Contacts of the helix formed by residues 351 - 372 (chain A) in PDB entry 3TQO
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 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 5.6 1.0 - - - +
298A HIS* 4.1 12.1 + - - +
345A ALA* 3.1 24.4 + - - +
346A MSE 4.8 0.2 - - - -
348A ASP* 3.1 30.3 + - + +
349A ASP 3.3 0.8 - - - -
350A PHE* 1.3 70.0 - - - +
352A THR* 1.3 61.9 + - - +
353A PRO* 3.5 11.1 - - - +
354A ILE* 3.0 41.5 + - + +
355A ALA* 3.1 20.9 + - - +
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Residues in contact with THR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MSE 3.5 39.9 - - + -
295A LEU* 2.7 29.3 + - + +
296A SER 4.1 0.4 - - - -
297A GLY 3.1 11.1 + - - -
298A HIS* 4.1 1.2 + - - -
299A TYR* 4.9 1.2 + - + +
346A MSE 4.2 3.4 - - - -
350A PHE 2.8 11.4 + - - +
351A ASN* 1.3 68.1 - - - +
353A PRO* 1.3 70.4 - - - +
355A ALA* 3.9 6.5 - - - -
356A PHE* 2.6 45.8 + - - -
392A PHE* 3.9 14.6 - - + -
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Residues in contact with PRO 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER 3.7 17.0 - - - +
297A GLY* 4.3 1.6 - - - -
298A HIS* 3.9 24.2 - - + +
351A ASN* 3.4 14.1 - - - +
352A THR* 1.3 99.4 - - - +
354A ILE* 1.3 66.6 + - + +
356A PHE* 4.1 3.2 - - + +
357A ALA* 3.2 24.9 + - - +
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Residues in contact with ILE 354 (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 ARG 5.5 0.7 - - - +
345A ALA* 3.4 22.7 - - + -
351A ASN* 3.0 38.8 + - + +
353A PRO* 1.3 81.9 - - + +
355A ALA* 1.3 61.2 + - - +
357A ALA* 3.7 5.8 + - - +
358A LEU* 3.1 23.1 + - + +
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Residues in contact with ALA 355 (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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342A PHE* 3.9 25.1 - - + -
345A ALA* 4.0 15.0 - - + -
346A MSE 4.2 6.1 - - - -
351A ASN 3.1 11.8 + - - +
352A THR* 3.0 12.9 + - - +
354A ILE* 1.3 77.4 - - - +
356A PHE* 1.3 65.4 + - - +
358A LEU* 3.1 8.4 + - - +
359A LEU* 3.1 26.1 + - - +
392A PHE* 4.2 9.2 - - + -
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 3.6 47.1 - + - +
295A LEU* 3.6 24.2 - - + -
296A SER* 3.9 27.8 - - - +
320A PHE* 5.6 1.8 - + - -
352A THR* 2.6 38.5 + - + +
353A PRO* 4.1 4.5 - - + +
355A ALA* 1.3 67.5 - - - +
357A ALA* 1.3 66.9 + - - +
358A LEU 3.0 1.8 - - - -
359A LEU* 3.0 24.8 + - + +
360A PHE* 3.0 25.7 + + + -
392A PHE* 3.7 35.2 - + - -
394A LEU* 4.0 12.8 - - + -
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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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353A PRO 3.2 16.8 + - - +
354A ILE* 3.9 6.5 - - - +
356A PHE* 1.3 77.9 - - - +
358A LEU* 1.3 57.6 + - - +
360A PHE* 3.8 11.6 - - - +
361A GLU* 3.1 24.9 + - - +
364A ARG* 4.8 2.9 + - - -
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Residues in contact with LEU 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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338A TYR* 3.8 17.7 - - + +
341A ARG* 3.4 50.9 - - + +
342A PHE* 3.4 41.5 - - + +
345A ALA* 5.4 0.9 - - + -
354A ILE* 3.1 16.6 + - + +
355A ALA* 3.3 11.7 - - - +
356A PHE 3.0 0.4 - - - -
357A ALA* 1.3 77.5 - - - +
359A LEU* 1.3 65.2 + - + +
361A GLU* 3.3 15.9 + - - +
362A MSE 3.1 27.4 + - - +
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Residues in contact with LEU 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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320A PHE* 4.1 19.7 - - + -
342A PHE* 4.5 7.2 - - + -
355A ALA 3.1 17.6 + - - +
356A PHE* 3.0 16.0 + - + +
358A LEU* 1.3 78.7 - - + +
360A PHE* 1.3 57.6 + - - +
362A MSE 3.3 17.2 + - - +
363A VAL* 3.0 29.5 + - - +
385A LEU* 3.5 29.7 - - + +
388A LEU* 4.1 20.6 - - + -
389A GLY* 4.5 11.4 - - - -
392A PHE* 4.0 29.6 - - + -
394A LEU* 5.7 2.9 - - + -
395A LEU* 5.2 2.7 - - + -
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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
----------------------------------------------------------
292A TYR* 3.1 30.1 - + - -
316A ALA* 3.8 22.0 - - + -
319A ARG* 4.2 33.3 + - + +
320A PHE* 3.4 38.4 - + - -
356A PHE* 3.0 28.5 + - + -
357A ALA* 3.8 11.4 - - - +
359A LEU* 1.3 75.2 - - - +
361A GLU* 1.3 64.5 + - - +
363A VAL* 3.1 8.9 + - + +
364A ARG* 2.9 35.6 + - - +
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Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 3.9 14.7 + - + +
341A ARG* 2.8 43.6 + - - -
357A ALA 3.1 12.6 + - - +
358A LEU* 3.3 15.5 + - - +
360A PHE* 1.3 76.7 - - - +
362A MSE 1.3 62.0 + - - +
364A ARG* 3.3 34.6 + - - +
365A GLU* 3.2 21.1 + - - +
