Contacts of the helix formed by residues 355 - 371 (chain A) in PDB entry 3QTC
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
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Residue Dist Surf HB Arom Phob DC
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353A GLY* 3.1 13.3 + - - -
354A CYS* 1.3 78.2 - - - +
356A ARG* 1.3 64.0 + - - +
357A GLU* 3.6 9.6 + - - +
358A ASN* 3.0 29.4 + - - +
359A LEU 3.0 16.6 + - - -
402A VAL* 4.7 1.6 - - - -
418A ILE* 3.6 9.4 - - - +
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Residues in contact with ARG 356 (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 THR* 1.3 71.7 - - - +
357A GLU* 1.3 57.9 + - - +
359A LEU* 3.3 3.2 + - - +
360A GLU* 2.7 58.0 + - + +
376A ILE* 4.7 5.3 + - - +
378A GLY* 3.9 26.3 + - - +
386A ASP* 3.0 39.6 + - - +
388A LEU* 3.1 29.8 - - + +
402A VAL* 4.0 21.7 - - + +
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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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355A THR* 3.2 9.8 + - - +
356A ARG* 1.3 79.3 - - - +
358A ASN* 1.3 68.1 + - - +
360A GLU* 3.4 6.9 + - - +
361A SER* 3.0 28.4 + - - -
817A EDO 2.4 51.9 + - - -
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Residues in contact with ASN 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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349A GLN* 6.2 0.4 - - - +
353A GLY* 2.9 33.4 - - - +
355A THR* 3.0 21.5 + - - +
357A GLU* 1.3 86.9 + - - +
359A LEU* 1.3 64.1 + - - +
361A SER* 3.4 9.3 + - - -
362A ILE* 3.1 31.7 + - + +
418A ILE* 4.2 7.6 - - + -
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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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347A PHE* 3.8 26.2 - - + -
355A THR 3.0 12.9 + - - +
356A ARG 3.3 8.0 + - - +
358A ASN* 1.3 74.7 - - - +
360A GLU* 1.3 65.2 + - - +
362A ILE* 3.3 4.3 + - - +
363A ILE* 3.1 39.1 + - + +
388A LEU* 4.2 12.1 - - + -
400A ALA* 3.9 13.7 - - + -
401A LEU 3.5 26.9 - - - +
402A VAL* 3.9 16.4 - - + -
418A ILE* 3.8 15.6 - - + +
419A GLY 3.7 22.9 - - - +
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Residues in contact with GLU 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 ARG* 2.7 62.2 + - - +
357A GLU* 3.8 7.0 - - - +
359A LEU* 1.3 72.0 - - - +
361A SER* 1.3 55.3 + - - +
363A ILE* 3.5 3.7 + - - +
364A THR* 2.8 38.6 + - - +
376A ILE* 4.0 28.2 - - + +
388A LEU* 3.8 16.8 - - + +
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Residues in contact with SER 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 GLU* 3.0 19.3 + - - -
358A ASN* 3.5 13.5 - - - -
359A LEU 3.2 0.2 - - - -
360A GLU* 1.3 74.1 - - - +
362A ILE* 1.3 60.1 + - - +
364A THR* 3.3 4.9 + - - -
365A ASP* 2.8 45.1 + - - +
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Residues in contact with ILE 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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253A PHE* 4.3 6.3 - - + -
254A PHE* 3.9 21.3 - - + -
257A ARG* 5.5 7.2 - - - +
259A PHE* 4.2 24.2 - - + -
347A PHE* 3.6 30.5 - - + -
349A GLN* 4.5 7.9 - - + +
358A ASN* 3.1 20.1 + - + +
359A LEU* 3.3 4.2 + - - +
361A SER* 1.3 76.5 - - - +
363A ILE* 1.3 58.0 + - - +
365A ASP* 3.9 5.6 - - - +
366A PHE* 2.9 32.1 + - - +
418A ILE* 4.2 19.7 - - + -
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Residues in contact with ILE 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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347A PHE* 4.1 15.9 - - + -
359A LEU* 3.1 27.3 + - + +
