Contacts of the helix formed by residues 325 - 342 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L PHE* 5.8 7.6 - - + -
176L ARG* 4.2 31.3 + - + +
323L VAL* 3.4 6.5 - - - +
324L ILE* 1.3 84.7 - - + +
326L ARG* 1.3 61.4 + - - +
327L GLN* 3.8 12.3 + - - +
328L HIS* 3.0 27.4 + - - +
329L GLN* 2.9 25.3 + - - +
362L PHE* 3.5 14.7 - - + +
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Residues in contact with ARG 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L GLY* 5.6 1.8 - - - -
325L THR* 1.3 72.6 - - - +
327L GLN* 1.3 59.9 + - - +
329L GLN* 3.2 28.8 + - - +
330L GLU* 3.0 49.7 + - + +
360L ASN* 3.3 35.7 + - - +
361L GLY 3.5 10.7 + - - -
362L PHE* 3.5 35.4 - - + -
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Residues in contact with GLN 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ARG* 5.2 7.4 + - - -
325L THR* 3.3 10.0 + - - +
326L ARG* 1.3 80.6 - - - +
328L HIS* 1.3 57.4 + - - +
330L GLU* 3.4 11.8 + - - +
331L LYS* 3.1 32.1 + - - +
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Residues in contact with HIS 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L PHE* 5.0 2.8 - + - -
176L ARG* 6.0 1.5 + - - +
278L GLU* 3.5 23.6 + - - -
323L VAL* 3.5 21.1 - - + -
324L ILE* 3.9 10.3 - - + -
325L THR* 3.0 20.8 + - - +
327L GLN* 1.3 75.3 - - - +
329L GLN* 1.3 64.6 + - - +
331L LYS* 3.7 30.7 + - + +
332L VAL* 3.1 36.8 + - + +
383L ILE 3.8 13.9 - - - -
384L PHE* 2.8 42.5 + + + +
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Residues in contact with GLN 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323L VAL* 3.4 10.5 - - + +
325L THR 2.9 15.6 + - - +
326L ARG* 3.2 41.4 + - - +
328L HIS* 1.3 76.4 - - - +
330L GLU* 1.3 66.6 + - + +
332L VAL* 3.3 3.0 + - - +
333L ILE* 3.1 37.2 + - + +
351L ARG 5.7 0.4 + - - -
353L PRO* 5.6 2.0 - - - +
361L GLY 4.1 4.6 + - - -
362L PHE* 3.4 15.6 - - + +
363L PHE 3.1 26.9 + - - +
364L VAL* 4.1 16.2 - - + +
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Residues in contact with GLU 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326L ARG* 3.0 39.9 + - + +
327L GLN* 3.7 11.5 - - - +
328L HIS 3.3 0.2 - - - -
329L GLN* 1.3 78.2 - - + +
331L LYS* 1.3 53.6 + - - +
333L ILE* 3.3 9.6 + - - +
334L GLY* 2.7 33.8 + - - -
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Residues in contact with LYS 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327L GLN* 3.1 20.4 + - - +
328L HIS* 3.7 34.5 + - + +
329L GLN 3.2 0.2 - - - -
330L GLU* 1.3 75.7 - - - +
332L VAL* 1.3 57.0 + - - +
334L GLY* 3.3 3.2 + - - -
335L TYR* 3.0 59.9 + - + +
382L GLU 5.6 1.3 + - - +
383L ILE 5.1 1.1 - - - +
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Residues in contact with VAL 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323L VAL* 4.5 5.2 - - + -
328L HIS* 3.1 41.7 + - + +
329L GLN 3.6 4.0 - - - +
331L LYS* 1.3 74.1 - - + +
333L ILE* 1.3 66.6 + - - +
335L TYR* 3.3 10.5 + - - +
336L ILE* 3.2 27.2 + - + +
364L VAL* 4.0 29.8 - - + -
383L ILE* 3.9 25.4 - - + +
384L PHE 4.2 4.7 - - - +
385L GLY* 4.3 2.9 - - - -
386L PRO* 4.5 5.4 - - + -
387L VAL* 4.4 5.8 - - + -
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Residues in contact with ILE 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329L GLN* 3.1 33.8 + - + +
330L GLU* 3.4 10.1 - - - +
332L VAL* 1.3 73.4 - - - +
334L GLY* 1.3 56.9 + - - +
336L ILE* 2.9 13.9 + - - +
337L ASN* 2.9 45.7 + - - +
351L ARG* 3.2 48.0 - - + +
363L PHE 5.5 0.4 - - - +
364L VAL* 4.8 16.8 - - + -
