Contacts of the helix formed by residues 350 - 358 (chain D) in PDB entry 3JCK
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 LEU 350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348D LEU 3.9 1.0 + - - -
349D SER* 1.3 69.1 + - - +
351D LYS* 1.3 56.6 + - + +
352D SER 2.7 0.9 + - - -
353D MET* 2.3 38.2 + - - +
354D ALA* 2.9 11.2 + - - -
361D VAL* 4.0 30.1 - - + -
364D LEU* 4.3 21.8 - - + -
365D ASP* 5.1 11.4 - - + +
368D LEU* 5.0 5.8 - - + -
381D ILE* 4.7 15.9 - - + -
382D ASP 5.1 0.2 - - - +
383D ARG* 5.5 5.8 - - + -
386D GLY* 2.8 39.0 + - - +
387D ILE 4.5 0.4 - - - +
388D VAL* 3.6 25.1 - - + -
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Residues in contact with LYS 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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349D SER* 3.4 19.9 + - - +
350D LEU* 1.3 78.2 - - + +
352D SER* 1.3 49.5 + - - +
354D ALA* 4.3 8.5 - - - -
355D SER* 2.7 39.3 + - - -
361D VAL* 3.9 19.7 - - + -
385D ASN 5.3 4.4 + - - -
386D GLY* 4.9 7.1 + - - -
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Residues in contact with SER 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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392C GLN* 2.6 40.6 + - - -
348D LEU* 4.5 2.9 - - - -
349D SER* 3.0 20.8 + - - -
350D LEU 2.7 4.2 + - - -
351D LYS* 1.3 74.8 - - - +
353D MET* 1.3 55.4 + - - -
355D SER* 2.3 24.6 + - - -
356D ALA* 2.9 13.7 + - - +
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Residues in contact with MET 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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338D TYR* 3.9 27.6 - - + -
341D LEU* 3.6 22.9 - - + -
342D LEU* 4.0 22.0 - - + -
348D LEU* 3.4 28.5 - - + -
349D SER 3.4 0.2 + - - -
350D LEU* 2.3 22.7 + - - +
352D SER* 1.3 68.7 - - - +
354D ALA* 1.3 66.9 + - - +
356D ALA* 2.8 18.9 + - - +
357D PHE* 2.9 24.3 + - + +
364D LEU* 3.6 21.8 - - + -
368D LEU* 4.1 13.5 - - + -
388D VAL* 4.8 13.9 - - - -
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Residues in contact with ALA 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 LEU 2.9 13.4 + - - +
351D LYS* 4.3 3.1 - - - -
353D MET* 1.3 72.6 - - - +
355D SER* 1.3 53.8 + - - +
357D PHE* 4.7 0.7 - - - +
358D GLY* 2.6 33.4 + - - -
359D VAL* 3.1 32.9 + - - +
360D SER 4.0 2.9 - - - +
361D VAL* 3.9 30.5 - - + +
364D LEU* 3.6 11.9 - - + +
84I TYR* 5.4 0.4 - - - -
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Residues in contact with SER 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 LYS 2.7 18.8 + - - -
352D SER* 2.3 32.1 + - - -
354D ALA* 1.3 75.5 - - - +
356D ALA* 1.3 65.5 + - - +
358D GLY* 3.1 11.4 + - - -
84I TYR* 4.3 17.5 + - - -
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Residues in contact with ALA 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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301D TYR* 4.0 19.5 - - + -
302D ALA* 3.2 27.0 - - - +
341D LEU* 5.1 6.7 - - + -
352D SER 3.5 8.7 - - - +
353D MET* 2.8 16.8 + - - +
355D SER* 1.3 81.5 + - - +
357D PHE* 1.3 67.0 + - + +
358D GLY* 3.0 0.5 + - - -
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Residues in contact with PHE 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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301D TYR* 3.4 46.5 - + + +
302D ALA* 4.2 11.3 - - - +
304D TYR* 5.2 2.9 - - + -
305D PHE* 4.1 36.1 - + + +
337D VAL* 3.3 26.0 - - + -
338D TYR* 3.8 31.6 - + - -
341D LEU* 4.0 24.7 - - + -
353D MET* 2.9 22.3 + - + +
354D ALA 4.2 1.3 - - - +
356D ALA* 1.3 74.4 - - + +
358D GLY* 1.3 63.4 + - - +
359D VAL* 4.3 7.6 - - + +
364D LEU* 4.4 10.3 - - + -
81I LEU* 4.0 12.5 - - - +
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Residues in contact with GLY 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 ALA 2.6 16.9 + - - -
355D SER 3.5 7.6 - - - -
356D ALA 3.0 4.8 + - - -
357D PHE* 1.3 74.6 - - - +
359D VAL* 1.3 61.4 + - - +
81I LEU* 3.4 15.8 - - - +
84I TYR* 3.6 34.8 - - - +
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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