Contacts of the helix formed by residues 356 - 376 (chain F) in PDB entry 4E2I
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 356 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F GLN 3.5 4.9 + - - +
355F LEU* 1.3 77.1 - - - +
357F ARG* 1.3 63.1 + - - +
358F GLU* 3.0 11.0 + - - +
359F GLN* 3.0 45.2 + - - +
360F MET* 3.1 9.9 + - - +
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Residues in contact with ARG 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F THR* 1.3 73.1 - - - +
358F GLU* 1.3 58.9 + - - +
360F MET* 3.5 24.2 - - + +
361F LEU* 3.6 14.7 + - - +
412F MET 2.8 23.0 + - - -
413F VAL* 3.7 18.8 - - + +
415F ASN* 3.7 33.3 + - - +
467F GLN 4.8 4.4 + - - -
468F PHE* 3.0 75.1 + - + +
522F PRO* 5.5 2.4 - - - +
523F PRO* 3.5 19.8 - - - +
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Residues in contact with GLU 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F THR* 3.0 9.2 + - - +
357F ARG* 1.3 79.3 - - - +
359F GLN* 1.3 54.8 + - + +
360F MET 3.3 0.2 - - - -
361F LEU* 3.3 6.7 + - + +
362F THR* 2.8 36.0 + - - +
410F LYS* 3.3 26.2 + - - +
413F VAL* 3.5 29.1 - - + +
587F GLU 5.1 1.4 - - - +
588F PHE 5.3 0.5 - - - -
589F ALA* 4.9 16.3 + - + -
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Residues in contact with GLN 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU* 5.6 4.8 + - - +
354F GLN 4.7 1.0 - - - +
355F LEU* 3.4 28.8 - - + +
356F THR* 3.0 41.0 + - - +
358F GLU* 1.3 77.1 - - + +
360F MET* 1.3 63.7 + - - +
362F THR* 3.0 20.0 + - - +
363F ASN* 2.8 22.4 + - - +
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Residues in contact with MET 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351F ASP* 4.0 17.0 - - + +
352F SER* 4.2 19.5 - - - +
355F LEU* 3.8 25.6 - - + +
356F THR 3.1 12.1 + - - +
357F ARG* 3.5 51.6 - - + +
359F GLN* 1.3 78.3 - - - +
361F LEU* 1.3 60.4 + - - +
363F ASN* 3.5 11.3 + - - +
364F ARG* 3.3 18.5 + - - +
443F CYS 5.4 0.4 - - - +
466F ASP 5.9 1.6 - - - +
467F GLN 5.6 5.2 - - - +
468F PHE* 4.6 13.7 - - + -
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Residues in contact with LEU 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F ARG 3.6 3.1 + - - +
358F GLU* 3.3 9.1 + - + +
359F GLN 3.1 0.6 - - - -
360F MET* 1.3 77.3 - - - +
362F THR* 1.3 57.8 + - - +
364F ARG* 2.9 4.9 + - + +
365F PHE* 2.8 54.3 + - + -
409F LEU* 4.2 19.3 - - + +
413F VAL* 3.5 32.1 - - + -
443F CYS* 3.7 31.6 - - + +
468F PHE* 3.5 38.4 - - + -
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Residues in contact with THR 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358F GLU* 2.8 22.3 + - - +
359F GLN* 3.0 17.5 + - - +
361F LEU* 1.3 77.1 - - - +
363F ASN* 1.3 58.7 - - - +
365F PHE* 3.5 6.8 + - - +
366F ASN* 2.7 43.2 + - - +
589F ALA* 3.6 25.1 - - + +
591F SER* 3.6 24.0 - - - +
592F ILE* 4.1 9.1 - - + +
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Residues in contact with ASN 363 (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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281F LYS* 5.7 3.1 - - - +
355F LEU* 3.6 28.3 - - - +
359F GLN* 2.8 22.3 + - - +
360F MET* 3.7 8.1 - - - +
361F LEU 3.2 0.2 - - - -
362F THR* 1.3 75.4 - - - +
364F ARG* 1.3 62.9 + - - +
366F ASN* 3.2 10.1 + - - +
367F ASP* 2.7 37.0 + - - +
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Residues in contact with ARG 364 (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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360F MET 3.3 10.7 + - - +
361F LEU* 2.9 10.4 + - - +
363F ASN* 1.3 79.5 - - - +
365F PHE* 1.3 63.5 + - + +
367F ASP* 3.0 15.3 + - - +
368F LEU* 2.9 39.4 + - + +
371F ARG* 4.0 18.0 - - - +
441F GLU* 2.8 51.1 + - - +
442F LEU 3.5 15.0 - - - +
443F CYS 3.2 27.1 + - - +
444F GLY* 4.2 9.2 - - - -
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Residues in contact with PHE 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361F LEU* 2.8 54.8 + - + +
362F THR* 3.8 2.7 - - - +
364F ARG* 1.3 72.8 - - + +
366F ASN* 1.3 62.1 + - - +
368F LEU* 3.6 10.7 + - + +
369F LEU* 3.3 27.3 + - + +
409F LEU* 3.9 27.6 - - + -
442F LEU* 3.9 21.1 - - + -
576F LEU* 3.5 21.6 - - + +
579F LEU* 3.5 28.7 - - + -
588F PHE* 4.2 24.5 - + - -
592F ILE* 3.7 20.6 - - + -
596F ILE* 5.6 0.2 - - + -
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Residues in contact with ASN 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362F THR* 2.7 32.1 + - - +
363F ASN* 3.2 12.4 + - - +
364F ARG 3.1 0.8 - - - -
365F PHE* 1.3 75.8 - - - +
367F ASP* 1.3 56.1 + - - +
368F LEU 3.2 0.2 - - - -
369F LEU* 3.1 2.2 + - - -
370F ASP* 2.7 38.5 + - - +
591F SER 5.3 3.1 + - - +
592F ILE* 3.4 27.5 - - - +
595F ARG* 3.2 32.2 + - - +
