Contacts of the helix formed by residues 358 - 375 (chain F) in PDB entry 5JLH
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 358 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F GLY 3.8 2.2 + - - -
357F PHE* 1.3 74.5 - - - +
359F HIS* 1.3 72.4 + - - +
360F GLU* 3.2 17.1 + - - +
361F GLU* 3.1 24.5 + - - +
362F ILE* 3.1 24.7 + - - +
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Residues in contact with HIS 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F LEU* 5.4 10.0 - - + +
349F LEU* 5.3 13.5 - - + +
353F ARG* 4.9 26.1 - - - +
357F PHE 4.0 0.2 + - - -
358F SER* 1.3 75.9 + - - +
360F GLU* 1.3 58.3 + - - +
362F ILE* 3.2 13.9 + - + +
363F ILE* 2.9 47.0 + - + +
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Residues in contact with GLU 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358F SER* 3.5 13.6 + - - +
359F HIS* 1.3 80.4 + - - +
361F GLU* 1.3 59.3 + - + +
363F ILE* 2.7 30.5 - - + +
364F SER* 2.9 18.1 + - - +
632F ARG* 3.2 35.7 + - - +
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Residues in contact with GLU 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F GLY 4.6 0.2 - - - +
357F PHE* 3.2 40.5 - - + +
358F SER* 3.1 22.6 + - - +
360F GLU* 1.3 81.6 - - + +
362F ILE* 1.3 58.2 + - - +
364F SER* 3.2 8.7 + - - -
365F MET* 2.9 37.1 + - - +
454F TRP* 5.1 14.2 - - + -
458F ARG* 3.5 26.8 + - - -
632F ARG* 5.7 5.4 - - - +
633F LEU* 4.8 3.5 - - + +
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Residues in contact with ILE 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F LEU* 5.7 2.2 - - + -
349F LEU* 4.6 19.5 - - + +
352F LEU* 3.2 45.3 - - + -
353F ARG* 5.8 2.0 - - + +
357F PHE* 4.0 15.3 - - + +
358F SER 3.1 18.5 + - - +
359F HIS* 3.2 15.9 + - + +
361F GLU* 1.3 75.2 - - - +
363F ILE* 1.3 64.0 + - - +
365F MET* 3.1 18.2 + - - +
366F LEU* 2.9 49.6 + - + +
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Residues in contact with ILE 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F LEU* 5.0 11.9 - - + -
318F ASP* 3.3 31.0 - - + +
319F LEU* 4.1 14.8 - - + +
359F HIS* 2.9 31.4 + - + +
360F GLU* 2.7 35.0 - - + +
362F ILE* 1.3 77.9 - - - +
364F SER* 1.3 59.1 + - - +
366F LEU* 3.5 5.6 + - - +
367F ARG* 2.9 52.6 + - - +
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Residues in contact with SER 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F GLU* 2.9 19.5 + - - +
361F GLU* 3.5 9.9 - - - -
363F ILE* 1.3 79.1 - - - +
365F MET* 1.3 63.5 + - - +
367F ARG* 3.2 16.6 + - - +
368F MET* 3.1 17.8 + - - +
632F ARG* 4.6 11.1 + - - -
633F LEU* 3.4 37.1 - - - +
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Residues in contact with MET 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F PHE* 3.8 30.3 - - + -
352F LEU* 4.4 17.9 - - + -
357F PHE* 5.5 5.6 - - - -
361F GLU* 2.9 22.4 + - - +
362F ILE* 3.3 28.0 - - - +
364F SER* 1.3 77.2 - - - +
366F LEU* 1.3 63.2 + - + +
368F MET* 3.1 9.4 + - - +
369F VAL* 2.9 32.0 + - - +
451F LEU* 4.9 7.2 - - + -
454F TRP* 4.0 30.3 - - + -
455F LEU* 4.3 18.8 - - + -
633F LEU* 3.8 9.9 - - + -
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Residues in contact with LEU 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F PHE* 5.7 3.1 - - + -
303F ILE* 5.5 11.9 - - + -
307F LEU* 3.6 17.6 - - + +
315F LEU* 3.9 18.6 - - + -
319F LEU* 3.1 21.4 - - + +
345F PHE* 3.5 37.9 - - + -
349F LEU* 4.8 2.0 - - + -
352F LEU* 5.0 7.6 - - + -
362F ILE* 2.9 37.6 + - + +
363F ILE* 4.0 3.8 - - - +
365F MET* 1.3 87.1 - - + +
367F ARG* 1.3 56.9 + - - +
369F VAL* 3.2 11.1 + - + +
370F SER 2.9 24.1 + - - -
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Residues in contact with ARG 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ASP* 4.0 23.6 + - - +
319F LEU* 3.6 19.0 - - + +
363F ILE* 2.9 46.5 + - - +
364F SER* 3.2 18.6 + - - +
366F LEU* 1.3 75.0 - - - +
368F MET* 1.3 58.0 + - - +
370F SER* 3.0 7.8 + - - -
371F ALA 2.9 20.4 + - - -
402F ARG 5.9 0.7 - - - -
403F LEU* 3.3 41.3 - - + +
631F ASP* 5.2 9.2 + - - -
