Contacts of the helix formed by residues 374 - 390 (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 GLN 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ARG* 5.1 0.9 - - - +
369A PHE* 2.7 50.2 + - + +
372A ASN* 3.1 38.7 + - - +
373A ASN* 1.3 70.2 - - - +
375A ILE* 1.3 63.1 + - - +
376A GLU 3.5 2.0 - - - -
377A LYS* 3.6 32.5 + - + +
378A ALA* 3.3 16.1 + - - +
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Residues in contact with ILE 375 (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 LEU* 4.2 10.8 - - + -
328A PRO* 4.0 28.7 - - + -
369A PHE 5.1 0.2 - - - -
370A ARG* 5.3 8.3 - - + +
373A ASN* 3.3 22.1 + - + +
374A GLN* 1.3 70.9 - - - +
376A GLU* 1.3 60.9 + - - +
378A ALA* 3.3 6.1 + - - +
379A ALA* 2.9 27.4 + - - +
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLN 3.5 1.0 - - - -
375A ILE* 1.3 77.2 - - - +
377A LYS* 1.3 65.9 + - + +
379A ALA* 3.2 7.3 + - - +
380A VAL* 3.0 30.3 + - + +
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Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A PHE* 3.7 42.7 - - + -
374A GLN* 3.6 29.5 + - + +
375A ILE 3.3 0.2 - - - -
376A GLU* 1.3 83.6 - - + +
378A ALA* 1.3 62.2 + - - +
380A VAL* 3.6 6.1 + - - +
381A LEU* 3.1 25.5 + - - +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.8 12.8 - - + +
366A ILE* 4.1 8.0 - - + +
369A PHE* 3.7 21.0 - - + +
370A ARG* 3.8 25.1 - - + -
374A GLN 3.3 13.2 + - - +
375A ILE* 3.6 9.2 - - - +
376A GLU 3.2 0.2 - - - -
377A LYS* 1.3 79.2 - - - +
379A ALA* 1.3 57.5 + - - +
381A LEU* 3.3 3.9 + - - +
382A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.2 9.1 - - - +
328A PRO* 3.7 40.8 - - + +
329A VAL 5.9 0.9 - - - +
375A ILE 2.9 17.1 + - - +
376A GLU* 3.6 6.1 - - - +
378A ALA* 1.3 77.6 - - - +
380A VAL* 1.3 63.8 + - + +
382A ALA* 3.2 4.0 + - - +
383A ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU* 3.0 23.4 + - + +
377A LYS* 4.0 5.8 - - - +
379A ALA* 1.3 76.1 - - + +
381A LEU* 1.3 63.1 - - - +
383A ALA* 3.3 16.3 + - + +
384A GLU* 3.3 12.7 + - + +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 5.3 0.9 - - - +
338A TYR* 3.8 20.2 - - + -
362A MSE 3.7 33.0 - - + +
365A GLU* 3.8 23.6 - - + +
366A ILE* 3.6 34.1 - - + +
369A PHE* 4.0 10.8 - - + -
377A LYS 3.1 19.0 + - - +
378A ALA* 3.7 4.0 - - - +
380A VAL* 1.3 78.3 - - - +
382A ALA* 1.3 57.2 + - - +
384A GLU* 3.4 9.2 + - - +
385A LEU* 3.0 25.6 + - - +
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Residues in contact with ALA 382 (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 LEU* 3.5 26.5 - - + +
327A LEU* 3.8 17.5 - - + -
328A PRO 5.8 0.7 - - - +
366A ILE* 3.8 12.3 - - + +
378A ALA 2.9 17.2 + - - +
379A ALA* 3.5 6.5 - - - +
380A VAL 3.2 0.2 - - - -
381A LEU* 1.3 74.5 - - - +
383A ALA* 1.3 58.5 + - - +
385A LEU* 3.2 2.4 + - - +
386A LYS* 2.9 34.7 + - - +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL 5.8 4.7 - - - +
379A ALA 3.0 12.5 + - - +
380A VAL* 3.5 13.0 - - + +
382A ALA* 1.3 78.4 - - - +
384A GLU* 1.3 61.0 + - - +
386A LYS* 3.4 11.3 + - - +
387A CYS* 3.1 21.7 + - - +
