Contacts of the helix formed by residues 336 - 351 (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 ASP 336 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291O ASN 3.1 24.1 - - - +
292O GLY* 3.5 12.6 - - - -
301O ARG* 3.2 37.6 + - - +
302O TYR* 4.1 4.3 + - - -
331O ALA 3.0 20.6 + - - +
334O SER* 4.2 3.9 - - - +
335O ASN* 1.3 75.9 - - - +
337O HIS* 1.3 62.9 + - - +
338O VAL* 5.3 0.3 - - - +
339O CYS* 3.0 27.6 + - - +
340O LEU* 3.5 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 337 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A PRO* 5.4 4.9 - - + +
1160A TYR* 2.8 41.3 + + - +
1164A LYS* 5.3 9.4 - - - -
289O LYS 3.9 13.0 + - - -
290O SER* 3.4 16.4 + - - +
335O ASN* 3.6 16.4 + - + -
336O ASP* 1.3 71.4 - - - +
338O VAL* 1.3 64.9 + - - +
340O LEU* 3.5 7.2 + - - +
341O GLN* 3.1 31.1 + - - +
371O PHE* 3.8 44.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 4.3 24.5 - - + -
290O SER* 3.4 29.3 + - - +
291O ASN* 3.9 25.1 - - + +
302O TYR* 5.5 1.3 - - - +
336O ASP* 3.5 0.4 - - - +
337O HIS* 1.3 74.0 - - - +
339O CYS* 1.3 63.3 + - - +
341O GLN* 3.5 5.7 + - - +
342O HIS* 3.0 30.3 + - + -
371O PHE* 4.8 8.7 - - + +
373O LEU* 4.3 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 339 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301O ARG* 3.7 26.5 - - - -
302O TYR* 3.7 25.5 - - + -
305O LEU* 4.7 5.1 - - - +
331O ALA* 3.7 23.1 - - - -
336O ASP* 3.0 27.6 + - - +
337O HIS 3.5 0.2 - - - -
338O VAL* 1.3 78.8 - - - +
340O LEU* 1.3 56.6 + - - +
342O HIS* 3.0 12.9 + - - +
343O CYS* 3.0 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A THR* 3.3 34.1 - - + +
1160A TYR* 3.6 38.6 - - + +
328O ILE* 3.7 43.1 - - + +
331O ALA* 3.9 15.7 - - + +
332O GLN* 4.2 13.2 - - + -
336O ASP 3.5 18.7 + - - +
337O HIS* 3.5 6.5 + - - +
338O VAL 3.3 0.8 - - - -
339O CYS* 1.3 79.4 - - - +
341O GLN* 1.3 57.7 + - - +
343O CYS* 3.1 9.2 + - - +
344O LEU 2.8 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A THR* 3.7 19.4 - - - +
1098A GLU* 5.7 1.8 - - - +
337O HIS* 3.1 20.7 + - - +
338O VAL 3.8 7.6 - - - +
339O CYS 3.3 0.2 - - - -
340O LEU* 1.3 76.3 - - - +
342O HIS* 1.3 57.5 + - - +
344O LEU* 3.1 16.5 + - - +
345O SER 2.8 24.3 + - - -
364O SER* 4.6 3.5 + - - +
367O LYS* 3.6 36.8 - - - +
368O ALA* 4.0 13.5 + - + +
371O PHE* 4.4 16.5 - - + -
373O LEU* 3.8 16.2 - - + -
376O LEU* 3.5 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 342 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PRO* 5.9 1.6 - - - +
14D GLU* 3.5 40.2 + - + +
16D LEU* 3.4 37.3 - - + +
17D TRP* 5.4 0.4 - + - -
305O LEU* 3.6 29.3 - - + +
338O VAL* 3.0 26.1 + - + -
339O CYS* 3.0 9.7 + - - +
341O GLN* 1.3 73.3 - - - +
343O CYS* 1.3 62.7 + - - +
345O SER* 3.3 17.9 + - - -
346O TRP* 3.6 10.5 + - + -
373O LEU* 3.8 14.0 - - + +
376O LEU* 3.5 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 343 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A THR* 4.3 0.7 - - - -
305O LEU* 4.0 13.9 - - - -
324O LEU* 4.0 8.4 - - + +
327O ALA* 4.1 16.6 - - - -
328O ILE* 3.9 49.4 - - + -
339O CYS* 3.0 23.9 + - - -
340O LEU* 3.2 15.9 - - - +
342O HIS* 1.3 74.1 - - - +
344O LEU* 1.3 51.3 + - - +
346O TRP* 3.4 2.8 + - - +
347O LEU* 2.6 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A VAL* 4.8 7.9 - - + -
