Contacts of the helix formed by residues 325 - 342 (chain B) in PDB entry 4ZZ7
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 THR 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 5.7 9.0 - - + -
176B ARG* 4.3 20.1 + - + +
323B VAL* 3.4 4.9 + - - +
324B ILE* 1.3 97.9 - - + +
326B ARG* 1.3 54.5 + - - +
327B GLN* 3.8 11.6 + - - +
328B HIS* 3.0 23.6 + - - +
329B GLN* 2.8 32.9 + - - +
362B PHE* 3.4 14.6 - - + -
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Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY* 5.4 2.0 + - - -
325B THR* 1.3 69.2 - - - +
327B GLN* 1.3 66.1 + - - +
329B GLN* 3.2 23.1 + - - +
330B GLU* 2.9 43.6 + - + +
360B ASN* 3.2 31.1 + - - +
361B GLY 3.1 26.3 + - - -
362B PHE* 3.4 36.8 - - + -
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 5.7 2.6 + - - -
325B THR* 3.3 9.2 + - - +
326B ARG* 1.3 78.1 - - - +
328B HIS* 1.3 57.3 + - - +
330B GLU* 3.2 14.1 + - - +
331B LYS* 2.9 34.8 + - - +
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Residues in contact with HIS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PHE* 4.9 3.3 - + - -
278B GLU* 3.5 15.6 + - - -
323B VAL* 3.4 28.7 - - + -
324B ILE* 4.0 11.4 - - + -
325B THR* 3.0 22.8 + - - +
327B GLN* 1.3 77.0 - - - +
329B GLN* 1.3 58.0 + - - +
331B LYS* 3.5 31.3 + - + +
332B VAL* 3.0 31.7 + - + +
383B ILE 4.0 13.9 - - - -
384B PHE* 3.0 40.7 + + + +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 3.5 11.8 - - + +
325B THR 2.8 17.2 + - - +
326B ARG* 3.3 37.9 + - - +
328B HIS* 1.3 70.5 - - - +
330B GLU* 1.3 68.4 - - - +
332B VAL* 3.4 2.3 + - - +
333B ILE* 3.0 38.7 + - + +
351B ARG 5.5 1.4 + - - -
353B PRO* 5.6 1.2 - - - +
361B GLY 3.9 4.6 + - - -
362B PHE* 3.6 15.6 - - + +
363B PHE 3.2 26.9 + - - +
364B VAL* 3.9 18.8 - - + +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG* 2.9 37.0 + - + +
327B GLN* 3.5 13.4 - - - +
329B GLN* 1.3 73.3 - - - +
331B LYS* 1.3 65.4 + - - +
333B ILE* 3.3 9.3 + - - +
334B GLY* 2.9 20.8 + - - -
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Residues in contact with LYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLN* 2.9 19.6 + - - +
328B HIS* 3.5 35.8 + - + +
329B GLN 3.3 0.2 - - - -
330B GLU* 1.3 74.3 - - - +
332B VAL* 1.3 59.2 + - + +
334B GLY* 3.0 5.9 + - - -
335B TYR* 3.0 60.5 + - + +
382B GLU 5.6 0.4 - - - +
383B ILE 5.3 0.4 - - - +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 4.4 5.8 - - + -
328B HIS* 3.0 37.8 + - + +
329B GLN 3.8 4.0 - - - +
331B LYS* 1.3 74.3 - - + +
333B ILE* 1.3 66.0 + - - +
335B TYR* 3.1 18.1 + - - +
336B ILE* 3.2 20.8 + - + +
364B VAL* 3.9 30.7 - - + -
383B ILE* 4.2 21.5 - - + +
385B GLY* 4.1 17.7 - - - -
386B PRO* 4.4 8.5 - - + -
387B VAL* 4.4 1.8 - - + -
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLN* 3.0 32.4 + - + +
330B GLU* 3.5 8.7 - - - +
332B VAL* 1.3 75.5 - - - +
334B GLY* 1.3 54.1 + - - +
336B ILE* 3.3 8.1 + - - +
337B ASN* 2.9 52.2 + - - +
351B ARG* 3.2 48.9 - - + +
352B GLN* 5.5 0.9 - - - +
364B VAL* 4.8 13.7 - - + -
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU 2.9 13.6 + - - -
331B LYS* 3.0 6.2 + - - -
