Contacts of the helix formed by residues 365 - 379 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363H GLY 3.7 3.2 + - - -
364H ASP* 1.3 72.8 + - - +
366H ILE* 1.3 70.6 + - - +
367H LEU* 2.7 18.4 + - - +
368H THR* 2.5 45.8 + - - +
369H ILE* 3.0 21.8 + - - +
394H LEU* 5.8 0.7 - - - +
397H LYS* 3.1 47.5 + - + +
398H LEU 3.7 15.3 + - - +
399H VAL* 4.7 6.5 - - - +
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Residues in contact with ILE 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G VAL* 6.1 0.4 - - + -
281G PHE* 4.8 12.3 - - + -
328H LEU* 3.5 28.5 - - + -
353H LEU* 5.5 1.6 - - + -
357H LEU* 5.1 5.8 - - + -
364H ASP 3.7 0.4 + - - -
365H ASP* 1.3 72.8 - - - +
367H LEU* 1.3 72.9 + - + +
369H ILE* 3.2 20.8 + - + -
370H LEU* 2.8 51.2 + - + +
394H LEU* 4.2 2.5 - - + -
398H LEU* 3.1 43.1 + - + +
399H VAL* 4.8 0.2 - - - +
400H PHE* 4.3 18.6 - - + -
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Residues in contact with LEU 367 (chain H).
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* 4.0 29.4 - - + -
371F THR* 3.9 15.0 - - - +
392F PHE* 4.2 20.3 - - + -
328H LEU* 4.4 12.6 - - + -
365H ASP* 2.7 21.8 + - - +
366H ILE* 1.3 91.0 - - + +
368H THR* 1.3 49.1 + - - +
370H LEU* 3.2 7.1 + - + +
371H THR* 2.8 39.8 + - - -
392H PHE* 3.7 39.3 - - + -
394H LEU* 4.8 8.5 - - + -
397H LYS* 4.6 3.6 - - - +
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Residues in contact with THR 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ASP* 3.7 23.3 - - - +
367F LEU* 6.0 0.7 - - - -
397F LYS* 2.9 27.2 + - + +
360H ARG* 4.1 21.8 - - - +
364H ASP* 4.4 7.9 + - - +
365H ASP* 2.5 42.1 + - - +
367H LEU* 1.3 71.8 - - - +
369H ILE* 1.3 65.0 + - - +
371H THR* 3.1 17.4 + - - +
372H GLU* 3.1 10.7 + - - +
397H LYS* 4.6 1.7 + - - -
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Residues in contact with ILE 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H LEU* 4.6 3.1 - - + +
356H SER* 3.7 30.5 - - - +
357H LEU* 4.1 13.7 - - + +
360H ARG* 3.4 30.1 - - + +
361H CYS* 4.4 18.4 - - - +
364H ASP* 3.0 19.7 - - + +
365H ASP 3.0 28.3 + - - +
366H ILE* 3.2 19.5 + - + +
368H THR* 1.3 78.4 - - - +
370H LEU* 1.3 57.4 + - - +
372H GLU* 2.8 29.8 + - - +
373H VAL* 2.9 17.1 + - + +
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Residues in contact with LEU 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F PHE* 4.5 8.5 - - + -
281G PHE* 4.5 8.5 - - + -
328H LEU* 4.0 30.3 - - + -
330H GLY* 5.1 1.6 - - - -
349H TYR* 3.8 28.0 - - + +
353H LEU* 4.4 17.5 - - + -
366H ILE* 2.8 31.8 + - + +
367H LEU* 3.6 9.9 - - + +
369H ILE* 1.3 72.7 - - - +
371H THR* 1.3 61.9 + - - +
373H VAL* 3.4 8.6 + - + +
374H ASN* 3.1 26.1 + - - +
389H PRO* 3.8 27.0 - - + +
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Residues in contact with THR 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F LEU* 3.6 22.9 - - - +
392F PHE* 3.7 11.6 - - - -
394F LEU* 4.5 3.3 - - - +
395F ARG* 3.8 6.4 - - - +
396F LYS* 3.8 37.8 + - - +
397F LYS* 4.4 6.3 - - + +
367H LEU 2.8 15.1 + - - -
368H THR* 3.2 13.4 - - - +
369H ILE 3.0 0.2 - - - -
370H LEU* 1.3 77.4 - - - +
372H GLU* 1.3 59.0 + - - +
374H ASN* 2.9 29.8 + - - +
375H TYR* 3.0 5.5 + - - +
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Residues in contact with GLU 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F ARG 5.2 0.4 - - - -
356H SER* 2.7 22.9 + - - +
359H GLU* 4.2 9.5 - - - +
