Contacts of the helix formed by residues 375 - 401 (chain C) in PDB entry 4U0Q
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 375 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C SER 4.3 0.4 + - - -
374C LYS* 1.4 68.9 - - - +
376C LEU* 1.3 62.2 + - - +
377C ASN* 3.5 15.2 + - - +
378C LYS* 3.1 45.0 + - + +
379C ASP* 3.3 18.6 + - - +
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C VAL* 4.3 12.1 - - + +
374C LYS* 3.4 29.2 + - + +
375C ASN* 1.3 71.6 + - - +
377C ASN* 1.3 63.0 + - - +
379C ASP* 3.5 16.9 - - - +
380C LEU* 3.3 25.2 + - - +
428C THR* 3.9 16.6 - - + +
431C ILE* 3.8 32.8 - - + -
432C ASN* 4.3 16.6 - - - +
476C ARG* 3.8 44.0 - - - +
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Residues in contact with ASN 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ASN* 3.2 11.7 - - - +
376C LEU* 1.3 74.2 + - - +
378C LYS* 1.4 62.2 + - - +
380C LEU* 3.2 23.2 + - + +
381C SER* 3.0 26.2 + - - -
428C THR* 5.5 0.2 - - - -
432C ASN* 3.3 31.5 + - - +
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Residues in contact with LYS 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ASN* 3.1 36.8 + - + +
377C ASN* 1.4 76.4 - - - +
379C ASP* 1.4 55.0 + - - +
381C SER* 3.0 12.5 + - - -
382C ASP* 2.8 65.6 + - - +
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Residues in contact with ASP 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C LYS* 5.3 3.9 - - - +
375C ASN 3.3 16.2 + - - +
376C LEU* 3.5 25.7 - - - +
377C ASN 3.3 0.2 - - - -
378C LYS* 1.4 79.1 - - - +
380C LEU* 1.4 56.9 + - + +
382C ASP* 3.5 12.3 + - - +
383C MET* 3.0 38.4 + - + +
424C ILE* 6.1 2.0 - - + -
476C ARG* 5.0 4.6 + - - -
480C TYR* 3.9 35.1 + - + -
484C TYR* 4.5 1.4 + - - -
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C LEU 3.4 14.8 - - - +
377C ASN* 3.2 26.2 + - + +
378C LYS 3.2 0.2 - - - -
379C ASP* 1.4 74.2 - - - +
381C SER* 1.4 59.8 + - - +
383C MET* 4.4 1.8 - - - -
384C THR* 3.0 33.0 + - - +
421C PHE* 3.6 21.8 - - + -
424C ILE* 3.9 18.6 - - + -
425C GLU* 3.7 40.2 - - + +
428C THR* 3.5 20.0 - - + +
429C LYS* 6.2 0.9 - - + -
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Residues in contact with SER 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ASN 3.0 14.5 + - - -
378C LYS* 3.0 12.8 + - - -
380C LEU* 1.4 73.9 - - - +
382C ASP* 1.3 61.9 + - - +
384C THR* 2.7 21.2 + - - -
385C ASN* 3.1 27.6 + - - +
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Residues in contact with ASP 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LYS* 2.8 54.1 + - - +
379C ASP* 3.8 12.2 - - - +
381C SER* 1.3 76.6 - - - +
383C MET* 1.4 60.8 + - - +
385C ASN* 3.6 15.2 + - - +
386C ILE* 3.3 29.6 + - + +
484C TYR* 4.1 11.0 - - - +
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Residues in contact with MET 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ASP* 3.0 22.9 + - + +
380C LEU* 3.8 6.1 - - - +
381C SER 3.3 0.2 - - - -
382C ASP* 1.4 74.5 - - - +
384C THR* 1.4 63.3 + - - +
386C ILE* 3.2 5.8 + - - +
387C LEU* 3.0 28.4 + - - +
421C PHE* 3.9 15.9 - - + -
424C ILE* 3.7 45.5 - - + -
480C TYR* 3.5 34.3 - - + -
