Contacts of the helix formed by residues 325 - 342 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 5.7 9.2 - - + -
176A ARG* 4.1 33.7 + - + +
323A VAL* 3.3 6.3 - - - +
324A ILE* 1.3 87.8 - - + +
326A ARG* 1.3 59.2 + - - +
327A GLN* 3.6 11.3 + - - +
328A HIS* 3.0 25.5 + - - +
329A GLN* 2.9 24.9 + - - +
362A PHE* 3.5 13.9 - - + +
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY* 5.9 1.0 + - - -
325A THR* 1.3 71.3 - - - +
327A GLN* 1.3 60.2 + - - +
329A GLN* 3.2 28.1 + - - +
330A GLU* 2.9 49.8 + - + +
360A ASN* 3.3 39.2 + - - +
361A GLY 3.8 7.5 + - - -
362A PHE* 3.5 37.1 - - + -
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 5.2 7.8 + - - -
325A THR* 3.3 10.3 + - - +
326A ARG* 1.3 80.0 - - - +
328A HIS* 1.3 55.4 + - - +
330A GLU* 3.4 12.5 + - - +
331A LYS* 3.0 31.7 + - - +
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 5.1 2.2 - + - -
176A ARG* 6.0 1.6 - - - +
278A GLU* 3.6 21.3 + - - -
323A VAL* 3.7 15.9 - - + -
324A ILE* 3.9 13.7 - - + -
325A THR* 3.0 22.6 + - - +
327A GLN* 1.3 73.6 - - - +
329A GLN* 1.3 60.7 + - - +
331A LYS* 3.4 28.2 + - + +
332A VAL* 3.0 33.9 + - + +
383A ILE 3.7 14.4 - - - -
384A PHE* 2.7 44.8 + + + +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 3.5 12.0 - - + +
325A THR 2.9 13.4 + - - +
326A ARG* 3.2 34.0 + - - +
328A HIS* 1.3 74.5 - - - +
330A GLU* 1.3 62.3 + - - +
332A VAL* 3.2 5.4 + - - +
333A ILE* 2.9 44.1 + - + +
351A ARG 5.5 1.4 + - - -
353A PRO* 5.5 1.2 - - - +
361A GLY 4.0 4.4 + - - -
362A PHE* 3.4 20.8 - - + +
363A PHE 3.1 26.5 + - - +
364A VAL* 3.8 16.7 - - + +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 2.9 43.6 + - + +
327A GLN* 3.7 9.3 - - - +
329A GLN* 1.3 77.5 - - + +
331A LYS* 1.3 53.4 + - - +
333A ILE* 3.4 8.0 + - + +
334A GLY* 2.7 33.8 + - - -
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A GLN* 3.0 19.5 + - - +
328A HIS* 3.5 34.0 + - + +
329A GLN 3.2 0.2 - - - -
330A GLU* 1.3 76.7 - - - +
332A VAL* 1.3 57.6 + - + +
334A GLY* 3.3 3.0 + - - -
335A TYR* 3.0 62.9 + - + +
382A GLU 5.6 1.3 - - - +
383A ILE 5.2 0.9 - - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 4.6 3.8 - - + -
328A HIS* 3.0 44.6 + - + +
329A GLN* 3.7 5.2 - - - +
331A LYS* 1.3 73.7 - - - +
333A ILE* 1.3 67.0 + - - +
335A TYR* 3.2 16.0 + - - +
336A ILE* 3.3 14.2 + - + +
364A VAL* 4.1 26.9 - - + -
383A ILE* 3.7 26.4 - - + +
384A PHE 3.9 4.9 - - - +
385A GLY* 4.1 13.0 - - - -
386A PRO* 4.4 0.2 - - + -
387A VAL* 4.3 8.7 - - + -
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN* 2.9 38.3 + - + +
330A GLU* 3.5 7.6 - - - +
332A VAL* 1.3 71.4 - - - +
334A GLY* 1.3 65.7 + - - +
336A ILE* 2.9 21.2 + - + +
337A ASN* 3.1 27.6 + - - +
351A ARG* 3.2 50.0 - - + +
364A VAL* 4.4 16.2 - - + -
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLU 2.7 22.1 + - - -
331A LYS* 3.4 4.3 - - - -
332A VAL 3.2 0.2 - - - -
333A ILE* 1.3 72.3 - - - +
