Contacts of the helix formed by residues 337 - 347 (chain A) in PDB entry 4E70
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 GLU 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A VAL* 3.9 13.7 - - + +
306A ASP* 2.8 25.2 + - - +
307A HIS* 6.0 1.6 - - - -
336A THR* 1.3 71.2 - - - +
338A LYS* 1.3 58.3 + - - +
340A TRP* 3.2 6.3 + - + +
341A ALA* 2.8 30.1 + - + +
352A TYR* 2.5 37.1 + - + +
354A ILE* 4.0 20.1 - - + +
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Residues in contact with LYS 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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306A ASP* 5.0 1.2 + - - -
336A THR* 3.2 10.0 + - - +
337A GLU* 1.3 77.3 - - - +
339A GLN* 1.3 64.5 + - + +
341A ALA* 3.8 5.8 - - - +
342A LYS* 3.1 27.3 + - + +
1094B VAL* 5.9 7.0 - - + -
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Residues in contact with GLN 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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275A ASP* 5.6 7.4 + - - +
333A SER* 5.4 3.9 + - - -
334A LEU 4.1 2.9 - - - +
335A ARG* 3.3 26.0 - - + +
336A THR* 2.9 44.1 + - - +
338A LYS* 1.3 77.1 - - + +
340A TRP* 1.3 66.1 + - - +
342A LYS* 3.5 7.1 + - - +
343A LEU* 3.2 27.8 + - - +
1072B ARG* 5.2 4.7 + - - +
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Residues in contact with TRP 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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270A LEU* 3.9 36.8 - - + -
271A CYS* 5.4 1.8 - - + -
278A VAL* 5.3 1.1 - - + -
282A LEU* 5.5 0.7 - - + -
300A ILE* 3.9 19.7 - - + -
302A ASP* 4.2 18.2 - - + -
303A HIS 2.9 27.3 + - - -
304A VAL* 3.8 20.1 - - + +
333A SER 6.2 0.2 - - - -
335A ARG* 3.5 41.3 - - + +
336A THR 3.0 23.3 + - - -
337A GLU* 3.6 8.1 - - + +
339A GLN* 1.3 77.3 - - - +
341A ALA* 1.3 64.8 + - - +
343A LEU* 3.0 16.3 + - + +
344A PHE* 3.0 55.0 + + + -
352A TYR* 6.5 0.2 - - + -
364A ILE* 4.0 10.5 - - + -
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Residues in contact with ALA 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 GLU* 2.8 21.2 + - + +
338A LYS* 3.8 6.5 - - - +
340A TRP* 1.3 72.6 - - - +
342A LYS* 1.3 57.1 + - - +
344A PHE* 3.4 14.1 + - - +
345A ALA* 3.0 29.3 + - - +
352A TYR* 4.1 24.4 - - + +
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Residues in contact with LYS 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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275A ASP* 5.7 2.2 + - - -
338A LYS* 3.1 19.5 + - + +
339A GLN* 3.7 7.9 - - - +
340A TRP 3.2 0.2 - - - -
341A ALA* 1.3 73.1 - - - +
343A LEU* 1.3 67.7 + - + +
345A ALA* 3.4 5.9 + - - +
346A GLU* 2.7 60.9 + - + +
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Residues in contact with LEU 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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275A ASP* 3.9 28.7 - - + +
278A VAL* 4.3 13.5 - - + -
279A LEU* 3.8 37.6 - - + +
282A LEU* 4.5 6.7 - - + +
335A ARG* 3.5 37.0 - - - +
339A GLN* 3.2 10.2 + - + +
340A TRP* 3.0 16.9 + - + +
342A LYS* 1.3 80.0 - - + +
344A PHE* 1.3 63.9 + - + +
346A GLU* 3.3 6.4 + - - +
347A ALA* 2.9 31.5 + - - +
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Residues in contact with PHE 344 (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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282A LEU* 4.4 13.0 - - + -
298A LEU* 4.8 1.8 - - + -
300A ILE* 3.6 24.9 - - + -
340A TRP* 3.0 55.5 + + + -
341A ALA* 3.8 6.3 - - - +
342A LYS 3.3 0.2 - - - -
343A LEU* 1.3 77.3 - - + +
345A ALA* 1.3 61.3 + - - +
347A ALA* 3.4 1.8 + - - -
348A GLY 3.2 4.2 + - - -
349A PHE* 2.9 37.5 + + + +
351A ASP 5.9 0.2 - - - +
352A TYR* 3.9 28.0 - + + -
364A ILE* 3.8 24.5 - - + -
366A VAL* 3.7 37.2 - - + -
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Residues in contact with ALA 345 (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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341A ALA 3.0 17.7 + - - +
342A LYS* 3.7 5.8 - - - +
343A LEU 3.3 0.2 - - - -
344A PHE* 1.3 77.6 - - - +
346A GLU* 1.3 64.0 + - + +
348A GLY* 3.1 14.6 + - - -
349A PHE 4.4 7.7 - - - +
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Residues in contact with GLU 346 (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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279A LEU* 3.5 32.7 - - + +
283A LYS* 3.4 16.9 - - - -
342A LYS* 2.7 61.2 + - + +
343A LEU* 3.9 5.0 - - - +
345A ALA* 1.3 77.5 - - + +
347A ALA* 1.3 59.7 + - - +
348A GLY* 3.2 1.1 + - - -
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Residues in contact with ALA 347 (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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279A LEU* 3.7 6.0 - - + +
282A LEU* 3.8 33.0 - - + -
283A LYS* 3.8 16.2 - - - +
286A LYS* 3.5 23.9 - - - +
343A LEU 2.9 17.3 + - - +
344A PHE* 3.9 0.7 - - - +
345A ALA 3.2 0.2 - - - -
346A GLU* 1.3 77.5 - - - +
348A GLY* 1.3 58.2 + - - +
349A PHE* 3.5 17.0 - - + -
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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