Contacts of the helix formed by residues 391 - 405 (chain B) in PDB entry 1YQZ
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 GLY 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ALA* 4.6 0.4 - - - -
368B LEU* 3.7 2.9 - - - -
390B GLU* 1.3 81.8 - - - +
392B ALA* 1.3 62.1 + - - +
393B ASP* 3.4 12.5 + - - -
394B LYS* 3.4 7.5 + - - -
395B ARG* 3.0 46.4 + - - +
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Residues in contact with ALA 392 (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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332B THR* 3.8 29.0 - - + +
334B ALA* 4.7 2.2 - - + -
368B LEU* 3.7 22.0 - - + -
386B ALA* 3.8 24.7 - - + +
388B GLY 4.3 2.9 - - - +
390B GLU 3.4 4.0 + - - -
391B GLY* 1.3 75.1 - - - +
393B ASP* 1.3 67.0 + - - +
395B ARG* 3.4 1.6 + - - +
396B ILE* 3.0 30.1 + - - +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 2.8 33.5 + - + +
418A ALA* 5.1 3.3 - - + +
423A TYR* 3.6 21.0 - - + -
325B ILE* 3.6 29.4 - - + -
332B THR* 4.3 3.3 + - - +
391B GLY* 3.9 8.8 + - - -
392B ALA* 1.3 81.6 + - - +
394B LYS* 1.3 67.5 + - - +
396B ILE* 4.0 3.4 - - - +
397B ASP* 3.0 30.2 + - - +
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Residues in contact with LYS 394 (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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393A ASP* 2.8 34.7 + - - +
394A LYS* 3.8 38.3 - - + +
397A ASP* 3.5 30.1 + - + +
391B GLY* 3.4 10.3 + - - +
392B ALA 3.2 0.4 - - - -
393B ASP* 1.3 86.0 + - - +
395B ARG* 1.3 90.5 + - - +
397B ASP* 4.0 1.6 - - - +
398B VAL* 3.1 29.8 + - + +
417B VAL* 5.8 0.2 - - - -
418B ALA 5.2 1.0 + - - -
423B TYR* 2.9 29.5 + - - +
424B SER* 4.7 2.7 - - - -
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASP* 5.9 0.4 + - - -
357B ALA* 3.1 26.1 + - - +
368B LEU* 3.7 19.8 - - + +
370B LEU* 4.4 28.3 - - + -
386B ALA* 4.8 1.1 - - + -
391B GLY* 3.0 37.6 + - - +
392B ALA* 3.4 4.5 + - - +
393B ASP 3.4 0.2 - - - -
394B LYS* 1.3 104.6 - - - +
396B ILE* 1.3 63.0 + - - +
398B VAL* 3.4 2.8 + - - +
399B LEU* 3.0 28.3 + - - +
423B TYR 3.8 9.1 + - - -
424B SER* 4.0 2.0 - - - -
428B ASP* 2.8 41.7 + - - -
429B LEU* 3.9 12.2 - - + +
430B ILE* 3.9 13.9 - - + +
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Residues in contact with ILE 396 (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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418A ALA* 5.0 1.6 - - + -
323B ASN* 3.3 25.4 - - - +
334B ALA* 3.7 17.3 - - + +
335B SER 3.9 8.1 - - - +
336B VAL* 3.7 14.6 - - + -
370B LEU* 4.3 6.1 - - + -
384B ALA* 3.8 32.3 - - + +
385B ALA* 3.9 2.0 - - - +
386B ALA* 3.7 32.1 - - + +
392B ALA 3.0 21.1 + - - +
393B ASP* 4.2 2.2 - - - +
395B ARG* 1.3 75.0 - - - +
397B ASP* 1.3 60.3 + - - +
399B LEU* 3.2 2.6 + - + +
400B SER* 2.8 26.7 + - - -
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Residues in contact with ASP 397 (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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394A LYS* 3.4 26.2 + - + +
395A ARG* 5.9 0.7 + - - -
398A VAL* 3.6 19.4 - - + +
415A PHE* 3.6 19.2 - - + -
417A VAL* 3.5 16.5 - - - +
418A ALA* 2.8 32.7 + - - +
323B ASN* 3.2 7.1 + - - -
393B ASP* 3.0 18.2 + - - +
394B LYS 4.0 1.8 - - - +
396B ILE* 1.3 75.7 - - - +
398B VAL* 1.3 63.8 + - - +
400B SER* 3.3 6.6 + - - -
401B MET* 3.1 19.1 + - - +
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASP* 3.7 38.4 - - + +
398A VAL* 4.0 8.7 - - + +
401A MET* 3.7 28.2 - - + +
394B LYS* 3.1 20.0 + - + +
395B ARG 3.7 0.2 - - - +
397B ASP* 1.3 75.8 - - - +
399B LEU* 1.3 58.8 + - + +
401B MET* 3.2 7.5 + - - +
402B ALA* 2.9 24.1 + - - +
415B PHE* 3.9 14.1 - - + -
430B ILE* 3.4 29.8 - - + -
