Contacts of the helix formed by residues 365 - 381 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F GLY 3.3 4.8 + - - -
364F ASP* 1.3 71.8 - - - +
366F ILE* 1.3 73.3 + - - +
367F LEU* 2.8 37.9 + - - +
368F THR* 2.8 38.4 + - - +
369F ILE* 3.0 10.7 - - - +
397F LYS* 3.4 48.1 + - + +
398F LEU 3.7 20.5 + - - +
399F VAL* 4.6 2.5 - - + -
367H LEU* 5.8 0.3 - - - +
397H LYS* 4.3 3.3 + - - -
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Residues in contact with ILE 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E VAL* 6.2 0.2 - - + -
281E PHE* 4.7 14.1 - - + -
328F LEU* 3.4 28.5 - - + -
353F LEU* 5.4 1.3 - - + -
357F LEU* 4.8 11.7 - - + -
361F CYS* 6.3 0.4 - - - -
364F ASP 3.6 1.0 + - - -
365F ASP* 1.3 75.7 + - - +
367F LEU* 1.3 65.8 + - + +
369F ILE* 3.3 14.0 + - + -
370F LEU* 2.8 48.1 + - + +
394F LEU* 4.3 2.0 - - + -
398F LEU* 2.7 43.8 + - + +
400F PHE* 4.2 19.3 - - + -
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Residues in contact with LEU 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328F LEU* 4.9 1.6 - - + -
365F ASP* 2.8 27.0 + - - +
366F ILE* 1.3 82.9 - - + +
368F THR* 1.3 63.0 + - - +
370F LEU* 3.3 13.4 + - + +
371F THR* 2.9 27.4 + - - -
392F PHE* 4.1 36.6 - - + -
394F LEU* 4.7 12.6 - - + -
396F LYS 5.9 1.6 - - - +
397F LYS* 6.0 2.5 - - + +
398F LEU 6.0 0.2 - - - +
367H LEU* 4.0 29.6 - - + -
368H THR* 5.7 0.7 - - - +
371H THR* 3.6 23.6 - - - +
392H PHE* 4.3 12.3 - - + -
397H LYS* 4.9 1.1 - - - +
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Residues in contact with THR 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F ARG* 3.8 27.3 + - - +
364F ASP* 4.1 6.9 - - + +
365F ASP* 2.8 28.6 + - - +
367F LEU* 1.3 77.5 - - - +
369F ILE* 1.3 65.7 + - - +
371F THR* 3.0 17.3 + - - -
372F GLU* 3.1 10.9 + - - +
397F LYS* 5.5 0.7 + - - -
150G ASP* 3.9 18.4 - - + +
397H LYS* 3.2 31.7 + - - +
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Residues in contact with ILE 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F LEU* 4.6 3.6 - - + +
356F SER* 3.8 25.6 - - - -
357F LEU* 4.1 23.1 - - + +
360F ARG* 3.4 29.8 - - + -
361F CYS* 4.8 11.4 - - - +
364F ASP* 2.8 38.8 - - + +
365F ASP 3.0 20.2 + - - +
366F ILE* 3.7 12.8 - - + +
368F THR* 1.3 77.5 - - - +
370F LEU* 1.3 66.1 + - - +
372F GLU* 3.0 10.3 + - - +
373F VAL* 2.9 28.6 + - + +
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Residues in contact with LEU 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E PHE* 4.5 13.5 - - + -
328F LEU* 3.9 33.0 - - + -
330F GLY* 5.1 2.2 - - - -
349F TYR* 4.0 28.3 - - + +
353F LEU* 4.8 6.1 - - + -
366F ILE* 2.8 30.0 + - + +
367F LEU* 3.5 11.4 - - + +
369F ILE* 1.3 73.6 - - - +
371F THR* 1.3 57.1 + - - +
373F VAL* 3.4 12.7 + - + +
374F ASN* 3.1 29.0 + - - +
389F PRO* 3.8 35.0 - - + +
392H PHE* 4.6 3.6 - - + -
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Residues in contact with THR 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F LEU 2.9 23.3 + - - -
368F THR* 3.0 11.5 + - - -
370F LEU* 1.3 73.5 - - - +
372F GLU* 1.3 68.1 + - - +
374F ASN* 2.9 19.5 + - - +
375F TYR* 2.9 10.7 + - - +
367H LEU* 3.9 17.5 - - + +
392H PHE* 4.0 6.3 - - - -
394H LEU* 3.8 11.2 - - + +
395H ARG 3.5 4.2 - - - +
396H LYS* 3.4 43.1 - - - +
397H LYS* 4.4 6.4 + - + +
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Residues in contact with GLU 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F SER* 3.5 25.5 + - - +
359F GLU* 4.8 7.1 - - - +
360F ARG* 2.8 46.8 + - - +
368F THR 3.1 6.5 + - - +
369F ILE* 3.0 9.8 + - - +
371F THR* 1.3 80.5 - - - +
373F VAL* 1.3 58.8 + - - +
375F TYR* 2.8 23.2 + - + +
376F GLU* 2.8 40.6 + - + +
395H ARG 5.0 0.7 - - - -
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Residues in contact with VAL 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349F TYR* 3.8 34.8 - - + -
