Contacts of the helix formed by residues 345 - 355 (chain A) in PDB entry 3C5F
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 GLY 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A SER* 4.4 7.7 - - - -
343A GLY 4.1 2.0 + - - -
344A ALA* 1.3 75.6 - - - +
346A THR* 1.3 60.8 + - - -
347A LYS 3.3 2.9 - - - -
348A THR* 3.3 7.8 + - - -
349A ALA* 3.0 27.9 + - - +
801A NA 4.6 0.4 - - - -
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Residues in contact with THR 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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268A SER 3.2 26.9 - - - +
269A VAL* 3.3 19.7 - - - +
271A GLY* 3.4 24.6 - - - +
339A SER* 5.2 4.7 - - - -
345A GLY* 1.3 69.0 - - - -
347A LYS* 1.3 67.8 + - - +
349A ALA* 3.7 6.7 - - - +
350A GLN* 2.9 40.2 + - - +
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Residues in contact with LYS 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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345A GLY 3.3 0.6 - - - -
346A THR* 1.3 82.5 + - - +
348A THR* 1.3 59.9 + - - +
350A GLN* 3.4 22.0 + - - +
351A MET* 3.0 26.5 + - - +
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Residues in contact with THR 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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343A GLY 5.1 0.2 + - - -
344A ALA* 4.1 2.2 - - + -
345A GLY 3.3 18.0 + - - -
346A THR 3.3 0.2 - - - -
347A LYS* 1.3 76.8 - - - +
349A ALA* 1.3 66.8 + - - +
351A MET* 3.2 15.2 + - + +
352A TRP* 2.9 65.5 + - + +
373A GLN* 4.0 19.0 + - - +
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Residues in contact with ALA 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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269A VAL 5.2 0.9 - - - +
335A LEU* 3.6 28.4 - - + +
338A PHE* 3.8 31.6 - - + -
339A SER* 4.3 4.7 - - - +
344A ALA* 5.4 0.4 - - - +
345A GLY 3.0 16.5 + - - +
346A THR* 3.7 8.7 - - - +
348A THR* 1.3 77.5 - - - +
350A GLN* 1.3 57.8 + - - +
352A TRP* 3.3 3.7 + - - +
353A TYR* 2.9 29.5 + - - +
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Residues in contact with GLN 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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269A VAL 5.5 1.1 - - - +
270A GLN* 3.5 24.4 + - - -
271A GLY* 4.6 2.2 - - - -
335A LEU* 4.0 20.4 - - + -
346A THR* 2.9 31.4 + - - +
347A LYS* 3.5 23.2 + - - +
349A ALA* 1.3 78.0 - - - +
351A MET* 1.3 63.9 + - - +
353A TYR* 3.1 3.6 + - - +
354A GLN* 2.9 37.5 + - + +
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Residues in contact with MET 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 LYS 3.0 15.3 + - - +
348A THR* 3.5 20.0 - - + +
350A GLN* 1.3 75.4 - - - +
352A TRP* 1.3 90.3 + - + +
354A GLN* 3.1 13.8 + - - +
355A GLN* 3.1 44.9 + - + +
368A SER* 4.9 11.0 - - - +
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Residues in contact with TRP 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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338A PHE* 3.7 32.8 - + + -
341A ILE* 3.8 24.7 - - + -
344A ALA* 3.9 17.9 - - + -
348A THR* 2.9 39.6 + - + +
351A MET* 1.3 94.0 - - + +
353A TYR* 1.3 60.7 + - - +
355A GLN* 3.3 24.9 + - - -
356A GLY 3.4 0.2 + - - -
357A PHE* 3.1 42.0 + + + +
363A ILE* 3.5 19.5 - - + -
367A ALA* 3.6 15.0 - - + +
368A SER 3.6 11.7 + - - +
369A LEU* 3.6 32.5 - - + -
373A GLN* 4.0 9.0 - - + -
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Residues in contact with TYR 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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330A GLU* 4.5 11.1 + - - +
331A SER* 3.4 40.8 + - - -
334A VAL* 3.7 29.2 - - + -
335A LEU* 4.0 13.7 - - + -
338A PHE* 4.2 2.0 - - + -
349A ALA 2.9 17.1 + - - +
350A GLN* 3.1 4.9 + - - +
352A TRP* 1.3 76.4 - - - +
354A GLN* 1.3 68.9 + - + +
356A GLY* 3.1 9.9 + - - -
357A PHE 4.0 4.9 - - - -
358A ARG* 3.2 56.5 + - - -
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Residues in contact with GLN 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 GLN* 2.9 26.8 + - + +
351A MET* 3.1 12.5 + - - +
353A TYR* 1.3 75.9 - - + +
355A GLN* 1.3 59.2 + - + +
356A GLY* 3.0 9.8 + - - -
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Residues in contact with GLN 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 MET* 3.1 33.8 + - + +
352A TRP* 3.3 35.5 - - - +
353A TYR 3.2 0.4 - - - -
354A GLN* 1.3 76.6 - - + +
356A GLY* 1.3 57.5 + - - +
357A PHE* 3.4 30.9 + - + -
366A GLN 5.8 0.4 + - - -
368A SER* 5.8 3.3 + - - +
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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