Contacts of the helix formed by residues 345 - 358 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B TYR 4.2 1.8 - - - -
269B ASP* 3.3 19.7 - - - +
270B LEU 3.1 21.1 - - - +
271B ALA* 3.5 14.8 - - + -
344B CYS* 1.3 75.7 - - - +
346B ALA* 1.3 54.0 - - - +
347B ARG* 3.2 15.3 - - + +
348B GLN* 2.8 41.0 + - - +
349B LEU* 2.5 37.5 + - - +
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Residues in contact with ALA 346 (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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196B LEU* 4.8 16.0 - - + +
261B ILE* 4.2 22.0 - - + +
267B LEU 5.0 1.1 - - - +
268B TYR* 3.2 38.9 + - + +
270B LEU 3.8 5.1 + - - -
344B CYS 3.7 1.6 + - - -
345B THR* 1.3 72.6 - - - +
347B ARG* 1.3 56.5 + - - +
349B LEU* 3.3 14.8 - - + +
350B ASP* 2.9 25.3 + - - -
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Residues in contact with ARG 347 (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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263B ALA 5.5 2.2 + - - -
268B TYR* 3.2 47.3 + - + +
269B ASP* 2.6 35.8 + - - +
345B THR* 3.0 11.8 - - - +
346B ALA* 1.3 75.8 - - - +
348B GLN* 1.3 60.1 + - + +
350B ASP* 3.1 6.2 + - - +
351B GLU* 2.9 46.7 + - + +
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Residues in contact with GLN 348 (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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344B CYS* 3.1 30.2 - - - +
345B THR* 2.8 30.1 + - - +
347B ARG* 1.3 71.9 - - + +
349B LEU* 1.3 60.9 + - - +
351B GLU* 3.4 25.2 - - - +
352B ASP* 2.9 32.2 + - - +
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Residues in contact with LEU 349 (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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191B LEU* 5.6 7.4 - - + -
194B GLY 6.2 0.4 - - - +
196B LEU* 4.3 16.2 - - + -
342B PRO* 3.9 33.4 - - + +
344B CYS* 3.2 31.9 - - - +
345B THR 2.5 31.1 + - - +
346B ALA* 3.3 16.2 - - + +
348B GLN* 1.3 72.5 - - - +
350B ASP* 1.3 60.7 + - - +
352B ASP* 3.8 3.2 - - + +
353B HIS* 2.8 31.9 + - + +
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Residues in contact with ASP 350 (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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195B ARG* 4.7 18.6 + - - -
263B ALA* 5.3 1.9 + - - +
268B TYR* 2.2 42.4 + - - +
346B ALA 2.9 13.3 + - - -
347B ARG 3.7 1.3 - - - +
349B LEU* 1.3 76.1 - - - +
351B GLU* 1.3 57.3 + - - +
353B HIS* 3.8 7.8 - - - +
354B SER* 2.9 32.6 + - - -
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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
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347B ARG* 2.9 34.0 + - + +
348B GLN* 3.4 32.9 - - - +
350B ASP* 1.3 79.6 - - - +
352B ASP* 1.3 58.0 + - - +
354B SER* 3.8 4.0 - - - -
355B LEU* 2.9 27.8 + - - +
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Residues in contact with ASP 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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348B GLN 2.9 18.6 + - - +
349B LEU* 4.1 3.4 - - + +
351B GLU* 1.3 73.7 - - - +
353B HIS* 1.3 57.7 + - - +
355B LEU* 3.3 8.4 + - - +
356B LEU* 2.9 30.3 + - - +
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Residues in contact with HIS 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 LEU* 2.8 21.2 + - + +
350B ASP* 3.8 10.8 - - - +
352B ASP* 1.3 74.5 - - - +
354B SER* 1.3 60.5 + - - +
356B LEU* 3.2 5.4 + - - +
357B GLU* 2.9 31.8 + - - +
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Residues in contact with SER 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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350B ASP 2.9 17.9 + - - -
351B GLU* 3.8 4.3 - - - -
353B HIS* 1.3 76.0 - - - +
355B LEU* 1.3 57.4 + - - +
357B GLU* 4.6 4.5 - - - -
358B ALA* 2.9 35.8 + - - +
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Residues in contact with LEU 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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351B GLU 2.9 17.2 + - - +
352B ASP* 3.6 9.6 - - - +
353B HIS 3.3 0.2 - - - -
354B SER* 1.3 78.8 - - - +
356B LEU* 1.3 59.4 + - - +
358B ALA* 4.3 1.6 - - - -
359B LEU* 3.6 19.4 + - - +
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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 ASP 2.9 17.3 + - - +
353B HIS* 3.9 4.9 - - - +
355B LEU* 1.3 76.4 - - - +
357B GLU* 1.3 61.5 + - - +
359B LEU* 3.7 15.1 - - - +
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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 HIS 2.9 17.0 + - - +
354B SER* 4.2 4.5 - - - +
356B LEU* 1.3 77.3 - - - +
358B ALA* 1.3 57.1 + - - +
359B LEU 3.1 11.3 + - - +
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Residues in contact with ALA 358 (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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354B SER* 2.9 19.2 + - - +
355B LEU* 4.3 3.6 - - - +
357B GLU* 1.3 75.3 - - - +
359B LEU* 1.3 61.2 + - - +
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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