Contacts of the helix formed by residues 345 - 358 (chain D) in PDB entry 6C3P
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 THR 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268D TYR 4.2 2.0 - - - -
269D ASP* 3.3 19.1 - - - +
270D LEU 3.1 21.1 - - - +
271D ALA* 3.5 15.0 - - + -
344D CYS* 1.3 75.9 - - - +
346D ALA* 1.3 54.3 + - - +
347D ARG* 3.2 14.6 - - - +
348D GLN* 2.8 41.6 + - - +
349D LEU* 2.5 36.5 + - - +
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D LEU* 4.8 17.1 - - + +
261D ILE* 4.2 21.3 - - + +
267D LEU 5.0 0.9 - - - +
268D TYR* 3.2 38.9 + - + +
270D LEU 3.8 5.6 + - - +
344D CYS 3.7 1.4 + - - -
345D THR* 1.3 72.2 - - - +
347D ARG* 1.3 56.3 + - - +
349D LEU* 3.3 14.4 - - + +
350D ASP* 2.9 25.3 + - - -
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Residues in contact with ARG 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D ALA 5.5 2.0 + - - -
268D TYR* 3.2 46.1 + - + +
269D ASP* 2.6 35.7 + - - +
345D THR* 3.0 10.7 - - - +
346D ALA* 1.3 75.0 - - - +
348D GLN* 1.3 60.0 + - + +
350D ASP* 3.1 6.4 + - - +
351D GLU* 2.9 47.9 + - + +
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Residues in contact with GLN 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D CYS* 3.1 31.9 - - - +
345D THR* 2.8 30.0 + - - +
347D ARG* 1.3 72.2 - - + +
349D LEU* 1.3 58.9 + - - +
351D GLU* 3.4 25.4 - - + +
352D ASP* 2.9 31.5 + - - +
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LEU* 5.6 7.2 - - + -
194D GLY 6.2 0.2 - - - +
196D LEU* 4.3 17.3 - - + -
342D PRO* 3.9 32.8 - - + +
344D CYS* 3.2 31.9 - - - +
345D THR 2.5 30.1 + - - +
346D ALA* 3.3 16.8 - - + +
348D GLN* 1.3 73.2 - - - +
350D ASP* 1.3 60.6 + - - +
352D ASP* 4.0 2.8 - - + +
353D HIS* 2.8 31.7 + - + +
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Residues in contact with ASP 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ARG* 4.7 20.1 + - - -
263D ALA* 5.3 1.6 + - - +
268D TYR* 2.2 42.0 + - - +
346D ALA* 2.9 13.3 + - - -
347D ARG 3.7 1.3 - - - +
349D LEU* 1.3 76.4 - - - +
351D GLU* 1.3 56.9 + - - +
353D HIS* 3.8 7.6 - - - +
354D SER* 2.9 32.4 + - - -
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Residues in contact with GLU 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D ARG* 2.9 33.1 + - + +
348D GLN* 3.4 33.2 - - - +
349D LEU 3.2 0.2 - - - -
350D ASP* 1.3 77.4 - - - +
352D ASP* 1.3 58.2 + - - +
354D SER* 3.8 3.4 - - - -
355D LEU* 2.9 28.3 + - - +
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Residues in contact with ASP 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D GLN 2.9 18.2 + - - +
349D LEU* 4.1 2.9 - - + +
351D GLU* 1.3 74.3 - - - +
353D HIS* 1.3 57.0 - - - +
355D LEU* 3.3 8.2 + - - +
356D LEU* 2.9 30.4 + - - +
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Residues in contact with HIS 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D LEU* 2.8 21.0 + - + +
350D ASP* 3.8 10.8 - - - +
352D ASP* 1.3 75.1 - - - +
354D SER* 1.3 61.1 + - - +
356D LEU* 3.2 5.8 + - - +
357D GLU* 2.9 32.2 + - - +
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Residues in contact with SER 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ASP 2.9 19.1 + - - -
351D GLU* 3.8 4.5 - - - -
353D HIS* 1.3 75.3 - - - +
355D LEU* 1.3 57.7 + - - +
357D GLU* 4.4 4.5 - - - +
358D ALA* 2.9 35.4 + - - +
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLU 2.9 16.5 + - - +
352D ASP* 3.6 9.4 - - - +
354D SER* 1.3 77.8 - - - +
356D LEU* 1.3 58.9 + - - +
358D ALA* 4.3 1.8 - - - -
359D LEU* 3.6 20.3 + - - +
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Residues in contact with LEU 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ASP 2.9 17.4 + - - +
353D HIS* 3.9 5.6 - - - +
354D SER 3.2 0.2 - - - -
355D LEU* 1.3 76.6 - - - +
357D GLU* 1.3 60.8 + - - +
359D LEU* 3.7 14.9 - - - +
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Residues in contact with GLU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D HIS 2.9 17.8 + - - +
354D SER* 4.2 4.0 - - - +
356D LEU* 1.3 76.6 - - - +
358D ALA* 1.3 57.9 + - - +
359D LEU 3.1 11.4 + - - +
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Residues in contact with ALA 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D SER* 2.9 18.8 + - - +
355D LEU* 4.3 3.1 - - - +
357D GLU* 1.3 74.4 - - - +
359D LEU* 1.3 61.1 + - - +
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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