Contacts of the helix formed by residues 365 - 379 (chain B) in PDB entry 1QDU
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 ASP 365 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B GLY 3.4 4.8 + - - -
364B ASP* 1.3 72.0 - - - +
366B ILE* 1.3 61.2 + - - +
367B LEU* 2.6 47.9 + - - +
368B THR* 2.8 46.2 + - - +
369B ILE* 3.0 5.2 - - - +
397B LYS* 3.5 50.2 + - + -
398B LEU 3.8 19.1 + - - +
399B VAL* 4.7 2.5 - - + -
367D LEU* 5.8 0.2 - - - +
368D THR 5.9 0.2 + - - -
397D LYS* 4.2 3.5 + - - -
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 6.3 0.2 - - + -
281A PHE* 4.7 12.3 - - + -
328B LEU* 3.4 29.6 - - + -
353B LEU* 5.2 1.6 - - + -
357B LEU* 4.7 12.1 - - + -
361B CYS* 6.3 0.2 - - - -
364B ASP 3.5 1.4 + - - -
365B ASP* 1.3 78.2 + - - +
367B LEU* 1.3 64.8 + - + +
369B ILE* 3.7 18.2 - - + -
370B LEU* 2.7 47.4 + - + +
394B LEU* 4.6 1.8 - - + -
398B LEU* 2.8 39.4 + - + +
400B PHE* 4.1 19.7 - - + -
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 4.7 11.4 - - + -
365B ASP* 2.6 29.8 + - - +
366B ILE* 1.3 85.2 - - + +
368B THR* 1.3 56.9 + - - +
370B LEU* 3.1 6.7 + - + +
371B THR* 2.8 33.2 + - - -
392B PHE* 4.2 33.0 - - + -
394B LEU* 4.9 11.0 - - + -
396B LYS 6.0 1.3 - - - +
397B LYS* 6.1 2.0 - - + +
398B LEU 6.1 0.4 - - - +
367D LEU* 4.1 29.8 - - + -
368D THR* 6.0 0.4 - - - -
371D THR* 3.6 24.0 - - + +
392D PHE* 4.4 11.0 - - + -
397D LYS* 4.9 1.1 - - - +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ARG* 3.9 28.2 + - - +
364B ASP* 4.1 8.2 - - + +
365B ASP* 2.8 29.0 + - - +
367B LEU* 1.3 80.2 - - - +
369B ILE* 1.3 62.0 + - - +
371B THR* 2.9 17.1 + - - -
372B GLU* 3.1 11.6 + - - +
397B LYS* 5.6 0.5 + - - -
150C ASP* 4.1 17.0 - - + +
397D LYS* 3.0 32.1 + - - +
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.5 4.0 - - + +
356B SER* 3.6 26.7 - - - +
357B LEU* 4.0 21.8 - - + +
360B ARG* 3.5 27.6 - - + -
361B CYS* 4.8 11.9 - - - +
364B ASP* 2.8 38.8 - - + +
365B ASP 3.0 21.3 + - - +
366B ILE* 3.7 13.7 - - + +
368B THR* 1.3 78.8 - - - +
370B LEU* 1.3 63.4 + - - +
372B GLU* 3.1 9.4 + - - +
373B VAL* 3.1 24.3 + - + +
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.5 12.1 - - + -
328B LEU* 3.9 31.0 - - + -
330B GLY* 4.9 5.4 - - - -
349B TYR* 4.1 21.1 - - + +
353B LEU* 4.5 14.8 - - + -
366B ILE* 2.7 28.2 + - + +
367B LEU* 3.5 9.6 - - + +
369B ILE* 1.3 74.1 - - - +
371B THR* 1.3 61.3 + - - +
373B VAL* 3.4 11.8 + - + +
374B ASN* 3.1 23.6 + - - +
389B PRO* 3.6 35.9 - - + +
392D PHE* 4.6 3.8 - - + -
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Residues in contact with THR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU 2.8 18.4 + - - -
368B THR* 2.9 10.8 + - - -
370B LEU* 1.3 75.0 - - - +
372B GLU* 1.3 61.6 + - - +
374B ASN* 2.9 28.2 + - - +
375B TYR* 3.0 6.6 + - - +
367D LEU* 3.9 19.4 - - + +
392D PHE* 3.9 8.0 - - - -
394D LEU* 3.8 9.2 - - + +
395D ARG 3.5 4.1 - - - +
396D LYS* 3.5 41.7 - - - +
397D LYS* 4.5 5.7 + - + +
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Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER* 3.2 29.7 + - - +
359B GLU* 5.0 6.1 - - - +
360B ARG* 2.8 48.3 + - - +
