
358A ILE* 2.8 17.2 + - + +
360A PHE* 1.3 72.0 - - - +
362A PHE* 1.3 56.0 + - - +
364A ALA* 3.1 5.2 + - - +
365A ILE* 2.8 46.0 + - + +
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Residues in contact with PHE 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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346A PHE* 3.2 40.0 - + + -
351A TRP* 4.0 21.3 - + - -
354A PHE* 4.5 2.9 - + + -
358A ILE 2.7 10.3 + - - +
359A ALA* 3.3 12.3 - - - +
360A PHE 3.1 0.2 - - - -
361A LEU* 1.3 73.4 - - - +
363A ARG* 1.3 64.8 + - - +
365A ILE* 3.2 3.1 - - - +
366A TYR* 3.0 29.5 + - + +
382A PHE* 3.9 24.0 - + - -
383A PRO* 4.1 7.0 - - + -
388A LEU* 4.1 23.1 - - + -
425A LEU* 3.8 21.3 - - + -
428A ALA* 4.1 21.1 - - + -
432A TYR* 4.0 20.9 - + - -
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A VAL* 3.4 29.6 - - - +
359A ALA 3.2 5.3 + - - +
360A PHE* 3.1 38.6 + - - +
362A PHE* 1.3 78.3 - - - +
364A ALA* 1.3 64.0 + - - +
367A LEU* 3.1 46.6 + - + +
424A GLN* 2.3 45.7 + - - +
427A ILE* 3.5 39.2 - - + +
428A ALA* 4.2 10.8 - - - +
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Residues in contact with ALA 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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327A VAL* 6.5 0.7 - - + -
330A ILE* 3.9 38.6 - - + -
331A GLU* 4.6 4.8 - - - +
334A PHE* 4.1 4.1 - - + -
360A PHE* 2.8 31.5 + - + +
361A LEU* 3.6 7.0 - - - +
363A ARG* 1.3 75.7 - - - +
365A ILE* 1.3 62.6 + - - +
367A LEU* 4.1 2.1 - - - +
368A TYR* 3.1 24.1 + - - +
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Residues in contact with ILE 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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334A PHE* 4.2 13.4 - - + -
341A LEU* 3.3 34.5 - - + -
344A ILE* 4.0 18.4 - - + -
346A PHE* 3.8 23.8 - - + -
361A LEU* 2.8 34.0 + - + +
362A PHE* 3.2 6.7 - - - +
364A ALA* 1.3 72.9 - - - +
366A TYR* 1.3 67.6 + - - +
368A TYR* 3.2 4.9 + - + +
369A CYS* 3.1 32.6 + - - -
377A MET* 4.2 3.4 - - - -
382A PHE* 3.8 20.6 - - + -
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Residues in contact with TYR 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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362A PHE* 3.0 21.1 + + + +
363A ARG 4.1 1.8 - - - +
365A ILE* 1.3 80.3 - - - +
367A LEU* 1.3 67.4 + - + +
368A TYR 3.2 0.9 + - - -
369A CYS* 3.3 3.1 + - - +
370A LEU* 3.3 37.7 + - + +
378A LEU* 4.3 10.9 - - + +
382A PHE* 3.6 43.5 - + + -
428A ALA* 3.6 32.1 - - + -
431A ARG* 3.1 26.6 + - + -
432A TYR* 2.9 49.2 - + - -
433A ASP* 3.9 7.9 + - - -
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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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331A GLU* 5.7 0.9 - - - +
363A ARG* 3.1 33.2 + - + +
364A ALA* 4.4 2.0 - - - +
366A TYR* 1.3 83.3 - - + +
368A TYR* 1.3 60.3 + - - +
370A LEU* 3.5 7.9 + - + +
371A ASP* 2.6 36.7 + - - +
427A ILE* 4.2 20.6 - - + +
428A ALA* 3.7 32.1 - - + +
430A GLU* 6.0 0.2 - - - +
431A ARG* 4.1 31.0 - - + +
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Residues in contact with TYR 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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331A GLU* 2.9 40.5 + - + +
334A PHE* 3.4 50.9 + + + +
335A GLN* 4.1 11.2 + - + +
341A LEU* 3.8 25.6 - - + +
364A ALA 3.1 20.5 + - - +
365A ILE* 3.3 6.1 - - - +
366A TYR 3.1 0.6 - - - -
367A LEU* 1.3 75.4 - - - +
369A CYS* 1.3 74.2 + - - +
371A ASP* 3.1 16.6 + - + +
372A ASN* 3.2 32.2 + - - +
374A ILE* 4.3 12.3 - - + -
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Residues in contact with CYS 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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341A LEU* 5.4 1.3 - - - -
365A ILE* 3.1 23.8 + - - -
366A TYR 3.3 3.5 + - - +
368A TYR* 1.3 81.5 - - - +
370A LEU* 1.3 52.3 + - - +
373A ASN* 2.7 31.4 + - - -
374A ILE* 2.9 39.9 + - + +
377A MET* 3.9 32.1 - - - -
378A LEU* 3.7 23.6 - - + +
382A PHE* 4.3 5.2 - - + -
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Residues in contact with LEU 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 TYR* 3.3 33.1 + - + +
367A LEU* 3.8 8.3 - - - +
368A TYR 3.2 0.6 - - - -
369A CYS* 1.3 78.8 - - - +
371A ASP* 1.3 62.9 + - - +
372A ASN 3.4 0.3 + - - -
373A ASN* 3.6 7.5 + - - +
378A LEU* 3.7 32.3 - - + -
431A ARG* 3.2 59.3 + - + +
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Residues in contact with ASP 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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331A GLU* 5.5 5.8 - - - +
367A LEU* 2.6 28.1 - - - +
368A TYR* 3.1 8.2 + - + +
370A LEU* 1.3 78.9 - - - +
372A ASN* 1.3 68.7 + - - +
373A ASN* 5.3 0.3 - - - +
431A ARG* 3.3 27.5 + - - +
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Residues in contact with ASN 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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331A GLU* 5.2 1.4 + - - -
368A TYR* 3.2 37.3 + - + +
371A ASP* 1.3 85.7 - - - +
373A ASN* 1.3 71.2 + - - +
374A ILE* 3.3 21.8 + - + +
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Residues in contact with ASN 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 CYS 2.7 16.6 + - - -
370A LEU* 3.6 6.3 + - - +
371A ASP 3.5 3.2 - - - +
372A ASN* 1.3 77.3 - - - +
374A ILE* 1.3 51.7 + - - +
375A THR* 2.6 43.2 + - - -
378A LEU* 5.0 7.1 - - - +
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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
------------------------------------------------------------
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