Contacts of the helix formed by residues 345 - 358 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A TYR 4.2 2.5 - - - -
269A ASP* 3.3 19.5 - - - +
270A LEU 3.1 21.1 - - - +
271A ALA* 3.5 15.3 - - + -
344A CYS* 1.3 76.5 - - - +
346A ALA* 1.3 52.8 + - - +
347A ARG* 3.2 14.3 - - - +
348A GLN* 2.8 41.7 + - - +
349A LEU* 2.5 36.5 + - - +
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Residues in contact with ALA 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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196A LEU* 4.8 16.6 - - + +
261A ILE* 4.2 22.0 - - + +
267A LEU 5.0 0.9 - - - +
268A TYR* 3.2 39.0 + - + +
270A LEU 3.8 5.2 + - - +
344A CYS 3.7 1.6 + - - -
345A THR* 1.3 72.0 - - - +
347A ARG* 1.3 56.1 + - - +
349A LEU* 3.3 14.2 - - + +
350A ASP* 2.9 24.9 + - - -
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Residues in contact with ARG 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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263A ALA 5.5 2.4 + - - -
268A TYR* 3.2 47.4 + - + +
269A ASP* 2.6 35.6 + - - +
345A THR* 3.0 11.2 - - - +
346A ALA* 1.3 75.0 - - - +
348A GLN* 1.3 60.4 + - + +
350A ASP* 3.1 6.1 + - - +
351A GLU* 2.9 46.9 + - + +
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Residues in contact with GLN 348 (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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344A CYS* 3.1 31.4 - - - +
345A THR* 2.8 31.2 + - - +
347A ARG* 1.3 71.9 - - + +
349A LEU* 1.3 59.4 + - - +
351A GLU* 3.4 25.6 - - + +
352A ASP* 2.9 32.1 + - - +
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Residues in contact with LEU 349 (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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191A LEU* 5.6 7.6 - - + -
194A GLY 6.2 0.2 - - - +
196A LEU* 4.3 17.3 - - + -
342A PRO* 3.9 33.4 - - + +
344A CYS* 3.2 31.9 - - - +
345A THR 2.5 30.2 + - - +
346A ALA* 3.3 16.8 - - + +
347A ARG 3.1 0.2 - - - -
348A GLN* 1.3 72.9 - - - +
350A ASP* 1.3 62.3 + - - +
352A ASP* 3.4 2.8 + - + +
353A HIS* 2.8 32.3 + - + +
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Residues in contact with ASP 350 (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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195A ARG* 4.7 18.7 + - - -
263A ALA* 5.3 1.4 - - - +
268A TYR* 2.2 42.4 + - - +
346A ALA 2.9 13.3 + - - +
347A ARG 3.7 0.7 - - - +
349A LEU* 1.3 76.6 - - - +
351A GLU* 1.3 58.6 + - - +
353A HIS* 3.8 7.4 - - - +
354A SER* 2.8 32.9 + - - -
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Residues in contact with GLU 351 (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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347A ARG* 2.9 34.3 + - + +
348A GLN* 3.4 34.1 - - - +
349A LEU 3.2 0.2 - - - -
350A ASP* 1.3 78.4 - - + +
352A ASP* 1.3 57.8 + - - +
354A SER* 3.3 4.0 + - - -
355A LEU* 2.9 28.4 + - - +
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Residues in contact with ASP 352 (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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348A GLN 2.9 18.6 + - - +
349A LEU* 4.1 2.5 - - + +
351A GLU* 1.3 75.2 - - - +
353A HIS* 1.3 58.1 + - - +
355A LEU* 3.3 8.0 + - - +
356A LEU* 2.9 30.9 + - - +
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Residues in contact with HIS 353 (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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349A LEU* 2.8 20.2 + - + +
350A ASP* 3.8 11.2 - - - +
352A ASP* 1.3 74.9 - - - +
354A SER* 1.3 60.8 + - - +
356A LEU* 3.2 5.7 + - - +
357A GLU* 2.9 31.4 + - - +
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Residues in contact with SER 354 (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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350A ASP 2.8 18.7 + - - -
351A GLU* 3.8 4.0 - - - -
353A HIS* 1.3 76.7 - - - +
355A LEU* 1.3 58.2 + - - +
357A GLU* 4.4 4.3 - - - +
358A ALA* 2.9 35.8 + - - +
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Residues in contact with LEU 355 (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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351A GLU 2.9 17.5 + - - +
352A ASP* 3.6 9.0 - - - +
354A SER* 1.3 79.3 - - - +
356A LEU* 1.3 58.4 + - - +
358A ALA* 4.3 2.2 - - - -
359A LEU* 3.6 19.4 + - - +
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Residues in contact with LEU 356 (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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352A ASP 2.9 17.0 + - - +
353A HIS* 3.2 5.6 + - - +
355A LEU* 1.3 77.2 - - - +
357A GLU* 1.3 61.6 + - - +
359A LEU* 3.7 14.3 - - - +
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Residues in contact with GLU 357 (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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353A HIS 2.9 17.8 + - - +
354A SER* 4.2 3.8 - - - +
356A LEU* 1.3 76.1 - - - +
358A ALA* 1.3 57.7 + - - +
359A LEU 3.1 10.4 + - - +
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Residues in contact with ALA 358 (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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354A SER* 2.9 18.8 + - - +
355A LEU* 4.3 2.5 - - - +
357A GLU* 1.3 74.6 - - - +
359A LEU* 1.3 60.7 + - - +
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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