Contacts of the helix formed by residues 348 - 357 (chain B) in PDB entry 5D0A
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 TYR 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B LEU* 3.6 39.0 - - + -
318B PRO* 3.6 26.6 - - + +
321B THR* 3.3 30.1 - - + -
340B ILE* 3.7 25.1 - - + +
345B ASP* 3.1 22.4 + - - +
346B PRO 3.1 1.6 - - - -
347B ALA* 1.3 85.0 - - + +
349B ALA* 1.3 64.8 + - - +
350B GLU 3.3 2.7 - - - -
351B GLU* 3.3 16.5 + - + +
352B LEU* 3.0 23.4 + - - +
375B LEU* 4.1 2.7 - - - -
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO* 3.1 17.8 + - + +
348B TYR* 1.3 76.0 - - - +
350B GLU* 1.3 64.2 + - - +
352B LEU* 3.1 9.3 + - - +
353B GLU* 3.0 29.9 + - + +
372B ILE* 4.9 3.8 - - + +
375B LEU* 3.7 27.9 - - + +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO 4.7 0.6 + - - -
347B ALA 4.7 6.2 + - - +
348B TYR 3.3 0.4 - - - -
349B ALA* 1.3 78.9 - - + +
351B GLU* 1.3 58.9 + - - +
353B GLU* 2.9 33.3 + - - +
354B LYS* 3.0 36.5 + - - +
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B THR* 3.9 19.9 - - + +
324B MET* 4.1 4.9 - - + +
325B HIS* 2.6 35.6 + - - +
347B ALA 5.2 1.2 + - - +
348B TYR* 3.3 22.0 + - + +
350B GLU* 1.3 77.9 - - - +
352B LEU* 1.3 56.8 + - - +
354B LYS* 3.6 23.8 - - - +
355B ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B MET* 3.8 26.5 - - + -
337B ALA* 3.9 12.8 - - + +
340B ILE* 3.6 25.1 - - + -
341B GLY* 4.3 2.0 - - - -
348B TYR 3.0 16.6 + - - +
349B ALA* 3.1 8.5 + - - +
351B GLU* 1.3 77.3 - - - +
353B GLU* 1.3 62.6 + - - +
355B ALA* 3.3 2.1 + - - -
356B LEU* 3.1 19.6 + - - +
368B ILE* 3.3 17.1 - - + +
371B GLY* 3.6 35.4 - - - +
372B ILE* 3.6 15.3 - - + +
375B LEU* 3.8 21.3 - - + -
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ALA* 3.0 20.6 + - - +
350B GLU* 2.9 21.3 + - - +
352B LEU* 1.3 76.5 - - - +
354B LYS* 1.3 61.9 + - + +
356B LEU* 3.6 16.8 - - - +
357B GLU* 3.7 14.9 + - - +
372B ILE* 3.5 36.4 - - - +
376B LYS* 4.4 8.8 + - - +
34D LYS* 5.7 2.6 + - - -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B HIS* 5.9 0.2 - - + -
350B GLU* 3.0 39.8 + - - +
351B GLU* 3.6 26.7 - - - +
352B LEU 3.2 0.2 - - - -
353B GLU* 1.3 79.1 - - + +
355B ALA* 1.3 63.8 + - - +
357B GLU* 3.3 14.6 + - - +
358B LYS* 3.5 24.1 - - + +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B MET* 3.6 25.8 - - + -
325B HIS* 3.6 27.6 - - + +
351B GLU 3.0 18.4 + - - +
352B LEU 3.3 3.6 + - - +
354B LYS* 1.3 76.6 - - - +
356B LEU* 1.3 56.4 + - - +
358B LYS* 2.9 7.3 + - - +
359B GLU* 2.9 31.2 + - - +
368B ILE* 4.1 8.5 - - + -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LEU 3.1 13.5 + - - +
353B GLU* 3.6 12.8 - - - +
354B LYS 3.2 0.2 - - - -
355B ALA* 1.3 78.2 - - - +
357B GLU* 1.3 75.1 + - - +
358B LYS 3.2 1.0 + - - -
359B GLU 3.7 13.3 + - - +
365B LYS* 3.6 52.7 - - + +
368B ILE* 3.8 13.6 - - + +
369B GLU* 3.8 28.9 - - + +
372B ILE* 4.1 13.7 - - + -
34D LYS* 5.8 2.9 - - - +
55D GLU* 4.3 17.3 - - + +
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLU 3.7 12.8 + - - +
354B LYS* 3.3 10.1 + - - +
355B ALA 3.2 1.0 - - - -
356B LEU* 1.3 89.7 - - - +
358B LYS* 1.3 62.5 + - + +
359B GLU 5.0 0.8 - - - +
360B LYS* 4.4 10.7 + - - -
365B LYS* 5.9 0.4 - - - -
55D GLU* 4.0 20.0 - - - +
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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