Contacts of the helix formed by residues 318 - 327 (chain B) in PDB entry 1ZQ1
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 SER 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ILE 3.3 3.4 + - - -
317B SER* 1.3 69.8 - - - +
319B GLU* 1.3 58.8 + - - +
320B ILE 3.1 0.9 - - - -
321B ILE* 3.1 8.2 + - - +
322B ASP* 2.9 34.8 + - - +
345B ASP* 4.4 12.3 + - - -
346B ILE* 4.2 19.9 - - - +
348B PRO* 6.3 0.2 - - - -
349B SER* 3.4 28.4 - - - -
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS* 4.9 8.8 + - - -
323A PHE* 3.6 9.5 - - + -
327A LYS* 3.0 43.5 + - - +
329A TYR* 5.0 2.4 + - - -
317B SER* 2.6 26.8 + - - +
318B SER* 1.3 81.2 + - - +
320B ILE* 1.3 55.9 + - - +
322B ASP* 3.6 11.4 - - - +
323B PHE* 2.8 29.5 + - - +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 4.7 1.1 - - + -
310A VAL* 6.5 0.2 - - + -
320A ILE* 5.6 11.0 - - + -
323A PHE* 4.3 20.2 - - + -
324A LEU* 4.4 13.2 - - + -
329A TYR* 3.8 17.9 - - + +
310B VAL* 5.1 16.8 - - + -
313B TYR* 3.6 13.7 - - + +
316B ILE* 3.5 28.3 - - + -
317B SER* 3.0 13.8 + - - +
319B GLU* 1.3 75.1 - - - +
321B ILE* 1.3 66.2 + - + +
323B PHE* 3.7 4.7 + - + +
324B LEU* 3.3 28.0 + - + +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 5.3 13.5 - - + -
312B VAL* 6.4 1.6 - - + -
317B SER 4.5 0.2 + - - -
318B SER* 3.1 5.6 + - - +
320B ILE* 1.3 77.8 - - + +
322B ASP* 1.3 67.5 + - - +
324B LEU* 3.1 13.1 + - + +
325B VAL* 3.0 28.7 + - + +
332B ILE* 4.6 15.5 - - + -
334B ILE* 4.8 9.4 - - + -
342B THR* 5.5 0.7 - - + -
346B ILE* 3.2 26.9 - - + -
349B SER* 3.2 43.7 - - - +
350B ILE* 3.5 20.4 - - + +
353B ALA* 4.6 1.8 - - + -
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS* 6.3 0.7 - - - +
318B SER* 2.9 29.7 + - - +
319B GLU* 3.6 11.2 - - - +
321B ILE* 1.3 77.6 - - - +
323B PHE* 1.3 62.9 + - - +
325B VAL* 3.1 8.0 + - - +
326B ASP* 2.8 38.5 + - - +
349B SER* 3.3 24.9 - - - +
352B ARG* 5.5 2.4 - - - +
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Residues in contact with PHE 323 (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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319A GLU* 3.6 40.4 - - + -
320A ILE* 4.0 22.2 - - + -
323A PHE* 3.3 46.7 - + + -
319B GLU 2.8 21.2 + - - +
320B ILE* 3.8 8.3 - - + +
322B ASP* 1.3 72.2 - - - +
324B LEU* 1.3 63.5 + - + +
326B ASP* 3.7 9.1 + - + +
327B LYS* 2.8 75.2 + - + +
329B TYR* 5.6 1.6 - + - -
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Residues in contact with LEU 324 (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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320A ILE* 3.5 33.4 - - + -
308B ALA* 3.9 13.5 - - + -
310B VAL* 3.6 31.6 - - + -
320B ILE* 3.3 18.4 + - + +
321B ILE* 3.1 10.7 + - - +
323B PHE* 1.3 84.5 - - + +
325B VAL* 1.3 64.0 + - - +
328B GLY 3.3 3.5 + - - -
329B TYR* 3.2 53.5 + - + -
332B ILE* 3.8 26.0 - - + -
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Residues in contact with VAL 325 (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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321B ILE* 3.0 20.4 + - + +
322B ASP* 3.5 9.4 - - - +
324B LEU* 1.3 72.6 - - - +
326B ASP* 1.3 62.5 + - - +
328B GLY* 2.6 28.1 + - - -
329B TYR* 4.8 2.6 - - - +
332B ILE* 4.8 4.5 - - + -
349B SER 4.8 1.3 - - - +
352B ARG* 6.1 1.1 - - + -
353B ALA* 3.2 34.1 - - + +
356B GLU* 4.1 35.2 - - + +
358B VAL* 4.6 10.3 - - + -
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Residues in contact with ASP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 2.8 35.3 + - - +
323B PHE* 3.7 7.9 + - + +
325B VAL* 1.3 76.8 - - - +
327B LYS* 1.3 60.1 + - + +
328B GLY* 3.0 5.2 + - - -
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Residues in contact with LYS 327 (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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319A GLU* 2.8 34.9 + - - +
306B LYS* 3.3 15.5 + - - +
323B PHE* 2.8 57.6 + - + +
324B LEU 3.8 4.9 - - - +
325B VAL 3.1 0.2 + - - -
326B ASP* 1.3 77.5 - - + +
328B GLY* 1.3 60.8 + - - +
329B TYR* 4.2 14.4 - - + -
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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
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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