Contacts of the helix formed by residues 332 - 343 (chain H) in PDB entry 4D1Q
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 ASN 332 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307H LEU* 3.9 19.7 - - + +
308H ARG* 3.8 14.4 + - - +
309H SER* 2.7 50.5 + - - -
311H LEU* 4.0 0.8 - - + +
328H SER* 3.0 29.4 + - - +
329H ILE 3.4 3.8 - - - -
331H ASP* 1.3 83.2 - - - +
333H TRP* 1.3 59.3 + - - +
334H GLU* 3.6 1.3 - - - -
335H SER* 4.0 16.5 + - - +
336H VAL* 3.0 28.8 + - + +
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Residues in contact with TRP 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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329H ILE* 3.6 33.0 - - + -
330H LEU* 3.3 20.7 + - + +
331H ASP 3.5 2.4 + - - -
332H ASN* 1.3 71.2 - - - +
334H GLU* 1.3 79.8 + - - +
335H SER 2.8 3.0 + - - -
336H VAL* 3.0 27.9 + - + +
337H ILE* 3.1 29.3 - - + +
349H ILE* 4.6 16.8 - - + -
352H ILE* 4.1 27.4 - - + -
354H LYS* 3.6 59.3 - - + +
357H ILE* 6.1 2.7 - - + -
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Residues in contact with GLU 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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331H ASP 6.1 0.2 - - - +
332H ASN* 6.0 0.4 - - - -
333H TRP* 1.3 87.4 - - - +
335H SER* 1.3 63.5 + - - +
337H ILE* 3.0 33.1 - - + +
338H GLN* 3.3 9.5 + - - +
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Residues in contact with SER 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 5.7 1.6 - - - -
307H LEU* 4.7 19.6 - - - -
308H ARG* 5.3 7.1 + - - +
332H ASN* 3.9 24.1 + - - +
333H TRP 2.8 1.0 + - - -
334H GLU* 1.3 74.5 - - - +
336H VAL* 1.3 53.6 + - - -
337H ILE 2.7 17.3 + - - -
338H GLN* 3.1 15.0 + - - +
339H ILE* 3.3 22.6 + - - +
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Residues in contact with VAL 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H ILE* 5.1 7.2 - - + -
298H PHE* 3.9 29.3 - - + -
307H LEU* 4.6 2.2 - - + -
311H LEU* 4.0 31.0 - - + -
329H ILE* 4.4 7.2 - - + +
332H ASN* 3.0 23.3 + - + +
333H TRP* 3.0 34.4 + - + +
335H SER* 1.3 70.0 - - - +
337H ILE* 1.3 61.5 + - + +
339H ILE* 4.3 0.7 - - - -
340H LEU* 3.1 31.7 - - + +
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Residues in contact with ILE 337 (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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333H TRP* 3.1 43.0 + - + +
334H GLU* 3.0 25.1 - - - +
335H SER 2.7 5.5 + - - -
336H VAL* 1.3 78.9 - - + +
338H GLN* 1.3 84.8 + - + +
339H ILE 2.9 1.8 - - - -
340H LEU* 2.8 5.1 + - - +
341H SER* 2.8 27.0 + - - -
349H ILE* 4.3 31.2 - - + -
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Residues in contact with GLN 338 (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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334H GLU 3.3 16.5 + - - +
335H SER* 3.5 5.6 - - - +
337H ILE* 1.3 87.3 - - + +
339H ILE* 1.3 73.3 + - + +
341H SER* 3.2 19.0 - - - -
342H GLU* 3.4 33.2 + - - +
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Residues in contact with ILE 339 (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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298H PHE* 3.9 14.6 - - + -
303H LEU* 3.8 25.6 - - + -
306H ARG* 3.9 49.1 - - + +
307H LEU* 5.8 0.9 - - + -
335H SER* 3.3 25.3 + - - +
336H VAL 4.3 3.6 - - - -
337H ILE 2.8 0.2 + - - -
338H GLN* 1.3 90.1 - - + +
340H LEU* 1.3 80.7 + - + +
341H SER 3.0 5.1 + - - -
342H GLU* 3.2 12.4 + - - +
343H ALA* 3.0 25.3 + - + +
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Residues in contact with LEU 340 (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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294H ILE* 4.8 17.0 - - + -
297H TYR* 4.0 22.0 - - + -
298H PHE* 4.0 21.1 - - + -
303H LEU* 5.5 0.2 - - + -
336H VAL 3.1 20.9 - - - +
337H ILE* 2.8 9.3 + - - +
339H ILE* 1.3 83.4 - - + +
341H SER* 1.3 64.9 + - - +
343H ALA* 3.9 5.8 - - + +
344H GLY 3.3 0.9 + - - -
345H GLU* 3.1 33.3 + - + +
346H THR* 3.1 20.8 + - + +
348H ARG* 5.3 3.8 - - + -
349H ILE* 3.9 28.0 - - + +
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Residues in contact with SER 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H ILE 2.8 14.7 + - - -
338H GLN* 3.2 15.5 - - - -
340H LEU* 1.3 70.3 - - - +
342H GLU* 1.3 56.1 + - - +
344H GLY* 2.8 28.6 + - - -
346H THR* 3.6 12.6 + - - +
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Residues in contact with GLU 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 3.8 20.1 + - - +
338H GLN* 3.5 31.9 - - - +
339H ILE* 3.5 12.7 - - - +
341H SER* 1.3 77.7 - - - +
343H ALA* 1.3 56.6 + - + +
344H GLY 3.3 2.0 - - - -
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Residues in contact with ALA 343 (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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297H TYR* 4.9 4.8 + - + +
303H LEU* 5.8 5.4 - - + -
339H ILE* 3.0 23.6 + - + +
340H LEU* 3.7 8.0 + - + +
341H SER 3.0 0.2 + - - -
342H GLU* 1.3 77.9 - - + +
344H GLY* 1.3 64.1 + - - +
345H GLU* 3.0 17.1 + - + +
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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