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Residues in contact with ASP 367 (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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281F LYS* 3.5 27.0 + - - -
363F ASN* 2.7 29.2 + - - +
364F ARG* 3.0 19.2 + - - +
366F ASN* 1.3 76.5 - - - +
368F LEU* 1.3 62.1 + - + +
370F ASP* 3.1 27.3 + - - +
371F ARG* 3.5 19.7 + - - +
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Residues in contact with LEU 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F ARG* 2.9 36.9 + - + +
365F PHE* 3.7 11.2 - - + +
367F ASP* 1.3 77.5 - - - +
369F LEU* 1.3 60.0 + - - +
371F ARG* 3.7 12.6 + - - +
372F MET* 3.1 23.7 + - - +
441F GLU* 3.7 21.3 - - + +
442F LEU* 3.5 41.3 - - + +
572F GLY 4.6 2.7 - - - +
573F ILE* 3.3 30.3 - - + +
576F LEU* 3.5 20.4 - - + -
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Residues in contact with LEU 369 (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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365F PHE 3.3 18.6 + - - +
366F ASN* 3.1 3.0 + - - +
368F LEU* 1.3 77.1 - - - +
370F ASP* 1.3 54.8 + - - +
371F ARG 3.2 0.7 - - - -
372F MET* 3.1 27.5 + - - +
373F ASP* 2.8 36.8 + - - +
576F LEU* 3.5 11.4 - - + -
580F ILE* 3.9 16.4 - - + -
592F ILE* 4.5 10.1 - - + -
595F ARG* 3.2 51.6 - - + +
596F ILE* 4.8 9.9 - - + -
599F TRP* 3.8 20.4 - - + +
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Residues in contact with ASP 370 (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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366F ASN* 2.7 24.4 + - - +
367F ASP* 3.1 25.9 + - - +
369F LEU* 1.3 78.0 - - - +
371F ARG* 1.3 62.4 + - + +
373F ASP* 3.3 11.0 + - - +
374F ILE* 3.2 25.9 + - + +
595F ARG* 3.2 18.3 + - - +
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Residues in contact with ARG 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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506E LYS* 6.0 1.4 - - - +
364F ARG* 4.0 25.1 - - - +
367F ASP* 3.5 19.1 + - - +
368F LEU* 3.8 15.7 - - - +
370F ASP* 1.3 76.9 - - + +
372F MET* 1.3 57.2 + - - +
374F ILE* 3.1 12.1 + - - +
375F MET* 2.9 41.6 + - - +
441F GLU* 3.4 29.9 + - - +
573F ILE* 4.1 17.1 - - + +
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Residues in contact with MET 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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368F LEU 3.1 11.7 - - - +
369F LEU* 3.2 32.5 - - + +
371F ARG* 1.3 73.1 - - - +
373F ASP* 1.3 57.5 + - - +
374F ILE 3.0 4.7 - - - -
375F MET* 3.4 9.4 - - - -
376F PHE* 2.8 59.5 + - + +
573F ILE* 3.5 20.4 - - + -
576F LEU* 3.5 18.4 - - + -
577F LEU* 3.4 40.2 - - + -
580F ILE* 5.5 0.7 - - + -
599F TRP* 3.6 19.3 - - + -
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Residues in contact with ASP 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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369F LEU 2.8 21.5 + - - +
370F ASP* 3.3 9.1 + - - +
372F MET* 1.3 75.1 - - - +
374F ILE* 1.3 60.0 - - + +
376F PHE 5.4 0.9 - - - -
377F GLY* 4.0 14.6 - - - -
595F ARG* 2.8 24.6 + - - -
599F TRP* 3.2 25.0 + - - -
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Residues in contact with ILE 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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311F PRO* 3.7 31.9 - - + -
314F TYR* 4.3 11.7 - - - +
315F LYS* 5.4 7.9 - - + +
370F ASP* 3.2 21.8 - - + +
371F ARG* 3.1 9.1 + - - +
372F MET 3.0 0.4 - - - -
373F ASP* 1.3 82.1 - - + +
375F MET* 1.3 62.4 + - - +
376F PHE 3.3 1.3 - - - -
377F GLY* 3.2 7.7 + - - -
379F THR* 3.5 27.8 + - - +
380F GLY* 3.1 22.5 + - - -
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Residues in contact with MET 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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371F ARG* 2.9 32.3 + - - +
372F MET* 3.4 18.6 - - - -
374F ILE* 1.3 77.7 - - - +
376F PHE* 1.3 85.9 + - + +
377F GLY 3.2 2.0 + - - +
380F GLY* 3.3 18.5 - - - -
381F SER 5.1 0.4 - - - +
382F ALA* 3.3 43.1 + - + +
387F TRP* 3.5 39.7 - - + -
573F ILE* 4.4 7.4 - - + -
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Residues in contact with PHE 376 (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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372F MET* 2.8 61.8 + - + +
373F ASP* 4.6 1.1 - - - -
375F MET* 1.3 101.7 - - + +
377F GLY* 1.3 60.3 + - - +
382F ALA* 3.8 13.9 - - + -
383F ASP 4.0 0.9 - - - -
384F ILE* 3.4 50.0 - - + -
387F TRP* 3.8 26.9 - + + -
573F ILE* 4.7 1.1 - - + -
577F LEU* 4.6 0.7 - - + -
599F TRP* 3.9 17.5 - + + -
602F ARG* 3.5 30.2 + - - +
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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
------------------------------------------------------------
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