Contacts of the helix formed by residues 358 - 370 (chain O) in PDB entry 5G04
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 TYR 358 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O ASP* 3.5 10.8 - - + +
357O SER* 1.3 77.2 - - - +
359O VAL* 1.3 73.6 + - + +
361O LEU* 3.1 16.8 + - - +
362O GLU* 3.4 30.4 + - + +
384O LEU* 4.4 6.3 - - + -
387O GLN* 3.4 32.0 + - + +
388O ARG* 4.1 25.0 + - + -
393O LYS* 5.6 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357O SER* 4.3 10.3 - - - +
358O TYR* 1.3 85.0 - - + +
360O LEU* 1.3 69.4 + - + +
361O LEU 3.1 0.7 + - - -
362O GLU* 3.1 10.3 + - + +
363O HIS* 2.8 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A VAL* 4.8 13.7 - - + -
344O LEU* 4.1 15.8 - - + +
347O LEU* 3.9 24.9 - - + +
348O TYR* 3.8 35.2 - - + +
351O GLY* 6.2 0.9 - - - -
357O SER* 3.8 33.4 - - - +
359O VAL* 1.3 89.9 - - + +
361O LEU* 1.3 53.1 + - - +
363O HIS* 3.4 9.9 - - - +
364O SER* 2.7 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348O TYR* 3.1 58.6 - - + +
358O TYR 3.1 10.1 + - - +
360O LEU* 1.3 74.4 - - - +
362O GLU* 1.3 64.9 + - - +
363O HIS 3.3 0.9 - - - -
364O SER* 3.6 9.4 - - - +
365O VAL* 3.2 30.5 + - - +
380O GLY* 4.1 17.9 - - - +
383O SER* 3.3 14.1 - - - -
384O LEU* 3.1 35.0 - - + +
387O GLN* 3.3 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358O TYR* 3.4 16.5 + - + +
359O VAL* 3.1 16.3 + - + +
361O LEU* 1.3 76.3 - - - +
363O HIS* 1.3 58.7 + - + +
365O VAL* 3.1 21.1 - - - +
366O LYS* 2.8 41.7 + - - +
384O LEU* 3.4 21.9 - - - +
388O ARG* 3.1 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 363 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092A TYR* 4.2 15.6 + - - -
1095A VAL* 4.0 27.6 - - + +
1098A GLU* 5.0 1.9 - - + +
344O LEU* 5.3 7.3 - - + +
359O VAL* 2.8 35.5 + - + +
360O LEU* 3.4 10.8 - - - +
362O GLU* 1.3 74.8 - - - +
364O SER* 1.3 54.4 + - - +
366O LYS* 3.3 4.9 + - - +
367O LYS* 2.8 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341O GLN* 4.7 2.3 + - - -
344O LEU* 3.8 33.1 - - - +
345O SER* 4.4 8.1 + - - -
348O TYR* 5.8 1.2 - - - +
360O LEU 2.7 21.0 + - - -
361O LEU* 3.5 19.0 + - - -
363O HIS* 1.3 70.5 - - - +
365O VAL* 1.3 61.5 - - - +
367O LYS* 4.2 1.1 - - - +
368O ALA* 3.0 36.4 + - - +
376O LEU 5.6 2.6 + - - -
377O ALA* 5.2 1.3 - - - -
380O GLY* 5.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361O LEU 3.2 13.4 + - - +
362O GLU 3.1 16.6 - - - +
364O SER* 1.3 76.9 - - - +
366O LYS* 1.3 79.6 + - + +
369O VAL* 3.2 35.9 + - + +
377O ALA* 3.5 14.8 - - + +
380O GLY* 3.5 9.4 - - - -
381O ILE* 3.5 38.4 - - + +
384O LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 366 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362O GLU* 2.8 49.5 + - - +
363O HIS* 3.3 7.7 + - - +
365O VAL* 1.3 96.2 - - + +
367O LYS* 1.3 67.0 + - + +
369O VAL* 3.6 14.1 + - - +
370O HIS* 3.7 10.7 + - - +
384O LEU* 5.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098A GLU* 3.8 25.6 - - + +
1099A PRO* 4.1 17.4 - - - +
1101A PRO* 5.5 11.9 - - - +
341O GLN* 3.6 28.3 - - - +
344O LEU* 5.0 4.7 - - + -
363O HIS* 2.8 43.5 + - + +
364O SER* 4.2 1.8 - - - +
366O LYS* 1.3 74.7 - - + +
368O ALA* 1.3 58.1 + - - +
370O HIS* 2.9 28.9 + - - +
371O PHE* 3.7 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341O GLN* 4.0 15.9 + - + +
364O SER* 3.0 21.4 + - - +
367O LYS* 1.3 73.1 - - - +
369O VAL* 1.3 53.3 + - - +
370O HIS 2.9 8.5 - - - +
372O GLY 2.8 28.1 - - - +
373O LEU* 3.5 11.9 - - + +
376O LEU* 4.1 14.6 - - + +
377O ALA* 3.7 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365O VAL* 3.2 25.6 + - + +
366O LYS* 3.7 8.7 - - - +
367O LYS 3.3 0.2 - - - -
368O ALA* 1.3 77.6 - - - +
370O HIS* 1.3 61.6 + - + +
372O GLY* 3.3 16.4 + - - +
377O ALA* 4.1 11.9 - - + -
381O ILE* 6.4 0.9 - - + -
408O LEU* 5.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 370 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366O LYS 3.7 5.6 + - - +
367O LYS* 2.9 25.2 + - - +
368O ALA* 2.9 15.6 - - - +
369O VAL* 1.3 77.9 - - + +
371O PHE* 1.3 104.1 + + + +
372O GLY 3.1 0.8 - - - -
373O LEU* 4.8 0.5 - - - +
----------------------------------------------------------
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