Contacts of the helix formed by residues 333 - 342 (chain C) 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 LEU 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C LEU* 3.7 24.2 - - + -
268C ILE* 3.9 29.8 - - + -
319C PHE* 4.5 12.1 - - + -
322C LEU* 3.3 31.2 - - + +
323C ILE* 3.5 4.2 + - - +
325C ARG 3.2 6.7 + - - -
327C ILE* 4.3 4.9 - - + +
332C ARG* 1.3 73.2 - - - +
334C GLY* 1.3 57.8 + - - +
336C GLU* 2.9 32.5 + - + +
337C PHE* 3.1 30.0 + - + -
399C ARG* 4.2 20.0 - - - +
403C ALA* 4.6 7.0 - - + -
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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
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323C ILE* 2.9 34.8 + - - +
332C ARG* 3.0 1.3 - - - -
333C LEU* 1.3 75.6 - - - +
335C THR* 1.3 56.9 + - - +
336C GLU 3.1 0.2 - - - -
337C PHE* 3.3 9.0 - - - +
338C ALA* 2.8 30.7 + - - +
348C ILE* 4.0 3.9 - - - +
350C HIS* 4.4 13.0 - - - -
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Residues in contact with THR 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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330C GLY 5.6 0.4 - - - +
331C ARG* 3.2 37.3 - - + +
332C ARG* 2.6 54.3 + - - +
334C GLY* 1.3 72.9 - - - +
336C GLU* 1.3 55.6 + - - -
338C ALA* 3.8 6.4 - - + +
339C ASP* 2.9 36.2 + - - +
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Residues in contact with GLU 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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261C ARG* 2.6 31.9 + - - -
265C LEU* 4.7 0.3 - - - +
327C ILE* 3.6 26.1 - - + +
331C ARG* 3.4 10.0 + - - +
332C ARG 4.0 0.4 - - - +
333C LEU* 2.9 19.0 + - + +
335C THR* 1.3 76.1 - - - +
337C PHE* 1.3 64.7 + - - +
339C ASP* 3.0 17.7 + - - +
340C ARG* 2.9 28.8 + - + +
399C ARG* 3.8 31.8 + - - +
410C GLU* 5.2 0.4 - - - -
412C ARG* 3.2 22.8 + - - -
422C TYR* 4.9 0.9 - - - +
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Residues in contact with PHE 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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316C LEU* 3.8 20.6 - - + -
319C PHE* 3.8 16.4 - + - -
323C ILE* 3.9 31.6 - - + -
333C LEU* 3.1 31.7 + - + -
334C GLY* 3.3 7.4 - - - +
336C GLU* 1.3 80.2 - - + +
338C ALA* 1.3 65.2 + - - +
340C ARG* 3.1 2.9 + - - +
341C ALA* 2.9 22.9 + - - +
348C ILE* 3.7 13.7 - - + -
380C VAL* 4.4 7.9 - - + -
396C VAL* 3.9 23.1 - - + +
399C ARG* 4.0 24.9 - - + -
400C ALA* 3.8 33.7 - - + -
403C ALA* 4.9 0.7 - - + -
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Residues in contact with ALA 338 (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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334C GLY 2.8 20.0 + - - +
335C THR* 3.8 8.5 - - + +
337C PHE* 1.3 72.8 - - - +
339C ASP* 1.3 53.3 + - - +
341C ALA* 3.1 6.7 + - - +
342C LYS* 2.8 35.5 + - - +
345C VAL 4.8 1.0 - - - +
347C GLY* 5.3 5.0 - - - -
348C ILE* 3.5 29.5 - - + +
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Residues in contact with ASP 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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331C ARG* 2.9 26.3 + - - -
335C THR* 2.9 21.1 + - - +
336C GLU* 3.0 19.9 + - - +
338C ALA* 1.3 74.7 - - - +
340C ARG* 1.3 63.7 + - - +
342C LYS* 3.0 30.9 + - - +
343C LYS 4.3 0.7 + - - -
421C GLU* 3.9 12.4 - - - +
422C TYR* 3.2 43.1 + - + -
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Residues in contact with ARG 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 GLU 2.9 19.1 + - - +
337C PHE 3.7 4.5 - - - +
339C ASP* 1.3 73.8 - - + +
341C ALA* 1.3 61.7 + - - +
343C LYS* 3.2 21.5 + - - +
395C GLU* 3.9 35.6 + - - +
398C LYS* 3.6 20.6 - - - +
399C ARG* 3.4 30.7 - - + +
402C GLU* 2.6 40.1 + - - -
408C PRO* 4.3 5.1 - - - +
409C GLU 5.8 1.0 + - - -
410C GLU* 3.3 21.6 + - - +
422C TYR* 3.6 45.6 + - + -
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Residues in contact with ALA 341 (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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337C PHE 2.9 12.6 + - - +
338C ALA 3.4 8.7 - - - +
340C ARG* 1.3 71.5 - - - +
342C LYS* 1.3 52.2 + - - +
343C LYS* 2.7 17.7 + - - +
344C TYR* 2.8 18.0 + - - +
345C VAL* 2.9 13.0 + - + +
348C ILE* 3.7 24.9 - - + -
392C ALA* 4.1 12.2 - - + +
395C GLU* 4.1 12.3 - - - +
396C VAL* 3.9 14.8 - - + -
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Residues in contact with LYS 342 (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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338C ALA 2.8 11.6 + - - +
339C ASP* 3.0 25.5 + - - +
341C ALA* 1.3 74.7 - - - +
343C LYS* 1.3 60.9 + - - +
344C TYR* 3.0 2.6 + - - -
345C VAL 3.1 21.3 + - - +
346C PRO* 5.6 5.4 - - + +
413C ARG* 6.0 1.0 - - - +
421C GLU* 4.5 19.0 + - - -
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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