Contacts of the helix formed by residues 361 - 378 (chain B) in PDB entry 4OE4
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 GLU 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B LEU 3.5 0.4 + - - -
360B PRO* 1.3 69.9 - - - +
362B SER* 1.3 62.2 + - - +
363B LYS 3.1 1.4 + - - -
364B SER* 3.3 20.1 + - - -
365B GLU* 4.6 1.7 + - - +
468B GLU* 4.3 22.2 - - + +
469B TYR 2.8 16.5 + - - +
470B PRO* 3.3 37.2 - - + +
471B ASP* 3.3 5.8 + - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PRO* 4.6 0.3 - - - +
360B PRO* 4.6 0.3 - - - +
361B GLU* 1.3 76.8 - - - +
363B LYS* 1.3 77.6 + - - +
365B GLU 5.5 0.6 + - - -
366B GLU* 5.8 0.7 + - - +
471B ASP* 2.4 35.2 + - - -
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Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 5.7 0.2 - - + -
328B PRO* 3.4 27.1 - - + +
330B ALA 5.6 0.7 - - - -
332B ILE* 4.0 32.9 - - + +
359B LEU* 5.8 0.7 - - + -
360B PRO* 3.0 26.6 + - + +
362B SER* 1.3 95.3 - - - +
364B SER* 1.3 59.5 + - - +
365B GLU 3.4 2.5 - - - -
366B GLU* 3.4 15.6 + - + +
367B PHE* 2.9 31.8 + - + +
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Residues in contact with SER 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.8 19.6 - - - +
360B PRO 2.9 17.8 + - - -
361B GLU* 3.3 18.3 + - - -
363B LYS* 1.3 77.6 - - - +
365B GLU* 1.3 55.5 + - - +
367B PHE* 3.6 0.3 - - - +
368B LEU* 2.8 42.1 + - - +
468B GLU* 3.7 35.2 - - - +
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU 4.6 1.8 + - - +
362B SER 5.5 0.6 + - - -
363B LYS 3.4 0.2 - - - -
364B SER* 1.3 78.7 - - - +
366B GLU* 1.3 58.5 + - - +
368B LEU* 4.9 3.6 - - - -
369B SER* 2.9 33.1 + - - -
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 3.7 35.2 - - - +
333B SER 5.3 0.5 + - - -
362B SER 5.9 0.4 - - - +
363B LYS* 3.4 19.3 + - - +
364B SER 3.3 0.6 - - - -
365B GLU* 1.3 77.4 - - - +
367B PHE* 1.3 64.2 + - - +
369B SER* 3.6 3.8 - - - -
370B ASP* 2.9 44.4 + - - +
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Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 4.1 6.1 - - + -
332B ILE* 3.9 26.6 - - + +
335B ALA* 3.8 13.7 - - + -
336B VAL* 3.5 37.9 - - + +
339B THR* 3.7 21.8 - - - -
357B LEU* 3.5 28.3 - - + -
359B LEU* 3.7 32.3 - - + -
363B LYS* 2.9 18.0 + - + +
364B SER 3.6 3.1 - - - +
366B GLU* 1.3 78.1 - - - +
368B LEU* 1.3 64.7 + - + +
370B ASP* 3.2 4.2 + - - +
371B MET* 3.0 41.8 + - + +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 4.9 2.0 - - + -
359B LEU* 3.8 21.5 - - + -
364B SER 2.8 24.4 + - - +
365B GLU* 4.3 2.9 - - - +
367B PHE* 1.3 80.4 - - + +
369B SER* 1.3 60.1 + - - +
371B MET* 3.2 6.0 + - - -
372B PHE* 2.9 64.6 + - + -
427B LEU* 3.7 21.8 - - + -
444B VAL* 4.5 11.9 - - + -
466B VAL* 4.8 7.2 - - + -
468B GLU* 3.5 25.1 - - - +
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Residues in contact with SER 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU 2.9 21.3 + - - -
366B GLU* 3.6 5.1 + - - -
368B LEU* 1.3 76.6 - - - +
370B ASP* 1.3 66.6 + - - +