483C PHE* 3.5 34.8 - - + -
484C TYR* 3.6 19.1 - - + +
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Residues in contact with THR 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU 3.0 18.9 + - - +
381C SER* 2.7 25.5 + - - -
383C MET* 1.4 70.1 - - - +
385C ASN* 1.4 55.2 + - - +
387C LEU* 3.3 9.9 + - + +
388C GLN* 2.8 49.1 + - - +
418C LYS* 6.4 0.4 - - - -
421C PHE* 3.4 29.4 - - + -
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Residues in contact with ASN 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C SER* 3.1 24.0 + - - +
382C ASP* 3.6 19.8 + - - +
383C MET 3.3 0.2 - - - -
384C THR* 1.4 75.6 + - - +
386C ILE* 1.4 56.5 + - + +
388C GLN* 3.2 17.9 + - - +
389C GLN* 2.9 40.3 + - + +
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Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ASP* 3.3 17.5 + - + +
383C MET 3.2 7.2 + - - +
385C ASN* 1.4 75.2 - - + +
387C LEU* 1.4 61.8 + - - +
389C GLN* 3.4 9.2 + - - +
390C SER* 3.2 23.6 + - - -
417C MET* 3.7 23.6 - - + -
483C PHE* 4.2 6.7 - - + -
484C TYR* 3.6 35.7 - - + +
487C GLU* 3.5 33.2 - - - +
490C LEU* 5.3 3.6 - - + -
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Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C MET 3.0 24.0 + - - +
384C THR* 3.6 10.5 - - + +
386C ILE* 1.4 71.7 - - - +
388C GLN* 1.3 61.0 + - + +
390C SER* 2.8 20.3 + - - +
391C GLU* 3.0 17.1 + - - +
414C HIS* 3.2 25.7 - - + +
417C MET* 3.7 39.7 - - + +
418C LYS* 3.7 20.9 - - + +
421C PHE* 3.7 37.5 - - + -
483C PHE* 4.1 7.4 - - + -
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Residues in contact with GLN 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C THR* 2.8 34.8 + - - +
385C ASN* 3.6 16.1 - - - +
387C LEU* 1.3 72.3 - - + +
389C GLN* 1.4 57.8 + - + +
391C GLU* 3.3 20.0 + - - +
392C LEU* 3.0 31.8 + - - +
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Residues in contact with GLN 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ASN* 2.9 31.9 + - + +
386C ILE* 3.4 9.2 + - - +
388C GLN* 1.4 75.7 - - - +
390C SER* 1.4 56.3 + - - +
392C LEU* 3.7 10.4 - - - +
393C LEU* 3.2 25.3 + - - +
494C PHE* 5.7 4.4 - - + -
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Residues in contact with SER 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ILE 3.2 11.3 + - - -
387C LEU* 2.8 13.3 + - - -
389C GLN* 1.4 77.5 - - - +
391C GLU* 1.3 57.2 + - - +
392C LEU 3.3 0.2 - - - -
393C LEU* 3.3 7.4 + - - +
394C LEU* 2.8 34.3 + - - +
410C ILE* 5.0 2.3 - - - +
414C HIS* 2.8 32.5 + - - -
417C MET* 6.0 0.5 - - - +
490C LEU* 3.8 27.1 - - - +
494C PHE* 4.3 11.2 - - - -
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Residues in contact with GLU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LEU* 3.0 22.7 + - - +
388C GLN* 3.6 24.7 - - - +
390C SER* 1.3 73.0 + - - +
392C LEU* 1.4 58.1 + - - +
394C LEU* 3.6 8.2 - - + +
395C THR* 2.9 32.1 + - - +
414C HIS* 3.5 26.6 + - + +
418C LYS* 5.5 4.7 - - - +
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLN 3.0 16.9 + - - +
389C GLN* 3.7 10.5 - - - +
390C SER 3.3 0.2 - - - -
391C GLU* 1.4 72.7 - - - +