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Residues in contact with GLY 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330L GLU 2.7 18.3 + - - -
331L LYS* 3.5 6.5 - - - -
332L VAL 3.3 0.2 - - - -
333L ILE* 1.3 73.4 - - - +
335L TYR* 1.3 55.8 + - - +
337L ASN* 3.7 12.7 - - - +
338L SER* 3.0 26.0 + - - -
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Residues in contact with TYR 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331L LYS* 3.0 54.9 + - + +
332L VAL* 3.6 6.3 - - - +
333L ILE 3.2 0.6 - - - -
334L GLY* 1.3 73.5 - - - +
336L ILE* 1.3 56.2 + - - +
338L SER* 3.3 7.5 + - - -
339L ALA* 2.7 33.8 + - - +
377L THR* 4.8 4.9 - - + -
378L SER* 3.5 27.5 - - - -
381L GLU* 2.9 44.2 + - + +
382L GLU 3.8 11.8 + - - -
383L ILE* 3.8 46.4 - - + -
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Residues in contact with ILE 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332L VAL* 3.2 26.0 - - + +
333L ILE* 2.9 6.9 + - - +
335L TYR* 1.3 72.1 - - + +
337L ASN* 1.3 65.3 + - - +
339L ALA* 3.1 7.9 + - - +
340L GLU* 2.9 23.4 + - - +
346L ILE* 3.9 22.8 - - + +
349L ASP* 5.1 0.4 - - - +
351L ARG* 3.6 38.4 - - + +
364L VAL* 4.6 6.3 - - + -
367L THR* 4.0 19.1 - - + +
369L ILE* 4.3 11.2 - - + -
383L ILE* 5.8 0.7 - - + -
387L VAL* 4.0 28.7 - - + -
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Residues in contact with ASN 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333L ILE* 2.9 35.9 + - - +
334L GLY* 3.7 10.4 - - - +
336L ILE* 1.3 73.7 - - - +
338L SER* 1.3 58.4 + - - +
340L GLU* 3.2 4.6 + - - +
341L GLN* 2.9 32.3 + - - +
351L ARG* 2.9 35.2 + - - +
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Residues in contact with SER 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334L GLY 3.0 20.1 + - - -
335L TYR* 3.3 11.2 + - - -
337L ASN* 1.3 74.3 - - - +
339L ALA* 1.3 61.2 + - - +
341L GLN* 4.1 13.7 - - - -
342L GLN* 3.2 42.8 + - - +
377L THR* 3.9 15.9 + - - -
378L SER* 4.1 4.7 + - - -
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Residues in contact with ALA 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335L TYR 2.7 14.5 + - - +
336L ILE 3.1 9.1 + - - +
338L SER* 1.3 70.8 - - - +
340L GLU* 1.3 67.2 + - - +
342L GLN* 3.3 10.8 + - - +
343L GLY 3.5 0.7 + - - -
344L ALA* 3.1 25.4 + - + +
346L ILE* 4.4 0.4 - - + -
369L ILE* 3.8 35.7 - - + -
376L MET* 4.4 2.1 - - - +
378L SER* 3.5 20.8 + - - +
389L GLN* 4.9 1.3 - - - +
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Residues in contact with GLU 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336L ILE 2.9 10.5 + - - +
337L ASN* 3.6 7.3 - - - +
339L ALA* 1.3 74.8 - - - +
341L GLN* 1.3 66.5 + - - +
343L GLY* 3.1 12.1 + - - -
344L ALA 3.5 18.3 + - - +
346L ILE* 3.7 22.0 - - + +
351L ARG* 2.9 36.8 + - - +
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Residues in contact with GLN 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337L ASN 2.9 16.6 + - - +
338L SER* 3.8 14.9 - - - +
340L GLU* 1.3 77.1 - - - +
342L GLN* 1.3 65.9 + - + +
343L GLY* 2.9 8.0 + - - -
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Residues in contact with GLN 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338L SER* 3.2 26.9 + - - +
339L ALA 3.3 5.1 + - - +
341L GLN* 1.3 86.3 + - + +
343L GLY* 1.3 55.7 + - - +
344L ALA 3.7 1.8 - - - -
375L GLU 4.6 4.4 + - - -
376L MET* 3.2 33.5 - - + +
377L THR* 3.0 43.6 + - - +
378L SER* 4.2 0.5 + - - -
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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
------------------------------------------------------------
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