360H ARG* 2.4 51.5 + - - +
368H THR 3.1 7.0 + - - +
369H ILE* 2.8 16.4 + - - +
371H THR* 1.3 75.9 - - - +
373H VAL* 1.3 61.0 + - - +
375H TYR* 2.8 24.0 + - + +
376H GLU* 2.9 33.9 + - + +
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Residues in contact with VAL 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H TYR* 3.8 34.5 - - + -
352H SER* 4.0 11.4 - - - +
353H LEU* 3.8 26.0 - - + +
356H SER* 3.9 16.4 - - - -
369H ILE* 2.9 24.8 + - + +
370H LEU* 3.6 13.0 - - + +
371H THR 3.3 0.2 - - - -
372H GLU* 1.3 74.1 - - - +
374H ASN* 1.3 61.5 + - - +
376H GLU* 4.0 7.6 - - - +
377H VAL* 3.0 40.7 + - + +
387H PRO* 5.1 1.1 - - + -
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Residues in contact with ASN 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F PHE* 3.6 24.2 - - - -
393F THR* 3.8 11.3 - - - +
394F LEU 3.0 25.2 + - - +
395F ARG* 4.1 2.2 - - - -
370H LEU* 3.1 12.7 + - - +
371H THR 2.9 13.2 + - - +
373H VAL* 1.3 75.0 - - - +
375H TYR* 1.3 60.4 + - - +
377H VAL* 4.1 1.4 - - - +
378H SER* 2.9 27.9 + - - -
386H MET* 3.9 10.3 - - + +
387H PRO* 3.1 37.4 - - - +
389H PRO* 3.8 12.5 - - - +
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Residues in contact with TYR 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LYS* 5.1 10.3 - - + +
319F ARG* 4.5 6.9 + - - -
395F ARG* 3.3 53.5 - - + +
396F LYS* 4.7 9.9 - - + -
299G ASP* 3.4 31.0 + - + +
371H THR 3.0 4.6 + - - +
372H GLU* 2.8 16.4 + - + +
374H ASN* 1.3 76.2 - - - +
376H GLU* 1.3 75.1 + - - +
378H SER* 2.6 33.4 + - - -
379H ASN* 3.1 30.5 + - - +
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Residues in contact with GLU 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352H SER* 4.4 16.4 - - - +
355H GLN* 6.2 0.4 - - - +
356H SER* 4.9 4.3 - - - +
372H GLU* 2.9 44.9 + - + +
373H VAL* 4.0 5.4 - - - +
375H TYR* 1.3 93.6 - - - +
377H VAL* 1.3 62.8 + - - +
379H ASN* 3.2 18.0 + - - +
381H LYS* 3.4 18.5 - - - +
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Residues in contact with VAL 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H TRP* 4.3 11.8 - - + +
349H TYR* 4.3 9.6 - - - -
352H SER* 3.8 19.1 - - - +
373H VAL* 3.0 26.7 + - + +
374H ASN 4.2 0.2 - - - +
376H GLU* 1.3 76.7 - - - +
378H SER* 1.3 63.3 + - - +
379H ASN 3.1 0.9 + - - -
381H LYS* 3.2 23.5 + - - +
385H GLN* 3.4 47.0 + - + +
387H PRO* 3.6 22.2 - - + -
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Residues in contact with SER 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F TYR 3.7 2.3 - - - +
321F ILE* 4.7 1.1 - - - -
322F PRO* 3.5 32.0 - - - +
395F ARG* 3.1 29.6 - - - +
374H ASN 2.9 17.1 + - - -
375H TYR 2.6 18.8 + - - -
377H VAL* 1.3 73.4 - - - +
379H ASN* 1.3 61.3 + - - -
384H LYS* 3.0 29.3 + - - -
385H GLN 4.3 2.2 - - - +
386H MET* 3.9 5.2 - - - +
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Residues in contact with ASN 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ARG* 5.7 6.2 - - - +
320F TYR 4.5 2.8 - - - +
321F ILE* 4.5 7.6 - - - +
395F ARG* 4.4 9.2 + - - -
299G ASP* 5.3 3.1 + - - +
375H TYR* 3.1 39.9 + - - +
376H GLU* 3.2 9.9 + - - +
377H VAL 3.1 1.2 - - - -
378H SER* 1.3 86.3 - - - +
381H LYS* 1.3 76.1 + - - +
384H LYS* 4.2 3.8 + - - +
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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
------------------------------------------------------------
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