368B THR 3.1 7.4 + - - +
369B ILE 3.5 8.1 - - - +
371B THR* 1.3 80.5 - - - +
373B VAL* 1.3 57.5 - - - +
375B TYR* 2.9 12.4 + - + +
376B GLU* 2.8 47.4 + - + +
395D ARG 5.0 0.7 - - - -
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Residues in contact with VAL 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TYR* 3.9 27.1 - - + -
352B SER* 3.7 27.6 - - - +
353B LEU* 3.8 27.1 - - + +
356B SER* 3.9 9.0 - - - +
369B ILE* 3.1 21.2 + - + +
370B LEU* 3.5 12.8 - - + +
372B GLU* 1.3 72.9 - - - +
374B ASN* 1.3 65.1 + - - +
376B GLU* 4.5 0.9 - - - -
377B VAL* 2.8 42.0 + - + +
387B PRO* 4.8 2.0 - - + -
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Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU 3.1 12.9 + - - +
371B THR 2.9 14.6 + - - +
373B VAL* 1.3 77.6 - - - +
375B TYR* 1.3 59.0 + - - +
377B VAL* 4.1 1.4 - - - +
378B SER* 2.8 29.7 + - - -
386B MET* 3.5 14.4 - - + +
387B PRO* 3.3 30.9 + - - +
389B PRO* 3.9 10.5 - - - +
392D PHE* 3.5 17.0 - - - -
393D THR* 3.5 20.4 - - - +
394D LEU 3.0 24.6 + - - +
395D ARG* 4.0 2.9 - - + -
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Residues in contact with TYR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ASP* 3.1 31.6 - - + +
371B THR 3.0 4.4 + - - -
372B GLU* 2.9 15.9 + - + +
374B ASN* 1.3 76.3 - - - +
376B GLU* 1.3 74.1 + - - +
378B SER* 2.6 32.2 + - - -
379B ASN* 3.3 24.8 + - - +
151C LYS* 4.0 36.8 - - + -
319D ARG* 3.8 13.2 + - - -
395D ARG* 3.6 53.5 - - + +
396D LYS* 5.7 3.1 - - + -
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B SER* 3.6 21.8 - - - +
355B GLN* 5.7 6.1 + - - +
356B SER* 4.8 3.6 - - - +
372B GLU* 2.8 45.5 + - + +
373B VAL* 4.3 0.4 - - - +
375B TYR* 1.3 90.5 - - - +
377B VAL* 1.3 62.0 + - - +
379B ASN* 3.2 18.2 + - - +
381B LYS* 3.7 20.0 + - - +
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B TRP* 4.0 26.9 - - + +
349B TYR* 4.4 3.1 - - - -
352B SER* 3.8 17.3 - - - +
373B VAL* 2.8 39.9 + - + +
375B TYR 3.0 1.0 + - - -
376B GLU* 1.3 75.3 - - - +
378B SER* 1.3 61.9 + - - +
381B LYS* 3.2 24.2 + - - +
385B GLN* 3.8 39.8 + - + +
387B PRO* 3.7 16.8 - - + -
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ASN 2.8 17.3 + - - -
375B TYR 2.6 18.8 + - - -
377B VAL* 1.3 72.3 - - - +
379B ASN* 1.3 56.8 + - - -
384B LYS* 2.9 31.8 + - - +
385B GLN 4.3 5.3 + - - +
386B MET* 3.7 6.4 - - - +
320D TYR 3.8 2.8 - - - +
321D ILE* 4.7 0.7 - - - -
322D PRO* 3.4 30.4 - - - +
395D ARG* 3.5 28.2 - - - -
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Residues in contact with ASN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP* 4.9 3.0 + - - +
375B TYR* 3.6 41.1 + - - +
376B GLU* 3.2 12.0 + - - +
377B VAL 3.2 1.0 - - - -
378B SER* 1.3 77.7 - - - +
381B LYS* 1.3 73.8 + - - +
384B LYS* 4.2 3.5 + - - +
319D ARG* 4.1 19.5 - - - +
320D TYR 4.0 10.9 - - - +
321D ILE* 4.4 0.9 - - - +
395D ARG* 4.3 7.4 + - - -
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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
------------------------------------------------------------
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