Contacts of the helix formed by residues 352 - 363 (chain A) in PDB entry 1OJ7
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 SER 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LEU* 5.5 0.2 - - - +
276A MET* 4.2 5.2 - - - -
277A HIS* 2.7 40.2 + - - -
348A LEU* 5.4 2.6 - - - +
349A ASP* 4.7 0.2 + - - -
350A GLY* 3.0 5.4 + - - -
351A SER* 1.3 80.1 + - - +
353A ILE* 1.3 64.7 + - - +
354A PRO* 3.4 0.9 - - - -
355A ALA* 3.1 6.5 + - - +
356A LEU* 3.0 29.4 + - - +
372B HIS* 3.8 25.1 - - - -
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Residues in contact with ILE 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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343A LEU* 4.7 4.5 - - + -
350A GLY* 3.1 31.8 + - - +
352A SER* 1.3 77.2 - - - +
354A PRO* 1.3 72.3 - - + +
356A LEU* 3.0 13.0 + - + +
357A LEU* 3.0 24.9 + - + +
380A ARG* 4.0 26.7 - - + +
383A TYR* 3.7 45.3 - - + +
384A GLU* 3.7 28.3 - - + +
387A ARG* 4.4 5.4 - - - +
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Residues in contact with PRO 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 GLY 4.3 1.1 - - - +
351A SER* 3.5 16.8 - - - +
352A SER 3.7 0.2 - - - -
353A ILE* 1.3 96.1 - - + +
355A ALA* 1.3 60.5 + - - +
357A LEU* 3.2 14.2 + - + +
358A LYS* 3.1 30.1 + - + +
380A ARG* 4.0 19.7 - - - +
372B HIS 5.6 2.5 - - - +
373B ASP* 6.5 1.8 - - + -
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Residues in contact with ALA 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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276A MET* 3.7 16.7 - - + +
352A SER 3.1 10.7 + - - +
354A PRO* 1.3 78.8 - - - +
356A LEU* 1.3 61.9 + - - +
358A LYS* 3.3 12.5 + - - +
359A LYS* 3.2 18.0 + - - +
367B GLN* 3.7 39.1 - - + +
372B HIS* 3.7 15.3 + - + +
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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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272A GLU* 3.4 39.4 - - + +
273A LEU* 3.7 25.8 - - + +
276A MET* 3.8 24.0 - - + -
277A HIS* 4.6 0.9 - - + -
343A LEU* 6.1 1.3 - - + -
352A SER* 3.0 29.5 + - - +
353A ILE* 3.5 17.0 - - + +
355A ALA* 1.3 76.7 - - - +
357A LEU* 1.3 58.7 + - - +
359A LYS* 3.2 6.4 + - - +
360A LEU* 2.9 31.0 + - - +
383A TYR* 3.9 29.2 - - + +
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Residues in contact with LEU 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 ILE* 3.0 19.8 + - + +
354A PRO* 3.2 7.8 + - + +
356A LEU* 1.3 73.2 - - - +
358A LYS* 1.3 62.3 + - - +
360A LEU* 3.3 13.7 + - + +
361A GLU* 3.0 28.8 + - - +
376A LEU* 3.7 35.4 - - + +
379A SER* 4.0 12.6 - - - -
380A ARG* 3.5 65.7 - - + +
383A TYR* 4.2 8.3 - - + -
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Residues in contact with LYS 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 PRO* 3.1 22.4 + - + +
355A ALA* 3.6 12.6 - - - +
356A LEU 3.3 0.2 - - - -
357A LEU* 1.3 76.1 - - - +
359A LYS* 1.3 59.3 + - + +
361A GLU* 3.5 16.6 + - - +
362A GLU* 3.0 27.8 + - - +
375B THR* 4.4 24.0 - - + -
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Residues in contact with LYS 359 (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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157A THR* 2.9 20.9 + - - -
158A GLY* 3.6 18.6 + - - +
159A ASP* 2.9 22.8 + - - -
272A GLU* 3.4 20.0 - - + +
276A MET* 4.0 15.3 - - + -
355A ALA 3.2 15.2 + - - +
356A LEU* 3.5 9.4 - - - +
358A LYS* 1.3 75.0 - - + +
360A LEU* 1.3 65.4 + - - +
362A GLU* 3.1 25.9 + - - +
363A HIS* 3.0 39.2 + - + -
366B THR* 5.0 6.2 + - - -
367B GLN* 4.7 16.4 - - - +
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Residues in contact with LEU 360 (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 MET 4.0 13.5 - - - +
269A LEU* 3.5 31.2 - - + -
272A GLU* 3.5 25.8 + - + +
356A LEU 2.9 14.8 + - - +
357A LEU* 3.6 17.5 - - + +
359A LYS* 1.3 76.2 - - - +
361A GLU* 1.3 57.2 + - - +
363A HIS 3.2 2.4 + - - -
364A GLY 3.1 4.3 + - - -
365A MET* 2.8 60.4 + - + +
368A LEU* 4.7 0.4 - - + -
376A LEU* 4.0 4.7 - - + -
379A SER* 3.9 18.6 - - - +
383A TYR* 4.0 12.3 - - + +
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Residues in contact with GLU 361 (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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357A LEU 3.0 16.7 + - - +
358A LYS* 3.6 18.9 + - - +
360A LEU* 1.3 75.5 - - - +
362A GLU* 1.3 63.9 + - - +
364A GLY* 3.1 13.7 + - - -
366A THR* 3.9 19.2 - - + +
376A LEU* 3.8 25.6 - - + +
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Residues in contact with GLU 362 (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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154A ARG* 5.8 0.9 + - - -
159A ASP* 3.9 14.2 - - - +
358A LYS 3.0 17.1 + - - +
359A LYS* 3.1 35.6 + - - +
361A GLU* 1.3 76.7 - - - +
363A HIS* 1.3 69.6 + - + +
364A GLY 3.3 1.1 + - - -
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Residues in contact with HIS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASP* 2.6 45.7 + - + -
160A LYS 4.4 3.7 + - - -
161A GLN* 3.7 36.0 + - + +
272A GLU* 2.7 33.9 + - - +
359A LYS* 3.0 21.3 + - + +
360A LEU 3.8 3.6 - - - +
361A GLU 3.1 0.4 - - - -
362A GLU* 1.3 89.0 + - + +
364A GLY* 1.3 61.8 + - - +
365A MET* 3.3 29.0 + - + +
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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