1097A THR* 3.8 16.8 - - + +
1098A GLU* 5.6 2.7 - - + +
340O LEU 2.8 12.8 + - - +
341O GLN* 3.1 28.5 + - - +
343O CYS* 1.3 73.4 - - - +
345O SER* 1.3 69.4 + - - +
347O LEU* 2.8 35.3 + - + +
348O TYR* 3.0 12.5 + - + +
360O LEU* 4.1 29.8 - - + +
363O HIS* 5.3 6.1 - - + +
364O SER* 3.8 28.0 - - - +
367O LYS* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 345 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PRO* 3.2 27.8 - - - +
341O GLN 2.8 14.3 + - - -
342O HIS* 3.3 17.0 - - - -
344O LEU* 1.3 73.0 - - - +
346O TRP* 1.3 59.6 + - - -
348O TYR* 3.6 8.0 + - - +
349O VAL* 3.6 17.2 + - - +
361O LEU* 6.0 0.2 - - - +
364O SER* 4.4 6.8 + - - -
376O LEU* 3.5 29.2 + - - +
379O LEU* 4.2 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 346 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 2.8 43.5 - + + -
10D PRO* 3.1 51.7 - - + +
11D ARG 5.2 1.4 + - - -
305O LEU* 3.9 15.1 - - + +
306O ASN* 6.0 0.8 - - - +
309O ALA* 3.3 28.3 - - + +
312O CYS* 3.7 26.0 - - + -
313O ARG* 3.6 31.0 - - + +
324O LEU* 4.3 14.8 - - + -
342O HIS* 3.6 15.5 - - + +
343O CYS 3.4 6.7 + - - +
344O LEU 3.2 0.6 - - - -
345O SER* 1.3 74.5 - - - +
347O LEU* 1.3 55.8 + - - +
348O TYR 3.0 2.7 - - - -
349O VAL* 2.9 11.3 + - + +
350O LEU* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A VAL* 4.5 9.9 - - + -
1096A PRO* 4.8 12.6 - - + -
1097A THR* 3.3 30.3 - - - +
324O LEU* 3.7 15.7 - - + -
328O ILE* 4.1 15.7 - - + -
343O CYS 2.6 19.2 + - - +
344O LEU* 2.8 25.3 + - + +
346O TRP* 1.3 71.5 - - - +
348O TYR* 1.3 56.9 + - - +
350O LEU* 3.4 4.3 + - - +
351O GLY* 3.1 20.6 + - - -
360O LEU* 3.9 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 348 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344O LEU* 3.0 11.6 + - + +
345O SER 3.7 9.4 - - - +
347O LEU* 1.3 74.2 - - - +
349O VAL* 1.3 80.8 + - + +
350O LEU 3.2 1.6 - - - -
351O GLY* 3.1 19.5 - - - +
352O GLN* 3.4 40.0 + - + +
357O SER* 3.9 18.6 - - - -
360O LEU* 3.8 22.8 - - + +
361O LEU* 3.1 47.0 - - + +
364O SER* 5.8 1.1 - - - +
383O SER* 3.2 29.8 + - - -
386O GLN* 5.6 1.4 + - - -
387O GLN* 3.5 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU 3.4 24.9 - - - +
9D PHE* 3.6 39.7 - - + -
10D PRO* 4.2 5.8 - - + -
312O CYS* 5.7 0.7 - - + -
317O TYR* 4.4 14.7 - - + +
345O SER 4.0 7.9 - - - +
346O TRP* 2.9 19.3 + - + +
348O TYR* 1.3 96.3 - - + +
350O LEU* 1.3 56.0 + - - +
351O GLY 2.8 13.9 - - - +
352O GLN* 4.3 13.0 - - - +
353O LYS* 4.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308O ALA* 5.8 0.2 - - + -
312O CYS* 3.9 19.7 - - - -
317O TYR* 3.4 38.6 - - + +
320O ALA* 3.5 28.9 - - + +
321O GLU* 3.5 43.1 - - + +
324O LEU* 3.8 20.6 - - + -
346O TRP 2.7 13.0 + - - +
347O LEU* 3.6 7.0 - - - +
349O VAL* 1.3 74.5 - - - +
351O GLY* 1.3 60.8 + - - +
353O LYS* 4.2 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 351 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347O LEU 3.1 13.9 + - - -
348O TYR* 3.1 9.7 + - - +
349O VAL 2.8 18.7 - - - +
350O LEU* 1.3 73.5 - - - +
352O GLN* 1.3 53.6 + - - +
353O LYS* 2.6 21.9 + - - -
355O SER* 4.9 12.3 - - - -
357O SER* 5.3 4.7 - - - -
360O LEU* 6.2 0.9 - - - -
----------------------------------------------------------
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