372B PHE* 4.0 6.8 - - - +
373B GLY* 3.0 20.1 + - - -
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Residues in contact with ASP 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 4.3 7.4 - - - +
333B SER* 4.5 12.1 - - - -
336B VAL* 3.9 18.7 - - + +
366B GLU* 2.9 43.2 + - - +
367B PHE* 3.2 9.8 + - - +
369B SER* 1.3 78.0 + - - +
371B MET* 1.3 63.3 + - - +
373B GLY* 3.2 3.2 + - - -
374B ILE* 3.0 29.5 + - + +
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Residues in contact with MET 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 3.6 13.5 - - + +
339B THR* 3.6 36.8 - - + -
340B ILE* 4.0 20.8 - - + +
344B PHE* 4.7 2.9 - - + -
367B PHE* 3.0 36.3 + - + +
368B LEU* 3.2 10.7 + - - +
370B ASP* 1.3 74.9 - - - +
372B PHE* 1.3 66.8 + - + +
374B ILE* 3.2 2.8 + - - +
375B LEU* 2.9 49.1 + - + +
444B VAL* 4.1 23.6 - - - -
464B LEU* 4.4 9.2 - - + -
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Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 2.9 50.0 + - + +
369B SER* 4.1 4.7 - - - +
371B MET* 1.3 83.8 - - + +
373B GLY* 1.3 56.6 + - - +
375B LEU* 3.8 3.1 - - + +
376B GLN* 2.9 32.7 + - - +
427B LEU* 3.5 44.2 - - + -
428B TYR* 3.6 39.0 - + + -
444B VAL* 3.9 20.6 - - + -
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B SER 3.0 14.8 + - - -
370B ASP 3.2 4.2 + - - -
371B MET 3.1 0.2 - - - -
372B PHE* 1.3 77.1 - - - +
374B ILE* 1.3 56.6 + - - +
376B GLN* 3.5 4.6 + - - +
377B SER* 3.0 28.2 + - - -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 4.1 17.9 - - + -
337B LEU* 3.7 31.6 - - + -
340B ILE* 3.7 19.1 - - + -
370B ASP* 3.0 19.1 + - + +
371B MET 3.8 4.0 - - - +
373B GLY* 1.3 74.6 - - - +
375B LEU* 1.3 64.7 + - + +
377B SER* 3.1 9.3 + - - -
378B GLN* 3.0 23.4 + - + +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B ILE* 4.2 19.1 - - + -
344B PHE* 3.9 34.5 - - + -
371B MET* 2.9 38.6 + - + +
372B PHE* 3.8 3.8 - - + +
374B ILE* 1.3 77.5 - - + +
376B GLN* 1.3 62.1 + - - +
377B SER 3.3 0.3 + - - -
378B GLN* 3.3 22.5 + - + +
399B MET* 5.3 5.2 - - - -
428B TYR* 3.4 41.3 + - + +
442B PRO* 4.2 17.0 - - + -
444B VAL* 4.6 1.6 - - + -
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B PHE 2.9 19.8 + - - +
373B GLY* 3.9 4.5 - - - +
375B LEU* 1.3 76.5 - - - +
377B SER* 1.3 62.1 + - - +
378B GLN 4.5 2.3 - - - -
428B TYR* 3.3 15.4 + - + +
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B GLY 3.0 14.2 + - - -
374B ILE* 3.1 14.1 + - - -
376B GLN* 1.3 81.0 - - - +
378B GLN* 1.3 65.6 + - - +
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Residues in contact with GLN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ILE* 3.0 13.9 + - + +
375B LEU* 3.3 18.9 + - + +
376B GLN 4.5 2.2 - - - -
377B SER* 1.3 81.7 - - - +
397B GLY* 5.8 8.0 + - - -
399B MET* 5.9 12.1 - - + -
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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
------------------------------------------------------------
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