393C LEU* 1.4 65.9 + - - +
395C THR* 3.2 11.9 - - + +
396C ASN* 3.0 58.5 + - - +
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Residues in contact with LEU 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C GLN 3.2 12.7 + - - +
390C SER* 3.5 9.0 - - - +
392C LEU* 1.4 78.2 - - - +
394C LEU* 1.3 51.6 + - - +
396C ASN* 3.4 9.5 + - + +
397C LEU* 2.7 68.6 + - + +
410C ILE* 4.8 1.1 - - + -
494C PHE* 3.6 33.0 - - + -
497C LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C SER 2.8 13.9 + - - +
391C GLU* 3.6 7.2 - - + +
392C LEU 3.3 0.2 - - - -
393C LEU* 1.3 76.1 - - - +
395C THR* 1.3 55.7 + - - +
397C LEU* 3.4 8.0 + - + +
398C ASN* 2.9 47.4 + - - +
407C ILE* 4.3 10.1 - - + +
410C ILE* 3.7 22.2 - - + +
411C LYS* 3.8 41.7 - - + +
414C HIS* 3.7 42.2 - - + -
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Residues in contact with THR 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C GLU 2.9 18.1 + - - +
392C LEU* 3.2 25.8 - - + +
394C LEU* 1.3 74.0 - - - +
396C ASN* 1.3 64.9 + - - +
398C ASN* 3.3 8.3 + - - +
399C LYS* 3.0 56.0 + - - +
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Residues in contact with ASN 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C LEU* 3.0 42.5 + - - +
393C LEU* 3.8 9.6 - - + +
395C THR* 1.3 81.2 - - - +
397C LEU* 1.4 56.5 + - - +
399C LYS* 4.5 5.5 - - - +
400C LYS* 2.9 35.4 + - + +
401C MET* 4.0 0.5 + - - +
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Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LEU* 2.7 56.3 + - + +
394C LEU* 3.7 9.0 - - + +
396C ASN* 1.4 71.7 - - - +
398C ASN* 1.4 52.4 + - - +
401C MET* 2.8 31.0 + - + +
402C GLY 2.7 30.9 + - - -
404C TYR* 4.4 2.0 - - + -
407C ILE* 3.7 30.5 - - + -
410C ILE* 4.1 17.7 - - + -
497C LEU* 4.0 30.1 - - + -
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Residues in contact with ASN 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 2.9 37.9 + - - +
395C THR* 3.3 7.4 + - - +
397C LEU* 1.4 74.2 - - - +
399C LYS* 1.3 66.3 + - - +
402C GLY* 3.9 17.5 + - - -
407C ILE* 3.7 23.0 - - - +
411C LYS* 3.7 16.8 + - - +
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Residues in contact with LYS 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C THR* 3.0 42.7 + - - +
396C ASN* 4.0 6.4 - - - +
398C ASN* 1.3 83.2 - - + +
400C LYS* 1.3 78.0 + - + +
402C GLY 5.1 0.2 - - - -
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Residues in contact with LYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASN* 2.9 18.3 + - + +
399C LYS* 1.3 90.8 - - + +
401C MET* 1.4 61.8 + - + +
402C GLY 3.9 0.7 - - - -
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Residues in contact with MET 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASN 4.0 0.2 + - - -
397C LEU* 2.8 30.4 + - + +
400C LYS* 1.4 74.7 - - + +
402C GLY* 1.3 57.4 + - - +
403C SER* 3.0 16.1 + - - +
404C TYR* 3.1 52.4 + - + +
407C ILE* 3.3 8.5 - - - +
497C LEU* 4.0 2.2 - - + -
500C VAL* 4.8 3.8 - - + -
501C LEU* 3.9 39.3 - - + -
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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