Contacts of the helix formed by residues 356 - 376 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G GLN 3.5 4.9 + - - +
355G LEU* 1.3 78.4 - - - +
357G ARG* 1.3 64.2 + - - +
358G GLU* 3.0 10.6 + - - +
359G GLN* 3.0 45.3 + - - +
360G MET* 3.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 357 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355G LEU 3.8 0.2 + - - -
356G THR* 1.3 72.4 - - - +
358G GLU* 1.3 59.3 + - - +
360G MET* 3.5 23.4 - - + +
361G LEU* 3.6 15.2 + - - +
412G MET 2.8 23.0 + - - -
413G VAL* 3.7 19.9 - - + +
415G ASN* 3.6 32.6 + - - +
467G GLN 4.8 4.0 + - - -
468G PHE* 3.0 75.4 + - + +
522G PRO* 5.5 2.2 - - - +
523G PRO* 3.5 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G THR* 3.0 9.3 + - - +
357G ARG* 1.3 78.2 - - - +
359G GLN* 1.3 55.3 + - + +
360G MET 3.3 0.2 - - - -
361G LEU* 3.3 6.7 + - + +
362G THR* 2.7 36.3 + - - +
410G LYS* 3.4 26.9 + - - +
413G VAL* 3.5 28.6 - - + +
587G GLU 5.1 1.4 - - - +
588G PHE 5.3 0.3 - - - -
589G ALA* 4.9 15.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 359 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G GLN 4.6 1.0 - - - +
355G LEU* 3.4 30.3 - - + +
356G THR* 3.0 40.3 + - - +
358G GLU* 1.3 77.7 - - + +
360G MET* 1.3 63.0 + - - +
362G THR* 3.0 20.4 + - - +
363G ASN* 2.8 21.5 + - - +
309H GLU* 5.8 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351G ASP* 4.0 17.5 - - + +
352G SER* 4.2 20.0 - - - +
355G LEU* 3.8 26.2 - - + +
356G THR 3.1 12.1 + - - +
357G ARG* 3.5 52.9 - - + +
358G GLU 3.3 0.2 - - - -
359G GLN* 1.3 78.1 - - - +
361G LEU* 1.3 61.1 + - - +
363G ASN* 3.5 11.4 + - - +
364G ARG* 3.3 18.0 + - - +
443G CYS 5.4 0.6 - - - +
466G ASP 5.9 1.3 - - - +
467G GLN 5.6 5.2 - - - +
468G PHE* 4.5 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G ARG 3.6 3.3 + - - +
358G GLU* 3.3 9.3 + - + +
359G GLN 3.1 0.6 - - - -
360G MET* 1.3 76.5 - - - +
362G THR* 1.3 58.0 + - - +
364G ARG* 2.9 4.1 + - - +
365G PHE* 2.8 54.5 + - + -
409G LEU* 4.2 18.4 - - + +
413G VAL* 3.5 32.3 - - + -
443G CYS* 3.7 33.2 - - + +
468G PHE* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 362 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G GLU* 2.7 23.2 + - - +
359G GLN* 3.1 16.6 - - - +
361G LEU* 1.3 77.1 - - - +
363G ASN* 1.3 59.7 + - - +
365G PHE* 3.5 7.6 + - - +
366G ASN* 2.7 43.2 + - - +
589G ALA* 3.5 25.3 - - + +
591G SER* 3.6 23.6 - - - +
592G ILE* 4.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 363 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G LYS* 5.7 3.1 - - - +
355G LEU* 3.6 27.8 - - - +
359G GLN* 2.8 22.5 + - - +
360G MET* 3.7 9.0 - - - +
361G LEU 3.1 0.2 - - - -
362G THR* 1.3 76.2 - - - +
364G ARG* 1.3 64.1 + - - +
366G ASN* 3.3 10.8 + - - +
367G ASP* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G MET 3.3 10.5 + - - +
361G LEU* 2.9 10.0 + - + +
363G ASN* 1.3 79.8 - - - +
365G PHE* 1.3 62.8 + - + +
367G ASP* 3.0 15.7 + - - +
368G LEU* 2.9 38.5 + - + +
371G ARG* 4.0 18.0 - - - +
441G GLU* 2.8 49.5 + - - +
442G LEU 3.5 15.5 - - - +
443G CYS 3.2 26.7 + - - +
444G GLY* 4.2 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G LEU* 2.8 55.1 + - + +
362G THR* 3.8 2.9 - - - +
364G ARG* 1.3 72.8 - - - +
366G ASN* 1.3 60.9 + - - +
368G LEU* 3.6 10.1 + - + +
369G LEU* 3.3 27.4 + - - +
409G LEU* 3.9 27.1 - - + -
442G LEU* 3.9 21.3 - - + -
576G LEU* 3.6 21.9 - - + +
579G LEU* 3.5 27.6 - - + -
588G PHE* 4.2 24.5 - + - -
592G ILE* 3.6 19.3 - - + -
596G ILE* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 366 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G THR* 2.7 32.1 + - - +
363G ASN* 3.3 11.5 + - - +
364G ARG 3.1 0.6 - - - -
365G PHE* 1.3 76.3 - - - +