333B ILE* 1.3 73.1 - - - +
335B TYR* 1.3 57.4 + - - +
337B ASN* 3.3 11.2 + - - +
338B SER* 2.9 31.3 + - - -
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Residues in contact with TYR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LYS* 3.0 57.2 + - + +
332B VAL 3.1 6.4 + - - +
334B GLY* 1.3 74.4 - - - +
336B ILE* 1.3 60.2 + - + +
338B SER* 3.7 4.7 - - - -
339B ALA* 3.5 10.2 + - - +
369B ILE* 4.8 1.6 - - - +
377B THR* 5.1 1.6 - - + -
378B SER* 3.4 35.4 - - - -
381B GLU* 3.0 42.6 + - + +
382B GLU 3.6 22.1 + - - -
383B ILE* 3.8 47.2 - - + +
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Residues in contact with ILE 336 (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 VAL* 3.2 23.5 + - + +
333B ILE* 3.6 6.1 - - - +
334B GLY 3.1 0.8 - - - -
335B TYR* 1.3 76.6 - - + +
337B ASN* 1.3 67.2 + - - +
338B SER 3.3 1.1 - - - -
339B ALA 3.5 0.7 + - - -
340B GLU 3.4 13.3 + - - -
346B ILE* 3.7 27.8 - - + +
349B ASP* 5.1 0.2 - - - +
351B ARG* 3.5 41.2 + - + +
364B VAL* 4.6 5.2 - - + -
367B THR* 3.8 29.8 - - + +
369B ILE* 4.4 11.9 - - + -
387B VAL* 4.0 21.3 - - + -
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Residues in contact with ASN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 2.9 35.5 + - - +
334B GLY* 3.6 8.7 - - - +
336B ILE* 1.3 72.6 - - - +
338B SER* 1.3 66.0 + - - +
340B GLU* 3.1 6.2 + - - +
341B GLN* 3.0 23.3 + - - +
351B ARG* 2.9 32.6 + - - +
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY 2.9 17.7 + - - -
335B TYR* 3.7 10.8 - - - -
337B ASN* 1.3 72.6 - - - +
339B ALA* 1.3 57.6 + - - +
341B GLN* 3.0 17.4 + - - +
342B GLN* 2.7 57.8 + - - +
377B THR* 4.5 4.6 - - - -
378B SER* 4.1 11.4 + - - -
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Residues in contact with ALA 339 (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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335B TYR 3.5 5.3 + - - +
336B ILE 3.8 8.1 - - - +
337B ASN 3.3 0.6 - - - -
338B SER* 1.3 78.5 - - - +
340B GLU* 1.3 54.0 + - - +
342B GLN* 4.1 1.8 - - - +
343B GLY 3.3 3.6 + - - -
344B ALA* 2.7 39.4 + - + +
346B ILE* 4.4 1.1 - - + -
369B ILE* 3.8 37.7 - - + -
376B MET* 4.5 6.4 - - - +
378B SER* 3.8 19.0 + - - +
389B GLN* 4.9 1.8 - - - +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ILE 3.4 5.3 + - - +
337B ASN 3.1 9.4 + - - +
339B ALA* 1.3 77.4 - - - +
341B GLN* 1.3 67.2 + - - +
343B GLY* 3.3 11.8 + - - -
344B ALA 3.9 12.4 - - - +
346B ILE* 3.6 28.4 + - + +
351B ARG* 3.2 31.6 + - - -
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Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ASN 3.0 11.2 + - - +
338B SER* 3.0 21.4 + - - +
340B GLU* 1.3 72.1 - - - +
342B GLN* 1.3 63.8 + - + +
343B GLY* 2.8 9.0 + - - -
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER* 2.7 33.0 + - - +
339B ALA 4.1 1.1 - - - +
341B GLN* 1.3 77.9 - - + +
343B GLY* 1.3 54.4 + - - +
344B ALA 3.9 1.1 - - - -
375B GLU 4.7 3.4 + - - -
376B MET* 3.0 36.3 - - + +
377B THR* 2.9 44.3 + - - +
378B SER* 4.3 1.0 + - - -
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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