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Residues in contact with GLU 384 (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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336A SER* 2.9 40.0 + - - +
338A TYR* 4.0 9.3 - - - +
339A THR* 2.6 40.5 + - - +
362A MSE 3.9 10.8 - - + +
380A VAL 3.3 8.0 + - - +
381A LEU* 3.7 14.4 - - - +
382A ALA 3.2 0.4 - - - -
383A ALA* 1.3 76.2 - - - +
385A LEU* 1.3 65.8 + - - +
387A CYS* 3.1 8.5 + - + +
388A LEU* 3.1 32.9 + - + +
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Residues in contact with LEU 385 (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* 4.4 2.9 - - + +
323A ALA* 6.2 0.4 - - + -
324A LEU* 4.9 9.4 - - + -
359A LEU* 3.5 42.4 - - + +
362A MSE 3.5 21.7 - - + +
363A VAL* 3.8 23.6 - - + -
366A ILE* 3.7 24.0 - - + -
381A LEU 3.0 18.3 + - - +
382A ALA* 3.2 5.4 + - - +
384A GLU* 1.3 76.8 - - - +
386A LYS* 1.3 57.5 + - - +
388A LEU* 3.4 1.7 + - - -
389A GLY* 3.0 26.2 + - - -
395A LEU* 3.8 19.7 - - + +
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 5.2 17.1 - - + +
329A VAL* 4.3 28.4 - - - +
382A ALA* 2.9 18.8 + - - +
383A ALA* 3.8 9.6 - - - +
385A LEU* 1.3 77.5 - - - +
387A CYS* 1.3 62.0 + - - +
389A GLY 3.6 0.3 + - - -
390A ASN* 3.2 18.2 + - - +
395A LEU* 3.3 35.0 - - + +
396A GLN* 3.2 20.9 + - - +
397A TYR 5.6 4.1 + - - +
399A PRO* 5.9 5.7 - - - +
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Residues in contact with CYS 387 (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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57A MSE 4.3 21.2 - - - +
383A ALA 3.1 12.5 + - - +
384A GLU* 3.1 14.0 + - + +
386A LYS* 1.3 75.6 - - - +
388A LEU* 1.3 68.7 + - + +
390A ASN* 3.2 20.9 + - - +
391A ILE* 4.1 1.6 + - - +
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Residues in contact with LEU 388 (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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57A MSE 4.6 12.3 - - + -
338A TYR 4.5 7.2 - - - +
339A THR* 4.1 23.6 - - + +
342A PHE* 3.8 49.5 - - + -
358A LEU* 6.0 0.4 - - + -
359A LEU* 4.1 14.6 - - + -
362A MSE 3.7 33.2 - - + -
384A GLU* 3.1 22.1 + - + +
385A LEU 4.0 2.9 - - - +
387A CYS* 1.3 80.1 - - + +
389A GLY* 1.3 63.1 + - - +
391A ILE* 3.3 20.1 + - - +
392A PHE* 4.3 3.1 + - - -
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Residues in contact with GLY 389 (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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359A LEU* 4.5 12.9 - - - +
385A LEU 3.0 16.8 + - - -
386A LYS 4.0 1.3 - - - -
388A LEU* 1.3 74.3 - - - +
390A ASN* 1.3 59.2 + - - +
392A PHE* 2.9 23.2 + - - +
394A LEU* 3.0 30.1 + - - -
395A LEU* 4.5 10.8 - - - -
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Residues in contact with ASN 390 (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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53A ARG* 3.7 25.7 + - - +
386A LYS 3.2 13.2 + - - +
387A CYS* 3.2 17.9 + - - +
388A LEU 3.1 0.6 - - - -
389A GLY* 1.3 78.6 - - - +
391A ILE* 1.3 57.4 + - + +
393A GLY* 2.9 17.9 + - - +
394A LEU 3.8 2.0 + - - +
396A GLN* 3.1 33.7 + - - +
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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