367G ASP* 1.3 56.9 + - - +
368G LEU 3.2 0.2 - - - -
369G LEU* 3.1 2.0 + - - -
370G ASP* 2.7 37.4 + - - +
591G SER 5.3 2.4 + - - +
592G ILE* 3.4 27.5 - - - +
595G ARG* 3.2 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 367 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G LYS* 3.5 26.4 + - - -
363G ASN* 2.7 27.9 + - - +
364G ARG* 3.0 20.4 + - - +
366G ASN* 1.3 75.8 - - - +
368G LEU* 1.3 63.3 + - + +
370G ASP* 3.1 27.2 + - - +
371G ARG* 3.5 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ARG* 2.9 37.3 + - + +
365G PHE* 3.7 10.8 - - - +
366G ASN 3.2 0.2 - - - -
367G ASP* 1.3 77.3 - - + +
369G LEU* 1.3 58.6 + - - +
371G ARG* 3.7 13.1 + - - +
372G MET* 3.1 24.6 + - - +
441G GLU* 3.7 22.2 - - + +
442G LEU* 3.5 41.5 - - + +
572G GLY 4.6 2.7 - - - +
573G ILE* 3.3 29.9 - - + +
576G LEU* 3.5 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G PHE* 3.3 18.8 - - + +
366G ASN* 3.1 3.1 + - - +
368G LEU* 1.3 77.7 - - - +
370G ASP* 1.3 54.6 + - - +
371G ARG 3.2 0.4 - - - -
372G MET* 3.1 27.1 + - - +
373G ASP* 2.7 36.9 + - - +
576G LEU* 3.5 12.6 - - + -
580G ILE* 3.8 16.4 - - + -
592G ILE* 4.5 10.1 - - + -
595G ARG* 3.2 48.7 - - + +
596G ILE* 4.8 10.1 - - + -
599G TRP* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 370 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G ASN* 2.7 25.8 + - - +
367G ASP* 3.1 25.3 + - - +
369G LEU* 1.3 77.7 - - - +
371G ARG* 1.3 62.4 + - + +
373G ASP* 3.3 11.5 + - - +
374G ILE* 3.2 26.1 - - + +
595G ARG* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ARG* 4.0 24.5 - - - +
367G ASP* 3.5 19.5 + - - +
368G LEU* 3.8 15.2 - - - +
369G LEU 3.2 0.4 - - - -
370G ASP* 1.3 76.7 - - + +
372G MET* 1.3 58.7 + - - +
374G ILE* 3.1 12.2 + - - +
375G MET* 2.9 41.2 + - - +
441G GLU* 3.4 30.5 + - - +
573G ILE* 4.1 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 372 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368G LEU 3.1 12.8 - - - +
369G LEU* 3.1 19.9 + - + +
371G ARG* 1.3 72.2 - - - +
373G ASP* 1.3 57.3 + - - +
374G ILE 3.0 5.2 - - - -
375G MET* 3.4 9.9 - - - -
376G PHE* 2.8 58.4 + - + +
573G ILE* 3.5 20.2 - - + -
576G LEU* 3.5 31.6 - - + -
577G LEU* 3.4 39.7 - - + -
580G ILE* 5.5 0.9 - - + -
599G TRP* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G LEU* 2.7 22.2 + - - +
370G ASP* 3.3 9.1 + - - +
372G MET* 1.3 75.0 - - - +
374G ILE* 1.3 61.6 + - + +
376G PHE* 5.3 0.9 - - - -
377G GLY* 4.0 13.8 - - - -
595G ARG* 2.8 24.9 + - - -
599G TRP* 3.2 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G PRO* 3.7 32.1 - - + -
314G TYR* 4.3 12.1 - - - +
315G LYS* 5.3 7.6 - - + +
370G ASP* 3.2 22.0 - - + +
371G ARG* 3.1 8.9 + - - +
372G MET 3.0 0.6 - - - -
373G ASP* 1.3 82.4 - - + +
375G MET* 1.3 63.0 + - - +
376G PHE 3.3 1.1 - - - -
377G GLY* 3.2 7.5 + - - -
379G THR* 3.5 27.5 + - - +
380G GLY* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 375 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371G ARG* 2.9 31.6 + - - +
372G MET* 3.4 18.2 - - - -
374G ILE* 1.3 77.2 - - - +
376G PHE* 1.3 87.1 + - + +
377G GLY 3.2 1.9 + - - +
380G GLY* 3.3 18.5 - - - +
381G SER 4.5 0.9 - - - +
382G ALA* 3.3 43.3 + - + +
387G TRP* 3.5 39.3 - - + -
573G ILE* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G MET* 2.8 59.5 + - + +
373G ASP* 4.6 1.1 - - - -
375G MET* 1.3 101.8 - - + +
377G GLY* 1.3 60.3 + - - +
382G ALA* 3.8 13.7 - - + -
383G ASP 4.0 1.1 - - - -
384G ILE* 3.4 52.7 - - + -
387G TRP* 3.8 25.4 - + + -
573G ILE* 4.7 0.9 - - + -
577G LEU* 4.6 1.3 - - + -
599G TRP* 3.9 17.0 - + + -
602G ARG* 3.5 29.5 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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