Contacts of the helix formed by residues 375 - 386 (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 THR 375 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366D THR* 3.2 17.5 - - - +
367D GLN* 4.9 7.9 - - + -
372D HIS 5.5 0.2 - - - +
373D ASP* 3.2 13.9 + - - +
374D ILE* 1.3 75.3 - - - +
376D LEU* 1.3 68.0 + - - +
377D ASP* 4.0 7.7 + - - +
378D VAL* 3.0 20.8 + - - +
379D SER* 2.9 22.8 + - - -
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Residues in contact with LEU 376 (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* 3.7 35.2 - - + +
360D LEU* 4.0 24.7 - - + -
361D GLU* 3.9 37.2 - - + +
365D MET 4.2 12.3 - - - +
366D THR* 4.1 15.1 + - + -
375D THR* 1.3 75.8 - - - +
377D ASP* 1.3 61.9 + - - +
379D SER* 3.3 4.5 + - - -
380D ARG* 2.9 30.2 + - - +
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Residues in contact with ASP 377 (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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375D THR* 3.2 7.2 + - - +
376D LEU* 1.3 77.1 - - - +
378D VAL* 1.3 65.2 + - + +
380D ARG* 2.6 44.3 + - - +
381D ARG* 3.2 35.6 + - - +
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Residues in contact with VAL 378 (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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295D GLU* 3.7 28.9 - - + +
296D LYS* 4.8 4.9 - - + +
373D ASP 4.0 9.0 - - - +
374D ILE* 4.0 21.5 - - + -
375D THR* 3.0 30.6 + - - +
377D ASP* 1.3 75.5 - - + +
379D SER* 1.3 59.7 + - - +
381D ARG* 3.1 22.5 + - - +
382D ILE* 2.9 30.6 + - + +
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Residues in contact with SER 379 (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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269D LEU* 3.4 29.8 - - - +
357D LEU* 3.9 14.1 - - - -
360D LEU* 4.0 6.3 - - - +
365D MET 4.9 1.6 + - - -
368D LEU* 4.1 4.3 - - - +
374D ILE* 3.5 12.6 + - - +
375D THR 2.9 15.3 + - - -
376D LEU* 3.6 9.3 - - - -
378D VAL* 1.3 73.6 - - - +
380D ARG* 1.3 64.3 + - - +
382D ILE* 3.3 10.7 + - - +
383D TYR* 2.9 28.8 + - - -
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Residues in contact with ARG 380 (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* 4.4 10.3 - - + +
357D LEU* 3.6 33.9 - - + +
376D LEU* 2.9 17.0 + - - +
377D ASP* 2.6 49.6 + - - +
379D SER* 1.3 75.0 - - - +
381D ARG* 1.3 55.9 + - - +
383D TYR* 3.4 1.6 + - - +
384D GLU* 2.9 57.4 + - - +
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Residues in contact with ARG 381 (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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295D GLU* 2.8 47.7 + - - +
377D ASP* 3.2 29.0 + - - +
378D VAL* 3.1 25.2 + - - +
380D ARG* 1.3 78.9 - - - +
382D ILE* 1.3 58.4 + - - +
384D GLU* 3.5 11.4 + - - +
385D ALA* 3.0 30.5 + - + +
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Residues in contact with ILE 382 (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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269D LEU* 3.8 24.5 - - + -
288D VAL* 4.1 12.8 - - + -
291D ALA* 3.6 9.0 - - + +
292D LEU* 3.9 46.2 - - + +
295D GLU* 3.8 25.4 - - + -
296D LYS* 5.2 0.2 - - + -
374D ILE* 4.3 11.9 - - + -
378D VAL* 2.9 30.9 + - + +
379D SER 3.6 6.1 - - - +
380D ARG 3.2 0.2 - - - -
381D ARG* 1.3 73.7 - - - +
383D TYR* 1.3 68.2 + - + +
385D ALA* 3.2 4.3 + - - -
386D ALA* 3.1 21.3 + - - +
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Residues in contact with TYR 383 (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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269D LEU* 2.6 56.0 + - + +
272D GLU* 3.8 13.2 - - - +
273D LEU* 4.1 23.1 - - + -
287D ILE* 6.4 0.4 - - + -
288D VAL* 4.4 9.0 - - + -
343D LEU* 3.7 13.9 - - + +
353D ILE* 3.6 29.8 - - + -
356D LEU* 3.8 26.9 - - + +
357D LEU* 4.2 8.7 - - + -
360D LEU* 4.1 19.0 - - + +
379D SER 2.9 22.6 + - - +
380D ARG 3.8 2.5 - - - +
382D ILE* 1.3 76.2 - - + +
384D GLU* 1.3 62.2 + - - +
386D ALA* 3.0 19.9 + - + +
387D ARG* 3.5 6.2 + - - +
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Residues in contact with GLU 384 (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* 3.9 17.1 - - + +
380D ARG* 2.9 44.0 + - + +
381D ARG* 3.8 11.0 - - - +
383D TYR* 1.3 76.8 - - - +
385D ALA* 1.3 61.3 + - - +
386D ALA 3.3 0.3 + - - -
387D ARG* 2.9 56.2 + - - +
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Residues in contact with ALA 385 (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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291D ALA* 4.3 16.6 - - + +
294D ASN* 5.8 6.3 - - - +
331D ARG* 5.5 5.0 + - - -
342D HIS* 5.0 4.9 - - - -
381D ARG* 3.0 18.5 + - + +
382D ILE* 3.2 6.3 + - - +
384D GLU* 1.3 75.9 - - - +
386D ALA* 1.3 59.1 + - - +
387D ARG 3.3 4.8 + - - +
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Residues in contact with ALA 386 (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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287D ILE* 3.6 35.0 - - + +
288D VAL* 5.0 4.0 - - + -
291D ALA* 4.1 7.4 - - + -
331D ARG* 6.3 0.9 - - - +
341D THR 5.1 2.2 - - - -
342D HIS* 3.4 10.0 - - - -
343D LEU* 2.9 26.5 + - + -
382D ILE 3.1 12.0 + - - +
383D TYR* 3.0 16.2 + - + +
385D ALA* 1.3 75.0 - - - +
387D ARG* 1.3 62.6 + - - +
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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