Contacts of the helix formed by residues 325 - 342 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 6.0 5.6 - - + -
176C ARG* 3.8 35.5 + - + +
323C VAL* 3.5 5.3 - - - +
324C ILE* 1.3 85.9 - - + +
326C ARG* 1.3 65.8 + - - +
327C GLN* 3.5 10.2 + - - +
328C HIS* 2.9 25.8 + - - +
329C GLN* 2.9 19.8 + - - +
362C PHE* 3.5 13.5 - - + -
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Residues in contact with ARG 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLY* 5.5 1.6 + - - -
325C THR* 1.3 73.3 - - - +
327C GLN* 1.3 65.1 + - - +
329C GLN* 3.1 24.7 + - - +
330C GLU* 2.9 43.9 + - - +
360C ASN* 3.6 26.1 + - - +
361C GLY 3.3 25.5 + - - -
362C PHE* 3.5 38.6 - - + -
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Residues in contact with GLN 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ARG* 5.5 4.7 + - - -
325C THR* 3.7 9.3 + - - +
326C ARG* 1.3 79.1 - - - +
328C HIS* 1.3 59.3 + - - +
330C GLU* 3.2 13.3 + - + +
331C LYS* 2.9 32.5 + - + +
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Residues in contact with HIS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PHE* 5.0 2.7 - + - -
176C ARG* 6.2 0.7 - - - +
278C GLU* 3.7 15.0 - - - -
323C VAL* 3.6 24.9 - - + -
324C ILE* 4.0 12.8 - - + -
325C THR* 2.9 22.3 + - - +
327C GLN* 1.3 76.3 - - - +
329C GLN* 1.3 57.5 + - - +
331C LYS* 3.1 30.7 + - + +
332C VAL* 2.8 39.1 + - + +
383C ILE 3.8 14.6 - - - -
384C PHE* 2.8 43.6 + + + +
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Residues in contact with GLN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C VAL* 3.4 13.8 - - + +
325C THR 2.9 11.6 + - - +
326C ARG* 3.1 36.6 + - - +
328C HIS* 1.3 76.5 - - - +
330C GLU* 1.3 66.2 + - + +
332C VAL* 3.3 3.0 + - - +
333C ILE* 3.0 38.3 + - + +
351C ARG 5.6 1.0 + - - -
353C PRO* 5.5 1.4 - - - +
361C GLY 4.0 4.0 + - - -
362C PHE* 3.7 11.6 - - + +
363C PHE* 2.7 32.3 + - - +
364C VAL* 3.8 19.1 - - + -
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Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ARG* 2.9 35.7 + - + +
327C GLN* 3.5 16.0 - - - +
329C GLN* 1.3 79.9 - - + +
331C LYS* 1.3 56.7 + - - +
333C ILE* 3.7 7.1 - - - +
334C GLY* 2.9 26.9 + - - -
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C GLN* 2.9 17.8 + - + +
328C HIS* 3.1 34.3 + - + +
330C GLU* 1.3 72.8 - - - +
332C VAL* 1.3 67.0 + - - +
334C GLY* 3.1 4.2 + - - -
335C TYR* 3.0 55.6 + - + +
382C GLU 5.5 1.3 - - - +
383C ILE 5.2 0.9 - - - +
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C VAL* 4.4 5.6 - - + -
328C HIS* 2.8 47.2 + - + +
329C GLN 3.8 4.0 - - - +
331C LYS* 1.3 72.5 - - - +
333C ILE* 1.3 61.5 + - - +
335C TYR* 3.2 18.6 + - - +
336C ILE* 3.2 16.1 + - + +
364C VAL* 4.0 29.2 - - + -
383C ILE* 3.8 26.0 - - + +
385C GLY* 4.1 13.5 - - - -
386C PRO* 4.4 0.2 - - + -
387C VAL* 4.2 13.2 - - + -
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Residues in contact with ILE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLN* 3.0 33.1 + - + +
330C GLU* 3.7 7.2 - - - +
332C VAL* 1.3 75.8 - - - +
334C GLY* 1.3 63.3 + - - +
336C ILE* 3.3 4.0 + - + +
337C ASN* 3.0 36.9 + - - +
351C ARG* 3.2 55.0 - - + +
363C PHE 5.4 0.4 - - - +
364C VAL* 4.5 18.6 - - + -
