Contacts of the helix formed by residues 371 - 382 (chain D) in PDB entry 3OX4
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 ASP 371 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D LEU* 3.5 9.4 - - - -
370D GLY* 1.3 74.2 - - - +
372D GLN* 1.3 65.9 + - + +
373D LYS* 3.0 26.9 + - - +
374D GLU* 3.0 26.8 + - - +
375D VAL* 3.1 22.2 + - - +
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Residues in contact with GLN 372 (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 PRO* 2.9 15.3 + - - -
354D ALA* 3.5 6.1 - - - +
355D ASP* 2.8 50.8 - - - +
358D LEU* 3.3 17.5 - - + +
371D ASP* 1.3 74.0 - - + +
373D LYS* 1.3 61.8 + - + +
375D VAL* 3.8 0.4 + - - -
376D GLU* 2.8 62.9 + - - +
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Residues in contact with LYS 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 ASP* 3.0 12.4 + - - +
372D GLN* 1.3 78.2 - - + +
374D GLU* 1.3 67.2 + - + +
376D GLU* 3.1 26.5 + - - +
377D GLU* 3.1 19.7 + - + +
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Residues in contact with GLU 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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291D TYR* 2.7 40.3 + - + +
368D ARG* 3.5 23.1 + - - -
369D GLN 4.6 0.3 - - - +
370D GLY* 3.1 14.4 - - - -
371D ASP* 3.0 28.0 + - - +
373D LYS* 1.3 75.0 - - + +
375D VAL* 1.3 60.0 + - - +
377D GLU* 2.9 39.4 + - - +
378D LEU* 3.0 15.8 + - - +
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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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261D TYR* 3.9 30.1 - - + +
265D MET* 4.2 10.5 - - + -
291D TYR* 5.7 0.2 - - - +
354D ALA* 3.7 29.8 - - + +
357D ALA* 4.3 8.3 - - + -
358D LEU* 4.1 17.5 - - + -
370D GLY 5.1 0.2 - - - -
371D ASP 3.1 17.5 + - - +
372D GLN 4.1 4.0 - - - +
374D GLU* 1.3 77.4 - - + +
376D GLU* 1.3 61.3 + - - +
378D LEU* 3.4 9.4 + - + +
379D PHE* 3.2 33.0 + - + -
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Residues in contact with GLU 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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350D VAL* 3.5 18.9 - - + +
351D PRO* 2.9 34.4 - - - +
354D ALA* 3.4 15.7 - - + -
372D GLN* 2.8 39.1 - - - +
373D LYS* 3.1 22.2 + - - +
374D GLU 3.1 0.2 - - - -
375D VAL* 1.3 78.2 - - - +
377D GLU* 1.3 62.0 + - + +
379D PHE 3.5 0.3 + - - -
380D LEU* 3.1 33.5 + - + +
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Residues in contact with GLU 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 LYS* 3.1 18.1 + - - +
374D GLU* 2.9 23.7 + - - +
376D GLU* 1.3 75.4 - - + +
378D LEU* 1.3 55.3 + - + +
380D LEU* 3.1 11.3 + - + +
381D SER* 2.7 37.2 + - - -
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Residues in contact with LEU 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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261D TYR* 4.4 9.6 - - + -
265D MET* 3.6 26.0 - - + +
284D LEU* 5.5 0.3 - - - +
287D HIS* 3.7 20.8 - - + +
288D VAL* 4.5 8.5 - - + +
291D TYR* 3.6 55.9 - - + -
374D GLU 3.0 11.6 + - - +
375D VAL* 3.6 13.7 - - - +
377D GLU* 1.3 76.5 - - + +
379D PHE* 1.3 63.7 + - - +
381D SER* 2.6 27.1 + - - +
382D ALA* 3.3 8.1 + - - +
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Residues in contact with PHE 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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265D MET* 3.3 61.2 - - + -
268D GLN* 4.8 0.2 - - + -
269D LEU* 4.1 27.6 - - + -
284D LEU* 4.3 2.0 - - + -
340D LEU* 3.5 20.8 - - + +
350D VAL* 3.9 19.7 - - + -
353D LEU* 3.8 21.8 - - + -
354D ALA* 3.7 31.9 - - + -
357D ALA* 4.3 0.7 - - + -
375D VAL* 3.2 17.2 + - + -
376D GLU 3.7 7.2 - - - +
378D LEU* 1.3 77.1 - - - +
380D LEU* 1.3 59.7 + - - +
382D ALA* 2.9 22.6 + - - +
383D PHE* 3.2 14.6 - + + -
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Residues in contact with LEU 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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347D LYS* 4.1 31.9 + - + +
350D VAL* 3.9 24.7 - - + -
376D GLU* 3.1 20.8 + - + +
377D GLU* 3.1 11.3 + - + +
379D PHE* 1.3 71.3 - - - +
381D SER* 1.3 62.4 + - - +
382D ALA 3.0 6.3 + - - -
383D PHE* 3.1 23.5 + - + +
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Residues in contact with SER 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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287D HIS* 3.2 32.5 + - - +
377D GLU 2.7 17.2 + - - -
378D LEU* 2.6 28.7 + - - +
380D LEU* 1.3 73.2 - - - +
382D ALA* 1.3 56.8 + - - +
383D PHE 3.4 2.2 + - - -
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Residues in contact with ALA 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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283D VAL* 4.5 2.1 - - + +
284D LEU* 3.7 16.6 - - + -
287D HIS* 3.7 24.0 + - + -
339D ASN* 3.1 10.5 - - - +
340D LEU* 2.8 43.0 + - + -
378D LEU 3.8 5.8 - - - +
379D PHE 2.9 14.1 + - - +
381D SER* 1.3 79.9 + - - +
383D PHE* 1.3 57.5 + - - +
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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