335A TYR* 1.3 55.8 + - - +
336A ILE 3.2 0.3 + - - -
337A ASN* 3.2 12.0 + - - +
338A SER* 3.0 28.7 + - - -
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Residues in contact with TYR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LYS* 3.0 55.0 + - + +
332A VAL 3.2 6.4 + - - +
334A GLY* 1.3 74.7 - - - +
336A ILE* 1.3 56.4 + - - +
338A SER* 3.5 7.1 - - - -
339A ALA* 3.0 22.5 + - - +
369A ILE* 5.1 0.3 - - - +
377A THR* 4.5 5.8 - - + -
378A SER* 3.3 29.7 - - - -
381A GLU* 2.9 45.0 + - + +
382A GLU 4.0 16.5 + - - -
383A ILE* 3.8 42.2 - - + -
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A VAL* 3.4 23.3 - - + +
333A ILE* 2.9 8.1 + - - +
335A TYR* 1.3 75.8 - - + +
337A ASN* 1.3 64.7 + - - +
339A ALA* 3.3 6.1 + - - +
340A GLU* 3.1 21.5 + - - +
346A ILE* 3.8 23.0 - - + +
349A ASP* 4.9 0.9 - - - +
351A ARG* 3.6 35.2 - - + +
364A VAL* 4.6 5.8 - - + -
367A THR* 3.8 32.5 - - + +
369A ILE* 4.5 9.0 - - + -
383A ILE* 5.8 0.4 - - + -
387A VAL* 4.0 19.5 - - + -
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Residues in contact with ASN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ILE* 3.1 28.5 + - - +
334A GLY* 3.6 8.8 - - - +
336A ILE* 1.3 75.1 - - - +
338A SER* 1.3 50.9 + - - +
340A GLU* 2.8 8.6 + - - +
341A GLN* 2.7 37.1 + - - +
351A ARG* 2.7 41.5 + - - +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A GLY 3.0 17.0 + - - -
335A TYR* 3.5 13.4 - - - -
337A ASN* 1.3 75.0 - - - +
339A ALA* 1.3 57.5 + - - +
341A GLN* 3.8 12.8 - - - +
342A GLN* 3.0 46.7 + - - +
377A THR* 4.1 13.5 - - - -
378A SER* 4.0 6.5 + - - -
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A TYR 3.0 15.1 + - - +
336A ILE 3.6 5.2 - - - +
337A ASN 3.1 0.4 - - - -
338A SER* 1.3 75.2 - - - +
340A GLU* 1.3 61.0 + - - +
342A GLN* 3.5 9.7 + - - +
343A GLY 3.5 0.3 + - - -
344A ALA* 2.9 38.7 + - + +
346A ILE* 4.6 0.4 - - + -
369A ILE* 3.8 25.6 - - + -
376A MET* 4.6 3.5 - - - +
378A SER* 3.3 21.5 + - - +
389A GLN* 5.0 1.8 - - - +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ILE 3.1 11.1 + - - +
337A ASN* 2.8 9.5 + - - +
339A ALA* 1.3 74.7 - - - +
341A GLN* 1.3 65.0 + - - +
343A GLY* 3.3 13.5 + - - -
344A ALA 3.7 13.6 + - - +
346A ILE* 3.7 19.4 + - + +
351A ARG* 2.9 37.5 + - - +
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASN* 2.7 20.2 + - + +
338A SER* 3.8 13.1 - - - +
340A GLU* 1.3 73.6 - - - +
342A GLN* 1.3 61.0 + - + +
343A GLY* 3.3 4.3 + - - -
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A SER* 3.0 29.7 + - - +
339A ALA 3.5 3.1 + - - +
340A GLU 3.3 0.6 - - - -
341A GLN* 1.3 80.4 - - + +
343A GLY* 1.3 55.7 + - - +
344A ALA 3.7 2.2 - - - -
375A GLU 4.4 5.0 + - - -
376A MET* 3.3 33.7 - - + +
377A THR* 3.0 41.7 + - - +
378A SER* 4.2 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
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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