Contacts of the helix formed by residues 327 - 334 (chain H) in PDB entry 4HY0
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 CYS 327 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331C LEU* 4.5 0.4 - - - +
336C GLN* 4.0 2.0 - - - +
340C ASN* 4.2 3.0 - - - +
300H CYS* 3.6 9.6 - - - -
302H HIS* 3.8 0.9 - - - -
303H CYS* 3.6 20.4 - - + -
320H HIS* 3.6 9.0 - - - +
324H TYR 3.5 4.0 + - - +
325H PRO 3.3 4.6 - - - +
326H GLY* 1.3 75.7 - - - +
328H LYS* 1.3 60.8 + - - +
329H TYR* 3.5 13.0 - - - -
330H LEU* 3.4 25.4 - - + +
331H LEU* 3.1 24.3 + - - +
401H ZN 2.2 37.2 - - - -
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Residues in contact with LYS 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LEU* 3.7 26.2 - - + -
336C GLN* 3.0 24.4 - - - +
255H ASN* 3.4 35.8 + - + +
302H HIS* 3.8 13.9 - - - +
326H GLY 3.2 1.0 + - - -
327H CYS* 1.3 70.0 - - - +
329H TYR* 1.3 60.5 + - - +
331H LEU* 3.4 2.4 + - + +
332H GLU* 3.0 48.4 + - + +
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Residues in contact with TYR 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268H ARG* 3.9 14.4 + - - -
286H ARG* 2.7 21.0 + - - -
287H ALA 3.6 26.5 - - - -
288H GLY* 3.6 10.3 - - - -
300H CYS* 4.7 1.6 - - - -
301H PHE* 3.6 30.1 - + + -
302H HIS* 3.8 20.6 - - + +
317H TRP* 4.0 7.9 - + - -
320H HIS* 5.0 0.7 - + - -
327H CYS* 3.2 15.3 - - - -
328H LYS* 1.3 76.3 - - - +
330H LEU* 1.3 69.6 + - - +
332H GLU* 3.2 17.6 + - - +
333H GLN* 3.1 58.7 + - + +
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Residues in contact with LEU 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317H TRP* 3.8 43.7 - - + +
320H HIS* 4.0 14.6 - - + +
321H ALA* 3.7 31.6 - - + -
324H TYR 3.8 17.0 - - - +
325H PRO* 4.1 4.3 - - + +
327H CYS* 3.3 20.2 + - + +
329H TYR* 1.3 84.7 - - - +
331H LEU* 1.3 55.9 + - - +
334H LYS* 2.9 33.4 + - + +
335H GLY 3.3 4.5 + - - -
338H TYR* 5.0 0.7 - - + -
339H ILE* 3.8 22.1 - - + +
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Residues in contact with LEU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ASN* 3.0 28.7 + - - +
326C GLY 3.2 24.0 - - - +
328C LYS* 3.5 34.8 - - + -
331C LEU* 3.3 28.7 - - + -
327H CYS 3.1 13.6 + - - +
328H LYS* 3.7 9.2 - - + +
329H TYR 3.1 0.2 - - - -
330H LEU* 1.3 76.5 - - - +
332H GLU* 1.3 64.3 + - + +
335H GLY* 3.1 13.7 + - - +
336H GLN* 3.6 23.3 - - + +
339H ILE* 3.7 13.9 - - + +
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Residues in contact with GLU 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C THR* 4.9 5.4 + - - -
255C ASN* 4.5 8.1 + - - +
302H HIS* 5.2 2.4 + - - -
328H LYS* 3.0 45.0 + - + +
329H TYR* 3.2 23.0 + - - +
331H LEU* 1.3 75.9 - - - +
333H GLN* 1.3 73.8 + - + +
335H GLY 5.0 0.2 + - - -
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Residues in contact with GLN 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286H ARG 4.7 0.3 - - - +
317H TRP* 3.5 26.6 - - + -
329H TYR* 3.1 57.1 + - + +
332H GLU* 1.3 88.9 + - + +
334H LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315H ASP* 6.0 0.2 - - - -
317H TRP* 3.5 57.7 - - + +
330H LEU* 2.9 20.0 + - + +
333H GLN* 1.3 76.4 - - + +
335H GLY* 1.3 60.8 + - - +
338H TYR* 3.3 63.3 + - + +
339H ILE* 5.4 0.2 - - + -
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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