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Residues in contact with LEU 399 (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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336B VAL* 4.6 2.0 - - + -
370B LEU* 3.8 28.0 - - + -
372B VAL* 4.1 9.0 - - + -
381B ILE* 4.5 11.4 - - + -
384B ALA* 3.6 32.5 - - + -
395B ARG 3.0 18.0 + - - +
396B ILE* 3.2 5.4 + - + +
398B VAL* 1.3 76.8 - - + +
400B SER* 1.3 60.2 + - - +
402B ALA* 3.2 3.6 + - + +
403B MET* 2.9 39.4 + - - +
412B LEU* 3.9 38.1 - - + -
430B ILE* 4.4 12.6 - - + -
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Residues in contact with SER 400 (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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415A PHE* 4.3 2.1 - - - -
416A GLU* 2.8 25.9 + - - +
321B LEU* 3.4 21.9 - - - +
323B ASN* 3.5 24.1 + - - -
336B VAL* 4.1 16.9 - - - +
396B ILE 2.8 10.6 + - - -
397B ASP* 3.3 6.5 + - - -
399B LEU* 1.3 76.4 - - - +
401B MET* 1.3 62.4 + - - +
403B MET* 3.3 2.3 + - - -
404B MET* 3.0 19.4 + - - +
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Residues in contact with MET 401 (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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398A VAL* 3.7 35.7 - - + +
401A MET* 3.6 17.0 - - + -
402A ALA* 3.7 24.0 - - + +
407A LEU* 4.0 8.3 - - + -
412A LEU* 4.3 7.9 - - + -
415A PHE* 3.8 28.4 - - + -
397B ASP 3.1 12.2 + - - +
398B VAL* 3.5 8.7 - - - +
400B SER* 1.3 73.1 - - - +
402B ALA* 1.3 65.9 + - - +
404B MET* 3.4 18.9 + - - +
405B ASN* 2.8 51.0 + - - +
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Residues in contact with ALA 402 (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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401A MET* 3.7 29.5 - - + +
381B ILE* 4.4 11.7 - - + -
398B VAL 2.9 13.3 + - - +
399B LEU* 3.2 12.8 + - - +
401B MET* 1.3 77.1 - - - +
403B MET* 1.3 62.0 + - - +
405B ASN* 3.1 13.0 + - - -
406B GLN 3.3 0.2 + - - -
407B LEU* 3.1 36.4 + - + +
412B LEU* 4.4 2.7 - - + -
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Residues in contact with MET 403 (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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284B ARG* 5.4 1.2 + - - +
285B HIS* 3.5 38.1 - - + +
321B LEU* 4.1 15.8 - - + +
336B VAL* 3.8 26.9 - - - -
337B GLY* 3.7 13.5 - - - -
381B ILE* 3.8 34.3 - - + +
382B LEU 3.6 22.9 - - - +
383B ARG* 4.0 2.7 - - - +
384B ALA* 5.1 0.7 - - - -
399B LEU* 2.9 23.2 + - - +
400B SER 3.7 3.6 - - - +
402B ALA* 1.3 76.7 - - - +
404B MET* 1.3 62.1 + - - +
405B ASN 3.3 0.3 + - - -
406B GLN* 3.3 22.2 + - - +
407B LEU 4.8 2.0 - - - +
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Residues in contact with MET 404 (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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407A LEU* 3.5 43.3 - - + -
411A GLU* 4.0 16.8 - - + +
414A GLU* 4.0 9.0 - - - +
415A PHE* 4.0 25.4 - - - -
416A GLU 5.2 0.9 - - - -
284B ARG* 3.3 54.2 + - - +
321B LEU* 4.1 10.5 - - + +
400B SER 3.0 13.3 + - - +
401B MET* 3.5 25.8 - - + +
403B MET* 1.3 75.8 - - - +
405B ASN* 1.3 59.9 + - - +
406B GLN* 3.4 6.0 + - - +
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Residues in contact with ASN 405 (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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402A ALA* 4.5 2.0 - - - +
405A ASN* 3.2 51.7 - - - +
407A LEU* 3.5 24.3 - - - +
401B MET* 2.8 42.4 + - - +
402B ALA 3.1 7.8 + - - +
404B MET* 1.3 80.5 - - - +
406B GLN* 1.3 70.7 + - - +
407B LEU* 3.2 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
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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