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Residues in contact with GLY 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLU 2.9 15.2 + - - -
331C LYS* 3.1 6.7 + - - -
333C ILE* 1.3 77.1 - - - +
335C TYR* 1.3 56.4 + - - +
337C ASN* 3.2 12.9 + - - +
338C SER* 2.8 28.3 + - - -
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Residues in contact with TYR 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LYS* 3.0 54.0 + - + +
332C VAL 3.2 5.8 + - - +
334C GLY* 1.3 73.2 - - - +
336C ILE* 1.3 61.9 + - + +
338C SER* 3.3 8.3 + - - -
339C ALA* 3.0 28.1 + - - +
369C ILE* 5.7 0.4 - - - -
377C THR* 4.7 5.4 - - + -
378C SER* 3.6 23.8 - - - -
381C GLU* 2.6 43.4 + - + +
382C GLU 3.9 20.4 + - - -
383C ILE* 3.8 40.8 - - + -
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C VAL* 3.2 22.5 + - + +
333C ILE* 3.3 6.0 + - - +
335C TYR* 1.3 73.4 - - + +
337C ASN* 1.3 67.8 + - - +
339C ALA* 3.1 7.6 + - - +
340C GLU* 3.1 21.7 + - - +
346C ILE* 3.7 25.5 - - + +
349C ASP* 4.8 0.7 - - - +
351C ARG* 3.6 37.5 - - + +
364C VAL* 4.7 5.6 - - + -
367C THR* 3.6 37.7 - - + +
369C ILE* 4.4 9.2 - - + -
383C ILE* 6.0 0.4 - - + -
387C VAL* 4.0 17.7 - - + -
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Residues in contact with ASN 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ILE* 3.0 28.8 + - - +
334C GLY* 3.3 11.4 - - - +
336C ILE* 1.3 77.9 - - - +
338C SER* 1.3 57.7 + - - +
340C GLU* 3.3 2.7 + - - +
341C GLN* 2.9 33.2 + - - +
351C ARG* 2.7 41.8 + - - +
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C GLY 2.8 14.0 + - - -
335C TYR* 3.5 14.6 - - - -
336C ILE 3.3 0.2 - - - -
337C ASN* 1.3 76.6 - - - +
339C ALA* 1.3 60.7 + - - +
341C GLN* 3.9 9.8 - - - +
342C GLN* 3.0 44.6 + - - +
377C THR* 4.2 13.4 + - - +
378C SER* 4.5 5.5 + - - -
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Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C TYR 3.0 10.3 + - - +
336C ILE 3.1 8.9 + - - +
338C SER* 1.3 73.1 - - - +
340C GLU* 1.3 65.3 + - - +
342C GLN* 3.2 6.0 + - - +
343C GLY 3.2 5.5 + - - -
344C ALA* 2.9 36.6 + - + +
346C ILE* 4.6 0.4 - - + -
369C ILE* 4.0 26.0 - - + -
376C MET* 4.4 3.5 - - - +
378C SER* 3.5 22.0 + - - +
389C GLN* 5.0 0.9 - - - +
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Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ILE 3.1 8.4 + - - +
337C ASN* 3.6 7.4 - - - +
339C ALA* 1.3 78.8 - - - +
341C GLN* 1.3 58.9 + - - +
343C GLY* 3.0 21.1 + - - -
344C ALA 3.6 15.3 + - - +
346C ILE* 3.7 22.9 + - + +
351C ARG* 2.9 38.2 + - - +
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Residues in contact with GLN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ASN* 2.9 18.4 + - - +
338C SER* 3.9 10.8 - - - +
340C GLU* 1.3 76.9 - - - +
342C GLN* 1.3 62.8 + - + +
343C GLY* 3.3 1.4 + - - -
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Residues in contact with GLN 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C SER* 3.0 34.0 + - - +
339C ALA 3.9 2.9 - - - +
340C GLU 3.2 0.4 - - - -
341C GLN* 1.3 80.9 - - + +
343C GLY* 1.3 57.3 + - - +
344C ALA 3.7 1.3 - - - -
375C GLU 3.9 10.3 + - - -
376C MET* 3.4 28.8 - - + +
377C THR* 3.3 36.4 + - - +
378C SER 4.4 0.9 + - - -
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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