Contacts of the helix formed by residues 332 - 343 (chain A) in PDB entry 6DWZ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A LEU* 2.8 56.5 - - + +
308A ARG* 5.5 0.5 + - - -
309A SER* 3.0 37.1 + - - -
310A SER 5.2 0.2 - - - -
311A LEU* 4.3 13.4 - - + +
328A SER 3.4 13.3 + - - +
329A ILE 3.6 3.7 + - - +
330A LEU 3.6 0.2 - - - -
331A ASP* 1.3 77.2 - - - +
333A TRP* 1.3 53.9 + - - +
334A GLU* 3.3 2.7 - - - -
335A SER* 2.9 10.9 + - - -
336A VAL* 2.7 36.0 + - + +
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Residues in contact with TRP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A CYS* 5.9 1.1 - - - -
329A ILE* 3.5 31.5 + - + +
330A LEU* 3.7 19.7 - - + +
331A ASP 3.3 3.2 + - - -
332A ASN* 1.3 74.9 - - - +
334A GLU* 1.3 90.7 + - + +
336A VAL* 3.3 7.1 + - + +
337A ILE* 3.0 58.9 + - + +
349A ILE* 5.7 4.3 - - + -
351A HIS 4.7 7.9 - - - -
352A ILE* 4.6 9.9 - - + -
353A ASN 4.5 7.4 - - - -
354A LYS* 3.3 56.8 - - + +
357A ILE* 4.6 12.3 - - + -
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LEU 5.4 0.2 - - - +
331A ASP 4.7 4.5 - - - +
332A ASN 4.5 0.7 - - - -
333A TRP* 1.3 103.5 + - + +
335A SER* 1.3 65.6 + - - +
337A ILE* 4.0 3.8 - - - +
338A GLN* 3.1 26.0 + - - +
354A LYS* 4.8 7.6 - - - +
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Residues in contact with SER 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ARG 5.3 0.7 - - - -
307A LEU* 3.9 27.2 + - - -
308A ARG* 5.4 5.5 + - - -
332A ASN* 2.9 13.8 + - - -
334A GLU* 1.3 79.0 + - - +
336A VAL* 1.3 56.5 + - - +
338A GLN* 3.6 4.7 - - - +
339A ILE* 2.9 42.3 + - - +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ILE* 4.1 22.0 - - + -
298A PHE* 3.6 25.3 - - + -
307A LEU* 4.8 0.7 - - + -
311A LEU* 4.2 24.5 - - + -
329A ILE* 5.3 10.1 - - + +
332A ASN* 2.7 26.0 + - + +
333A TRP* 3.7 11.0 - - + +
334A GLU 3.2 0.2 - - - -
335A SER* 1.3 72.6 - - - +
337A ILE* 1.3 60.3 + - + +
339A ILE* 2.8 3.1 + - - +
340A LEU* 2.6 45.3 + - + +
349A ILE* 4.2 10.1 - - + -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A TRP* 3.0 55.9 + - + +
334A GLU* 4.0 4.0 - - - +
336A VAL* 1.3 74.8 - - + +
338A GLN* 1.3 53.8 + - - +
340A LEU* 3.4 0.9 + - - +
341A SER* 2.7 47.0 + - - +
349A ILE* 3.5 41.3 - - + -
352A ILE* 5.5 8.1 - - + -
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A GLU 3.1 15.7 + - - +
335A SER* 3.6 7.2 - - - +
337A ILE* 1.3 79.9 - - - +
339A ILE* 1.3 57.7 + - + +
341A SER* 3.5 3.7 - - - -
342A GLU* 2.5 65.2 + - - +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PHE* 4.5 16.8 - - + -
303A LEU* 4.6 15.7 - - + -
306A ARG* 3.4 51.6 - - + +
307A LEU* 4.3 8.1 - - + -
335A SER* 2.9 35.2 + - - +
336A VAL 2.8 7.2 + - - +
338A GLN* 1.3 74.1 - - + +
340A LEU* 1.3 57.4 + - - +
342A GLU* 3.3 24.6 - - - +
343A ALA* 3.0 32.7 + - + +
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ILE* 3.7 17.9 - - + -
297A TYR* 4.5 12.6 - - + -
298A PHE* 3.7 30.5 - - + -
336A VAL* 2.6 24.3 + - + +
337A ILE* 3.6 6.1 - - - +
339A ILE* 1.3 74.0 - - - +
341A SER* 1.3 59.2 + - - +
343A ALA* 3.5 1.9 + - + +
344A GLY 3.3 1.9 + - - -
345A GLU* 3.0 62.5 + - + +
346A THR* 3.2 5.3 + - - -
348A ARG* 4.2 20.9 - - + -
349A ILE* 4.5 12.3 - - + +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ILE* 2.7 31.3 + - - +
338A GLN* 3.7 4.9 - - - -
340A LEU* 1.3 72.7 - - - +
342A GLU* 1.3 54.3 + - - +
344A GLY* 2.5 27.7 + - - -
346A THR* 2.6 34.1 + - - +
349A ILE* 4.6 1.0 - - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ARG* 3.6 16.3 + - - -
338A GLN* 2.5 48.2 + - - +
339A ILE* 3.3 38.8 - - + +
341A SER* 1.3 72.4 - - - +
343A ALA* 1.3 61.8 + - + +
344A GLY 3.2 1.1 + - - -
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TYR* 4.7 14.8 - - + +
303A LEU* 6.3 1.8 - - + -
339A ILE* 3.0 21.2 + - + +
340A LEU* 4.1 3.8 - - + +
341A SER 3.2 0.2 - - - -
342A GLU* 1.3 77.2 - - + +
344A GLY* 1.3 54.8 + - - +
345A GLU* 2.9 16.7 + - + +
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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