Contacts of the helix formed by residues 372 - 383 (chain D) in PDB entry 1OEY
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 TYR 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371D PRO* 1.3 71.0 - - - +
373D SER* 1.3 56.8 + - - +
375D VAL* 3.2 1.0 + - - -
376D ARG* 2.7 86.0 + - + +
390D THR 4.5 2.8 + - - -
391D LYS* 5.5 0.9 - - - -
392D LEU* 4.8 8.1 + - + -
405D LEU* 3.3 44.7 + - + -
406D SER* 3.6 20.4 - - - +
407D GLU* 3.6 45.3 - - + +
410D MSE 3.6 19.3 - - + +
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Residues in contact with SER 373 (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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371D PRO* 3.1 15.5 - - - +
372D TYR* 1.3 85.3 - - - +
374D GLN* 1.3 59.8 + - - +
376D ARG* 3.8 4.9 + - - +
377D ASP* 3.2 26.3 + - - +
387D LEU* 5.3 1.2 - - - +
407D GLU* 5.3 9.9 - - - +
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Residues in contact with GLN 374 (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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370D LEU* 3.8 28.0 - - + -
371D PRO* 3.1 23.3 + - + +
373D SER* 1.3 78.9 + - - +
375D VAL* 1.3 65.7 + - - +
377D ASP* 3.4 16.8 + - - +
378D MSE 3.2 44.6 + - + +
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Residues in contact with VAL 375 (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 LEU* 4.2 14.6 - - + -
366D THR* 5.3 0.9 - - - +
370D LEU* 4.1 10.8 - - + -
371D PRO 3.1 13.0 + - - +
372D TYR 3.7 5.2 - - - +
374D GLN* 1.3 75.7 - - - +
376D ARG* 1.3 64.8 + - - +
378D MSE 3.4 7.7 - - - +
379D VAL* 3.2 23.7 + - + +
392D LEU* 4.3 4.7 - - + -
405D LEU* 4.2 21.3 - - + -
410D MSE 3.9 20.0 - - + -
414D TRP* 3.9 24.0 - - + -
424D LEU* 4.2 17.9 - - + -
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Residues in contact with ARG 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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372D TYR* 2.7 63.9 + - + +
373D SER* 4.1 5.6 - - - +
375D VAL* 1.3 73.6 - - - +
377D ASP* 1.3 57.5 + - - +
379D VAL* 4.0 1.6 - - - +
380D SER* 3.0 29.5 + - - -
387D LEU* 3.1 40.6 + - + +
388D GLU* 3.7 23.2 + - - +
390D THR* 3.1 31.2 + - - +
391D LYS* 4.6 8.5 - - - +
392D LEU* 4.1 12.8 - - + -
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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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373D SER 3.2 16.4 + - - +
374D GLN* 3.7 19.9 + - - +
375D VAL 3.2 0.8 - - - -
376D ARG* 1.3 81.0 - - - +
378D MSE 1.3 59.1 + - - +
380D SER* 3.2 5.4 + - - -
381D LYS* 2.9 60.0 + - - +
387D LEU* 3.8 20.8 - - + +
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Residues in contact with MSE 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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354D LEU* 4.5 9.0 - - - -
364D MSE 4.0 13.6 - - - +
365D LYS 4.4 13.5 - - - +
366D THR* 3.7 24.2 - - - -
367D GLN* 6.0 0.9 - - - +
370D LEU* 4.1 19.3 - - + -
374D GLN* 3.2 31.8 + - + +
375D VAL* 3.4 14.6 - - - +
377D ASP* 1.3 79.0 - - - +
379D VAL* 1.3 64.6 + - + +
381D LYS* 3.4 10.7 + - - +
382D LYS* 2.9 28.1 + - - +
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Residues in contact with VAL 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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354D LEU* 4.0 15.7 - - + -
356D VAL* 4.0 18.2 - - + -
364D MSE 3.9 22.9 - - + -
375D VAL* 3.2 22.1 + - + +
376D ARG 4.0 2.2 - - - +
378D MSE 1.3 74.6 - - + +
380D SER* 1.3 67.9 + - - +
382D LYS* 3.2 0.5 + - - +
383D LEU* 3.1 44.9 + - + +
390D THR* 5.4 2.7 - - - -
392D LEU* 3.9 29.4 - - + -
424D LEU* 5.0 1.1 - - + -
426D CYS* 4.9 1.3 - - - -
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Residues in contact with SER 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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376D ARG 3.0 16.9 + - - -
377D ASP* 3.2 10.9 + - - -
379D VAL* 1.3 78.6 - - - +
381D LYS* 1.3 63.1 + - - +
383D LEU 3.5 0.3 + - - -
384D GLU* 3.1 3.6 + - - -
385D LEU* 2.6 51.6 + - - +
387D LEU* 3.6 22.0 + - - +
390D THR* 3.7 23.6 - - - -
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Residues in contact with LYS 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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377D ASP* 2.9 47.6 + - - +
378D MSE 3.7 8.1 - - - +
379D VAL 3.2 0.2 - - - -
380D SER* 1.3 76.3 - - - +
382D LYS* 1.3 65.8 + - - +
384D GLU* 3.3 17.1 + - - +
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Residues in contact with LYS 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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362D VAL* 4.0 18.2 - - + -
363D VAL 4.1 12.1 + - - -
364D MSE 3.9 34.5 - - + +
378D MSE 2.9 18.2 + - - +
379D VAL 3.2 4.5 + - - +
381D LYS* 1.3 79.2 - - - +
383D LEU* 1.3 58.9 + - + +
384D GLU* 3.3 6.3 + - - +
298M LEU* 3.3 36.0 - - + +
299M SER* 3.7 13.9 + - - -
301M GLU* 5.7 1.6 + - - +
302M ASP* 2.8 41.8 + - - -
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Residues in contact with LEU 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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356D VAL* 4.3 5.8 - - + -
358D TYR* 3.9 34.2 - - + -
360D TYR* 3.6 44.6 + - + +
362D VAL* 4.0 22.0 - - + -
379D VAL* 3.1 34.5 + - + +
380D SER* 4.3 0.4 - - - +
382D LYS* 1.3 77.0 - - + +
384D GLU* 1.3 71.8 + - - +
385D LEU* 3.2 22.0 + - + +
426D CYS* 4.0 15.3 - - - -
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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