360A GLU* 3.7 7.4 - - - +
362A ILE* 1.3 77.2 - - - +
364A THR* 1.3 58.7 + - - +
366A PHE* 3.3 6.4 + - - +
367A LEU* 3.0 45.8 + - + +
374A PHE* 4.5 1.6 - - + -
376A ILE* 4.1 14.4 - - + -
388A LEU* 4.8 5.8 - - + -
390A VAL* 3.9 28.7 - - + -
400A ALA* 3.9 28.3 - - + -
420A ALA* 4.5 2.2 - - + -
422A PHE* 4.2 12.6 - - + -
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Residues in contact with THR 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 GLU* 2.8 23.3 + - - +
361A SER* 3.8 5.8 - - - -
363A ILE* 1.3 74.4 - - - +
365A ASP* 1.3 71.3 + - - +
367A LEU* 4.1 0.2 - - - -
368A ASN* 3.0 41.4 + - - +
374A PHE* 3.6 28.8 - - + -
376A ILE* 4.0 5.4 - - - +
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Residues in contact with ASP 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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253A PHE* 3.8 3.6 - - + -
257A ARG* 2.8 41.6 + - - +
361A SER* 2.8 34.7 + - - +
362A ILE* 3.9 2.4 - - - +
364A THR* 1.3 76.7 - - - +
366A PHE* 1.3 58.4 + - - +
368A ASN* 3.9 4.4 - - - +
369A HIS* 3.0 30.3 + - - +
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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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250A ILE* 3.9 24.9 - - + -
253A PHE* 3.4 34.3 - + + -
254A PHE* 3.8 18.6 - + + -
345A LEU* 3.7 28.3 - - + -
347A PHE* 5.4 0.2 - + - -
362A ILE 2.9 19.6 + - - +
363A ILE* 3.5 4.0 - - - +
365A ASP* 1.3 78.2 - - - +
367A LEU* 1.3 78.0 + - + +
369A HIS* 3.3 5.1 + + - +
370A LEU* 3.0 50.7 + - + +
422A PHE* 4.1 26.9 - + - -
427A LEU* 4.4 2.7 - - + -
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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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363A ILE* 3.0 21.4 + - + +
366A PHE* 1.3 85.2 - - + +
368A ASN* 1.3 61.3 + - - +
370A LEU* 3.3 5.8 + - + +
371A GLY 2.9 22.5 + - - -
372A ILE* 3.0 28.4 + - + +
374A PHE* 3.6 41.3 - - + -
390A VAL* 3.7 21.8 - - + -
397A LEU* 4.4 4.7 - - + -
422A PHE* 3.8 26.0 - - + -
427A LEU* 3.8 21.5 - - + -
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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 THR* 3.0 38.1 + - - +
365A ASP* 4.0 5.1 - - - +
367A LEU* 1.3 74.2 + - - +
369A HIS* 1.3 65.0 + - - +
371A GLY* 3.4 11.4 + - - +
372A ILE 4.9 3.0 + - - +
374A PHE* 3.9 16.0 - - - -
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Residues in contact with HIS 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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249A GLU* 4.8 10.3 + - + +
253A PHE* 3.7 39.7 + + + +
365A ASP 3.0 19.7 + - - +
366A PHE* 3.3 6.3 - + - +
368A ASN* 1.3 78.2 - - - +
370A LEU* 1.3 75.4 + - + +
371A GLY 3.5 0.5 + - - -
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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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246A LEU* 4.0 25.8 - - + -
249A GLU* 4.6 13.9 - - + +
250A ILE* 4.7 4.5 - - + +
366A PHE* 3.0 53.4 + - + +
367A LEU* 3.3 8.3 + - + +
369A HIS* 1.3 90.5 - - + +
371A GLY* 1.3 60.9 + - - +
372A ILE* 4.1 23.5 - - + +
427A LEU* 4.0 18.4 - - + -
431A LYS* 4.5 20.3 + - + +
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Residues in contact with GLY 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 2.9 5.8 + - - -
368A ASN* 3.4 9.3 + - - -
369A HIS 3.3 4.2 - - - -
370A LEU* 1.3 78.8 - - - +
372A ILE* 1.3 62.3 + - - +
373A ASP 4.3 0.7 + - - -
431A LYS* 5.4 4.5 - - - +
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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