Contacts of the helix formed by residues 352 - 363 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273D LEU* 5.2 0.3 - - - +
276D MET* 3.9 8.5 - - - -
277D HIS* 2.7 40.7 + - - -
348D LEU* 5.7 2.1 - - - +
349D ASP* 4.7 0.2 + - - -
350D GLY* 4.2 5.9 + - - -
351D SER* 1.3 80.5 + - - +
353D ILE* 1.3 59.0 + - - +
354D PRO* 3.4 1.1 - - - -
355D ALA* 3.1 12.2 + - - +
356D LEU* 2.9 35.0 + - - +
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Residues in contact with ILE 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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343D LEU* 4.8 4.0 - - + -
350D GLY* 3.2 32.5 - - - +
351D SER 3.2 0.4 - - - -
352D SER* 1.3 75.6 - - - +
354D PRO* 1.3 74.3 - - + +
356D LEU* 3.0 12.8 + - + +
357D LEU* 3.0 37.2 + - + +
380D ARG* 4.4 14.1 - - + +
383D TYR* 3.6 54.3 - - + +
384D GLU* 3.7 18.6 - - + +
387D ARG* 4.5 3.1 - - + +
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Residues in contact with PRO 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 GLY 4.5 1.3 - - - +
351D SER* 3.2 18.4 - - - +
352D SER 3.5 0.9 - - - -
353D ILE* 1.3 97.5 - - + +
355D ALA* 1.3 60.7 + - - +
357D LEU* 3.3 13.2 + - + +
358D LYS* 3.2 28.1 + - + +
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Residues in contact with ALA 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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276D MET* 3.6 24.9 - - + +
351D SER 5.2 0.4 + - - +
352D SER* 3.1 14.1 + - - +
354D PRO* 1.3 76.7 - - - +
356D LEU* 1.3 63.7 + - - +
358D LYS* 3.4 10.1 + - - +
359D LYS* 3.3 19.1 + - - +
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Residues in contact with LEU 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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272D GLU* 3.3 41.1 - - + +
273D LEU* 3.5 26.9 - - + +
276D MET* 3.6 22.7 - - + -
277D HIS* 4.8 0.2 - - - +
343D LEU* 6.2 1.1 - - + -
352D SER* 2.9 30.0 + - - +
353D ILE* 3.4 18.2 - - + +
355D ALA* 1.3 75.8 - - - +
357D LEU* 1.3 58.1 + - - +
359D LYS* 3.2 6.2 + - - +
360D LEU* 2.9 31.8 + - - +
383D TYR* 3.8 26.0 - - + +
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Residues in contact with LEU 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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353D ILE* 3.0 22.6 + - + +
354D PRO* 3.6 11.9 - - + +
355D ALA 3.3 0.2 - - - -
356D LEU* 1.3 72.2 - - - +
358D LYS* 1.3 61.1 + - + +
360D LEU* 3.3 14.0 + - + +
361D GLU* 2.9 29.8 + - - +
376D LEU* 3.7 33.3 - - + +
379D SER* 3.9 13.7 - - - -
380D ARG* 3.6 59.5 - - + +
383D TYR* 4.2 6.7 - - + -
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Residues in contact with LYS 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 PRO* 3.2 20.1 + - + +
355D ALA* 3.6 11.9 - - - +
356D LEU 3.3 0.2 - - - -
357D LEU* 1.3 77.0 - - + +
359D LYS* 1.3 58.0 + - + +
361D GLU* 3.4 17.1 + - - +
362D GLU* 3.0 27.9 + - - +
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Residues in contact with LYS 359 (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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157D THR* 2.7 24.7 + - - -
158D GLY* 3.5 17.5 - - - +
159D ASP* 2.7 25.7 + - - -
272D GLU* 3.4 19.3 - - - +
276D MET* 4.4 13.2 - - + -
355D ALA 3.3 11.3 + - - +
356D LEU* 3.2 10.6 + - - +
358D LYS* 1.3 78.0 - - + +
360D LEU* 1.3 64.0 + - - +
362D GLU* 2.8 28.3 + - - +
363D HIS* 3.0 38.7 + - + -
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Residues in contact with LEU 360 (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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268D MET 4.0 12.6 - - - +
269D LEU* 3.5 31.0 - - + -
272D GLU* 3.5 26.4 + - + -
356D LEU 2.9 11.9 + - - +
357D LEU* 3.3 23.3 + - + +
359D LYS* 1.3 77.1 - - - +
361D GLU* 1.3 60.3 + - - +
363D HIS 3.2 2.3 + - - -
364D GLY 3.1 4.3 + - - -
365D MET* 2.9 55.5 + - + +
368D LEU* 4.7 0.4 - - + -
376D LEU* 4.0 9.9 - - + -
379D SER* 4.0 16.8 - - - +
383D TYR* 4.1 7.6 - - + +
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Residues in contact with GLU 361 (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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357D LEU 2.9 17.0 + - - +
358D LYS* 3.6 18.1 + - - +
360D LEU* 1.3 76.8 - - - +
362D GLU* 1.3 61.7 + - - +
364D GLY* 3.2 12.5 + - - -
366D THR* 3.9 17.5 - - + +
376D LEU* 3.9 24.1 - - + +
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Residues in contact with GLU 362 (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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157D THR* 6.1 0.2 - - - -
159D ASP* 4.0 7.6 - - - +
358D LYS 3.0 17.8 + - - +
359D LYS* 2.8 44.4 + - - +
361D GLU* 1.3 76.3 - - - +
363D HIS* 1.3 68.3 + - + +
364D GLY 3.3 1.1 + - - -
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Residues in contact with HIS 363 (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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159D ASP* 2.6 39.8 + - - -
160D LYS 4.4 3.7 + - - -
161D GLN* 3.5 38.7 + - + +
272D GLU* 2.7 33.2 + - - +
359D LYS* 3.0 22.2 + - + +
360D LEU 3.2 3.3 + - - +
362D GLU* 1.3 87.8 - - + +
364D GLY* 1.3 61.6 + - - +
365D MET* 3.3 31.0 + - + +
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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