352F SER* 3.6 20.4 - - - +
353F LEU* 3.8 26.5 - - + +
356F SER* 3.9 15.5 - - - +
369F ILE* 2.9 20.8 + - + +
370F LEU* 3.5 13.5 - - + +
371F THR 3.1 0.2 - - - -
372F GLU* 1.3 76.8 - - - +
374F ASN* 1.3 62.3 + - - +
376F GLU* 4.5 0.7 - - - -
377F VAL* 2.8 37.0 + - + +
387F PRO* 4.8 1.8 - - + -
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Residues in contact with ASN 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F LEU 3.1 13.1 + - - +
371F THR 2.9 13.6 + - - +
373F VAL* 1.3 75.1 - - - +
375F TYR* 1.3 56.6 + - - +
377F VAL* 4.1 1.7 - - - +
378F SER* 2.6 34.4 + - - -
386F MET* 3.6 14.2 - - + +
387F PRO* 3.1 34.4 - - - +
389F PRO* 3.7 10.4 - - - +
392H PHE* 3.6 17.8 - - - -
393H THR* 3.6 20.2 - - - +
394H LEU 3.1 23.5 + - - +
395H ARG* 4.0 1.8 - - + -
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Residues in contact with TYR 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E ASP* 3.2 31.5 - - + +
371F THR 2.9 4.6 + - - -
372F GLU* 2.8 15.7 + - + +
374F ASN* 1.3 76.2 - - - +
376F GLU* 1.3 72.0 + - - +
378F SER* 2.7 32.1 + - - -
379F ASN* 3.4 27.7 + - - +
151G LYS* 3.8 38.2 - - + -
319H ARG* 3.8 14.2 + - - -
395H ARG* 3.5 50.8 - - + +
396H LYS* 5.7 2.7 - - + -
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Residues in contact with GLU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F SER* 3.8 19.7 - - - +
355F GLN* 5.9 5.0 + - - +
356F SER* 4.8 3.8 - - - +
372F GLU* 2.8 43.4 + - + +
375F TYR* 1.3 89.2 - - - +
377F VAL* 1.3 62.6 + - - +
379F ASN* 3.2 22.3 + - - +
381F LYS* 3.6 20.4 + - - +
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Residues in contact with VAL 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348F TRP* 4.0 20.8 - - + +
349F TYR* 4.4 2.9 - - - +
352F SER* 3.9 22.4 - - - +
373F VAL* 2.8 33.3 + - + +
375F TYR 3.1 0.2 + - - -
376F GLU* 1.3 76.9 - - - +
378F SER* 1.3 61.6 + - - +
381F LYS* 3.2 24.1 - - - +
385F GLN* 3.5 45.3 + - + +
387F PRO* 3.7 17.7 - - + -
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Residues in contact with SER 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F ASN 2.6 18.9 + - - -
375F TYR 2.7 19.1 + - - -
377F VAL* 1.3 72.3 - - - +
379F ASN* 1.3 49.4 + - - -
381F LYS 3.2 0.2 - - - -
384F LYS* 2.5 38.9 + - - +
385F GLN 4.3 3.3 + - - -
386F MET* 3.8 5.5 - - - +
320H TYR 3.6 2.8 - - - +
321H ILE* 4.6 0.9 - - - -
322H PRO* 3.6 28.0 - - - +
395H ARG* 3.4 31.4 - - - +
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Residues in contact with ASN 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E ASP* 5.1 2.8 - - - +
375F TYR* 3.6 45.0 + - - +
376F GLU* 3.2 15.0 + - - +
378F SER* 1.3 79.4 - - - +
381F LYS* 1.3 78.8 + - - +
384F LYS* 3.8 4.4 + - - +
319H ARG* 4.2 17.5 - - - +
320H TYR 4.4 7.9 - - - +
321H ILE* 4.7 1.4 - - - +
395H ARG* 4.4 2.9 + - - -
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Residues in contact with LYS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348F TRP* 3.4 66.2 + - + +
352F SER* 5.7 4.0 - - - -
376F GLU* 3.8 18.3 + - - +
377F VAL* 3.2 21.5 - - - +
378F SER 3.2 1.1 - - - +
379F ASN* 1.3 77.7 - - - +
381F ASP* 1.3 58.9 + - - +
384F LYS* 2.8 24.4 - - - +
4300V PHQ 5.9 3.1 - - + -
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Residues in contact with ASP 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F TYR* 3.0 46.7 - + + +
348F TRP* 3.7 18.5 - - + -
379F ASN 3.0 20.2 + - - +
381F LYS* 1.3 225.5 - - + +
382F MET* 3.3 31.2 + - + -
383F GLY 3.1 20.2 + - - +
384F LYS* 3.4 22.3 - - - +
320H TYR* 4.5 11.2 - - + -
4300V PHQ 4.5 25.9 - - - -
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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
------------------------------------------------------------
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