Contacts of the helix formed by residues 364 - 375 (chain A) in PDB entry 1QTI
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 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A HIS 3.7 1.6 + - - +
363A ALA* 1.3 73.1 - - - +
365A ASP* 1.3 60.6 + - - +
366A LEU* 3.7 7.8 - - - +
367A GLY* 2.5 36.1 + - - -
368A LEU* 2.9 33.2 + - - +
531A LEU* 4.3 0.3 - - - +
532A LEU* 3.8 10.3 + - + +
535A THR* 3.0 44.2 + - - +
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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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357A LYS* 5.0 5.4 + - - -
364A ASN* 1.3 74.4 - - - +
366A LEU* 1.3 67.2 + - - +
368A LEU* 3.0 18.0 + - - +
369A ASP* 2.8 30.3 + - - +
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Residues in contact with LEU 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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364A ASN* 3.2 12.1 + - - +
365A ASP* 1.3 78.3 - - - +
367A GLY* 1.3 57.5 + - - +
369A ASP* 3.2 16.6 + - + +
370A ALA* 2.9 27.6 + - + +
531A LEU* 3.9 23.1 - - + -
535A THR* 3.4 28.7 - - + -
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Residues in contact with GLY 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 ALA* 4.4 3.8 - - - -
364A ASN* 2.5 23.4 + - - -
366A LEU* 1.3 74.2 - - - +
368A LEU* 1.3 56.7 + - - +
370A ALA* 3.0 5.4 + - - +
371A VAL* 2.9 34.5 + - - +
528A LEU* 4.1 7.2 - - - +
531A LEU* 3.9 13.0 - - - +
532A LEU* 4.1 11.7 - - - -
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Residues in contact with LEU 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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356A VAL* 3.6 29.3 - - + +
357A LYS* 3.7 45.8 - - + +
360A VAL* 4.3 6.1 - - + +
363A ALA* 4.1 20.2 - - + +
364A ASN 2.9 25.8 + - - +
365A ASP* 3.0 17.2 + - - +
367A GLY* 1.3 72.0 - - - +
369A ASP* 1.3 62.2 + - - +
371A VAL* 3.5 3.9 + - - +
372A THR* 2.8 35.7 + - - +
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Residues in contact with ASP 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 ASP* 2.8 20.4 + - - +
366A LEU* 3.4 20.6 + - + +
368A LEU* 1.3 77.8 - - - +
370A ALA* 1.3 57.8 + - - +
372A THR* 3.8 5.4 + - - -
373A LEU* 2.9 32.7 + - - +
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Residues in contact with ALA 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 LEU* 2.9 13.4 + - + +
367A GLY* 3.1 11.4 - - - +
369A ASP* 1.3 77.0 - - - +
371A VAL* 1.3 64.0 + - - +
373A LEU* 3.3 6.6 + - - +
374A GLN* 3.0 23.4 + - - +
523A PHE* 3.9 22.1 - - + -
527A PHE* 4.5 5.4 - - + -
528A LEU* 4.4 1.8 - - + -
531A LEU* 4.0 20.2 - - + -
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Residues in contact with VAL 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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356A VAL* 4.3 12.6 - - + -
360A VAL* 4.0 13.9 - - + -
367A GLY 2.9 25.0 + - - +
368A LEU* 3.8 5.6 - - - +
370A ALA* 1.3 72.2 - - - +
372A THR* 1.3 62.7 + - - +
374A GLN* 3.0 13.9 + - - +
375A TYR* 3.1 14.3 + - + +
394A ILE* 3.8 38.4 - - + -
523A PHE* 3.6 21.7 - - + -
524A TRP* 3.9 21.5 - - + -
528A LEU* 4.2 7.4 - - + -
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Residues in contact with THR 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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349A ARG* 3.9 11.2 - - - +
352A PHE* 3.9 18.7 - - + -
353A MET* 5.2 11.1 - - + +
356A VAL* 3.7 17.5 - - - +
368A LEU* 2.8 22.8 + - - +
369A ASP* 3.8 6.2 - - - -
371A VAL* 1.3 77.1 - - - +
373A LEU* 1.3 63.1 + - - +
375A TYR 3.3 1.0 + - - -
376A THR* 2.6 42.8 + - - +
378A TRP* 4.8 8.1 - - + -
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Residues in contact with LEU 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 ASP 2.9 19.0 + - - +
370A ALA* 3.7 5.6 - - - +
372A THR* 1.3 77.0 - - - +
374A GLN* 1.3 63.2 + - - +
375A TYR 3.4 0.5 + - - -
376A THR 3.7 12.4 + - - +
378A TRP* 3.7 32.5 - - + +
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Residues in contact with GLN 374 (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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370A ALA 3.0 12.2 + - - +
371A VAL* 3.3 12.6 - - - +
373A LEU* 1.3 80.5 - - - +
375A TYR* 1.3 65.0 + - + +
376A THR 3.6 0.6 + - - -
519A GLN* 4.4 10.9 + - - -
520A MET* 3.2 46.0 - - - +
523A PHE* 4.0 35.9 - - + +
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Residues in contact with TYR 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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349A ARG* 5.2 0.2 + - - -
352A PHE* 4.2 12.8 - - + -
371A VAL* 3.1 18.8 + - + +
374A GLN* 1.3 85.9 - - + +
376A THR* 1.3 62.5 + - - +
377A ASP 4.1 0.9 + - - -
386A LYS 5.2 1.9 - - - +
390A GLY* 3.6 27.9 - - - +
393A ASP* 3.6 19.7 - - + -
394A ILE* 3.5 32.5 - - + -
397A ASP* 2.5 30.9 + - - +
520A MET* 3.3 30.5 - - + +
523A PHE* 4.6 2.2 - + - -
524A TRP* 2.7 34.9 + + - -
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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