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Residues in contact with MET 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364F SER 3.1 11.5 + - - +
365F MET 3.4 11.2 - - - +
367F ARG* 1.3 76.6 - - - +
369F VAL* 1.3 60.2 + - - +
371F ALA* 2.8 26.8 + - + +
372F VAL* 2.9 14.7 + - - +
403F LEU* 5.3 0.6 + - - -
404F LEU* 5.2 9.9 - - + -
447F THR* 3.3 42.9 - - + +
451F LEU* 3.6 28.0 - - + +
633F LEU* 4.4 9.4 - - + -
634F THR* 5.1 12.1 - - - +
637F ILE* 3.3 36.3 - - + -
638F TRP* 5.4 2.2 - - - +
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Residues in contact with VAL 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F PHE* 4.5 16.2 - - + -
303F ILE* 4.4 12.8 - - + -
304F PHE* 3.8 29.4 - - + -
307F LEU* 3.6 21.3 - - + -
365F MET 2.9 21.3 + - - +
366F LEU* 3.2 12.3 + - + +
368F MET* 1.3 74.4 - - - +
370F SER* 1.3 57.7 + - - +
372F VAL* 3.0 27.5 - - - +
373F LEU* 3.6 7.4 - - - +
448F TYR* 5.2 3.6 - - + -
451F LEU* 3.6 22.9 - - + -
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Residues in contact with SER 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F LEU* 4.4 1.5 - - - +
319F LEU* 3.7 15.1 + - - -
321F LEU* 3.3 33.3 - - - +
327F TYR* 4.3 1.0 + - - -
366F LEU 2.9 11.2 + - - -
367F ARG 3.0 9.8 + - - -
369F VAL* 1.3 78.3 - - - +
371F ALA* 1.3 50.2 + - - +
373F LEU* 2.9 11.0 + - - +
374F GLN* 2.8 50.9 + - - +
403F LEU* 3.7 7.2 - - - +
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Residues in contact with ALA 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F ARG 2.9 6.6 + - - +
368F MET* 2.8 25.2 + - + +
370F SER* 1.3 77.5 - - - +
372F VAL* 1.3 59.6 + - - +
374F GLN* 3.0 15.1 + - - +
375F PHE* 2.8 27.4 + - + -
400F LEU* 4.5 14.2 - - + +
403F LEU* 3.5 20.0 - - + -
404F LEU* 4.8 11.0 - - + -
447F THR* 5.5 2.7 - - + -
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Residues in contact with VAL 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ALA* 5.2 9.2 - - + -
304F PHE* 4.2 22.4 - - + -
329F PHE* 3.6 11.5 - - + -
368F MET 2.9 10.0 + - - +
369F VAL* 3.0 30.3 - - - +
371F ALA* 1.3 75.8 - - - +
373F LEU* 1.3 64.6 + - + +
375F PHE* 3.3 25.7 + - - +
444F ALA* 3.2 38.8 - - + +
447F THR* 4.5 8.2 - - + +
448F TYR* 4.3 16.8 - - + -
451F LEU* 6.3 0.7 - - + -
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Residues in contact with LEU 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ALA 5.7 2.7 - - - +
304F PHE* 4.4 33.2 - - + -
307F LEU* 4.8 9.0 - - + -
308F LEU* 4.8 15.5 - - + -
321F LEU* 5.2 1.3 - - + -
327F TYR* 3.3 33.2 - - + +
329F PHE* 4.4 14.1 - - + +
330F LEU* 3.9 38.6 - - + -
369F VAL 3.6 15.3 - - - +
370F SER* 2.9 12.8 + - - +
372F VAL* 1.3 79.6 - - + +
374F GLN* 1.3 64.4 + - - +
376F GLY* 3.0 14.7 + - - -
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Residues in contact with GLN 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F LEU 4.8 1.4 + - - -
320F LEU 3.7 1.8 + - - -
322F GLU* 5.8 0.2 - - - +
327F TYR* 3.5 21.6 + - - -
370F SER* 2.8 31.0 + - - +
371F ALA* 3.0 10.0 + - - +
373F LEU* 1.3 71.4 - - - +
375F PHE* 1.3 65.0 + - - +
376F GLY 3.0 2.9 - - - -
377F ASN* 2.7 47.3 + - - +
378F ILE* 3.6 7.4 + - - +
396F ALA* 4.6 5.8 - - - +
399F LYS* 3.2 43.1 - - - +
400F LEU* 5.0 18.3 - - + +
403F LEU* 3.9 12.5 - - + +
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Residues in contact with PHE 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F PHE* 3.6 21.9 - - + -
371F ALA* 2.8 41.8 + - + -
372F VAL* 3.4 19.5 - - - +
373F LEU 3.1 0.6 - - - -
374F GLN* 1.3 74.6 - - - +
376F GLY* 1.3 58.0 + - - +
378F ILE* 2.8 26.4 - - + +
400F LEU* 4.5 29.8 - - + -
404F LEU* 5.2 6.3 - - + -
411F PHE* 5.5 2.7 - + - -
440F LEU* 3.8 29.6 - - + +
443F LEU* 3.7 31.9 - - + -
444F ALA* 3.8 11.7 - - + -
447F THR* 4.1 18.6 - - + -
626F LEU* 5.8 3.6 - - + -
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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
------------------------------------------------------------
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