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Residues in contact with MSE 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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338A TYR* 3.4 42.2 - - + -
358A LEU* 3.1 14.4 + - - +
359A LEU* 3.3 15.9 - - - +
360A PHE 3.1 0.2 - - - -
361A GLU* 1.3 75.8 - - - +
363A VAL* 1.3 60.8 + - - +
365A GLU* 3.4 1.6 + - - +
366A ILE* 2.9 34.4 + - - +
381A LEU* 3.7 26.9 - - + +
384A GLU* 3.9 6.1 - - + -
385A LEU* 3.5 50.0 - - + +
388A LEU* 3.7 27.4 - - + -
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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
----------------------------------------------------------
319A ARG* 4.3 28.0 - - + +
320A PHE* 3.3 34.8 - - + +
323A ALA* 3.9 15.3 - - + -
359A LEU 3.0 19.4 + - - +
360A PHE* 3.1 13.6 + - + +
362A MSE 1.3 74.3 - - - +
364A ARG* 1.3 66.9 + - - +
366A ILE* 3.2 8.1 + - - +
367A ASN* 2.9 38.1 + - - +
385A LEU* 3.8 9.6 - - + -
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Residues in contact with ARG 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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319A ARG* 3.6 22.4 - - - +
357A ALA 4.8 2.0 + - - -
360A PHE* 2.9 21.0 + - - +
361A GLU* 3.5 51.1 + - - +
362A MSE 3.3 0.2 - - - -
363A VAL* 1.3 77.4 - - - +
365A GLU* 1.3 56.9 + - - +
367A ASN* 3.4 7.1 + - - +
368A ARG* 3.0 26.2 + - - +
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Residues in contact with GLU 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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338A TYR* 2.5 38.8 + - - +
361A GLU 3.2 12.9 + - - +
362A MSE 3.9 0.4 - - - +
364A ARG* 1.3 75.2 - - - +
366A ILE* 1.3 65.8 + - - +
368A ARG* 3.1 11.5 + - + +
369A PHE* 3.0 55.5 + - + -
381A LEU* 3.8 11.2 - - + -
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Residues in contact with ILE 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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323A ALA* 3.7 32.5 - - + +
324A LEU* 4.8 4.3 - - + -
327A LEU* 4.2 12.1 - - + -
362A MSE 2.9 23.0 + - - +
363A VAL* 3.4 9.6 - - - +
365A GLU* 1.3 76.0 - - - +
367A ASN* 1.3 62.9 + - - +
369A PHE* 3.2 8.1 + - - +
370A ARG* 3.0 26.7 + - + +
378A ALA* 4.4 4.7 - - + +
381A LEU* 3.6 24.2 - - + +
382A ALA* 3.8 26.2 - - + +
385A LEU* 3.7 26.5 - - + -
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Residues in contact with ASN 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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319A ARG* 5.3 5.4 + - - +
322A LEU* 5.3 1.0 - - - +
323A ALA* 3.8 24.2 - - - +
363A VAL* 2.9 32.1 + - - +
364A ARG* 3.7 6.6 - - - +
366A ILE* 1.3 75.0 - - - +
368A ARG* 1.3 57.1 + - - +
370A ARG* 3.8 11.0 - - - +
371A ASP* 3.0 47.3 + - - +
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Residues in contact with ARG 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 ARG 3.0 14.7 + - - +
365A GLU* 3.1 17.5 + - + +
367A ASN* 1.3 77.4 - - - +
369A PHE* 1.3 66.0 + - + +
371A ASP* 3.4 4.9 + - - +
372A ASN* 3.0 29.6 + - + +
374A GLN* 5.1 1.1 - - - +
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Residues in contact with PHE 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 GLU* 3.0 55.3 + - + -
366A ILE 3.6 5.8 - - - +
368A ARG* 1.3 78.5 - - + +
370A ARG* 1.3 60.2 + - - +
372A ASN 3.4 1.0 + - - -
373A ASN 3.1 2.9 + - - -
374A GLN* 2.7 70.1 + - + +
377A LYS* 3.7 49.6 - - + -
378A ALA* 3.7 7.9 - - + -
381A LEU* 4.0 12.6 - - + -
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Residues in contact with ARG 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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322A LEU 3.6 13.5 + - - -
323A ALA 3.1 29.3 + - - -
325A ARG* 3.5 23.2 - - - +
326A GLY* 3.5 32.3 - - - +
327A LEU* 3.8 21.7 - - + +
366A ILE* 3.0 23.1 + - + +
367A ASN* 3.8 13.7 - - - +
369A PHE* 1.3 73.2 - - - +
371A ASP* 1.3 66.4 + - - +
373A ASN* 2.9 24.7 + - - +
374A GLN 4.9 1.6 - - - +
375A ILE* 5.3 8.0 - - + +
378A ALA* 3.8 15.9 - - + -
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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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367A ASN* 3.0 29.2 + - - +
368A ARG* 4.0 4.4 - - - +
370A ARG* 1.3 80.2 - - - +
372A ASN* 1.3 57.6 + - - +
373A ASN* 3.1 13.9 + - - +
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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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368A ARG* 3.0 20.5 + - + +
370A ARG 3.2 0.2 - - - -
371A ASP* 1.3 75.5 - - - +
373A ASN* 1.3 72.7 + - - +
374A GLN* 3.1 35.2 + - - +
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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