Contacts of the helix formed by residues 406 - 421 (chain Y) 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 ARG 406 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279Y ASP* 5.6 4.2 - - - +
282Y PHE* 3.3 37.5 - - + -
283Y ARG* 3.5 50.7 - - - +
310Y VAL* 4.7 6.9 - - - +
373Y VAL* 5.2 10.9 - - + +
374Y GLN* 4.8 4.0 + - - -
403Y ALA* 4.1 15.5 - - + -
404Y PRO 3.3 11.0 + - - +
405Y CYS* 1.3 82.0 - - - +
407Y LEU* 1.3 63.8 + - - +
408Y ASP* 3.3 3.8 - - + +
409Y CYS* 2.9 39.6 + - + +
410Y TYR* 3.0 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Y PHE 5.9 1.3 - - - +
283Y ARG* 4.3 21.8 - - - +
284Y ALA 5.2 2.2 - - - +
285Y GLY* 4.8 13.0 - - - -
405Y CYS 4.1 11.7 - - - +
406Y ARG* 1.3 72.1 - - - +
408Y ASP* 1.3 62.4 + - - +
410Y TYR* 3.3 10.9 + - - +
411Y GLU* 3.1 23.1 + - - +
433Y VAL* 5.8 1.3 - - - -
437Y LEU* 3.5 31.4 - - + -
443Y THR* 3.4 38.4 - - + +
447Y LEU* 5.4 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Y PHE* 4.9 14.1 - - + -
313Y TYR* 2.9 50.4 + - + -
374Y GLN* 3.9 14.2 + - - +
377Y LEU* 4.2 12.0 - - + +
406Y ARG* 5.0 2.9 - - + -
407Y LEU* 1.3 80.0 - - - +
409Y CYS* 1.3 61.8 + - - +
411Y GLU* 3.0 41.5 + - - +
412Y GLY* 3.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 409 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377Y LEU* 4.1 30.7 - - + +
396Y PHE* 4.8 6.0 - - - -
399Y ALA* 5.2 2.9 - - + +
400Y ILE* 3.9 22.8 - - + +
403Y ALA* 3.3 34.3 - - + -
406Y ARG* 2.9 34.8 + - + +
408Y ASP* 1.3 79.4 - - - +
410Y TYR* 1.3 72.2 + - - +
411Y GLU 3.6 0.2 + - - -
412Y GLY* 3.7 1.4 + - - -
413Y LEU* 3.6 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 410 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400Y ILE* 4.4 25.4 + - + -
403Y ALA 4.1 4.7 + - - -
404Y PRO* 3.7 8.7 - - - +
405Y CYS* 3.1 35.1 + - - -
406Y ARG 3.0 29.1 + - - -
407Y LEU* 3.3 8.6 + - - +
408Y ASP 3.2 0.6 - - - -
409Y CYS* 1.3 77.2 - - - +
411Y GLU* 1.3 64.8 + - - +
413Y LEU* 3.4 12.0 + - + +
414Y ILE* 3.1 26.7 + - - +
429Y MET 5.6 1.8 - - - -
432Y ASN 5.8 0.7 - - - -
433Y VAL* 3.5 49.4 - - + -
436Y THR* 4.1 13.3 + - + +
437Y LEU* 4.7 1.3 - - + -
447Y LEU* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Y TYR* 4.0 6.3 + - - -
407Y LEU 3.1 13.0 + - - +
408Y ASP* 3.0 39.4 + - - +
410Y TYR* 1.3 73.9 - - - +
412Y GLY* 1.3 58.8 + - - +
414Y ILE* 3.2 11.2 - - - +
415Y GLU* 2.9 54.9 + - + +
447Y LEU* 4.2 15.0 - - + +
477Y LYS* 4.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 412 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384Y ARG* 4.4 4.9 + - - -
396Y PHE* 4.1 22.9 - - - -
408Y ASP 3.4 6.5 + - - -
409Y CYS 3.7 2.0 + - - -
410Y TYR 3.3 0.6 - - - -
411Y GLU* 1.3 81.7 - - - +
413Y LEU* 1.3 65.7 + - - +
415Y GLU* 3.5 4.9 + - - +
416Y CYS* 3.0 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393Y ILE* 4.7 0.9 - - - +
396Y PHE* 3.9 28.9 - - + -
397Y ARG* 4.0 21.8 - - + +
400Y ILE* 3.8 31.0 - - + -
409Y CYS 3.6 11.4 + - - +
410Y TYR* 3.4 15.1 + - + +
411Y GLU 3.4 0.2 - - - -
412Y GLY* 1.3 78.1 - - - +
414Y ILE* 1.3 61.3 + - - +
416Y CYS* 3.4 3.8 + - + +
417Y TYR* 3.1 49.6 + - + -
429Y MET* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 414 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410Y TYR 3.1 13.6 + - - +
411Y GLU* 3.2 23.6 - - - +
413Y LEU* 1.3 79.9 - - - +
415Y GLU* 1.3 63.7 + - + +
417Y TYR* 3.4 8.5 + - - +
418Y LEU* 3.2 21.6 + - + +
426Y ALA* 4.0 28.9 - - + +
429Y MET* 5.2 7.9 - - + -
430Y ALA* 4.8 5.6 - - + +
447Y LEU* 3.7 26.5 - - + +
450Y VAL* 4.6 13.5 - - + -
451Y CYS* 3.4 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384Y ARG* 3.0 40.8 + - - +
411Y GLU* 2.9 49.3 + - + +
412Y GLY* 3.8 1.3 - - - +
414Y ILE* 1.3 72.6 - - + +
416Y CYS* 1.3 66.2 + - - +
418Y LEU* 3.3 13.8 - - + +
419Y ALA 3.3 15.1 + - - -
447Y LEU* 6.5 0.2 - - + -
450Y VAL* 6.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 416 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384Y ARG* 3.6 37.2 - - - +
389Y VAL* 4.2 8.6 - - + +
392Y ALA* 5.2 2.9 - - - -
393Y ILE* 4.3 20.0 - - + -
396Y PHE* 3.5 32.1 - - + -
412Y GLY 3.0 22.9 + - - +
413Y LEU* 3.6 6.3 - - + +
414Y ILE 3.4 0.2 - - - -
415Y GLU* 1.3 75.7 - - - +
417Y TYR* 1.3 58.8 + - + +
419Y ALA* 3.2 8.2 + - - +
420Y SER* 3.0 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 417 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393Y ILE* 3.3 37.3 - - + +
397Y ARG* 3.7 18.4 + - - +
413Y LEU* 3.1 44.6 + - + -
414Y ILE 3.8 7.6 - - - +
415Y GLU 3.3 0.2 - - - -
416Y CYS* 1.3 76.0 - - + +
418Y LEU* 1.3 55.9 + - - +
420Y SER* 3.1 8.4 + - - -
421Y ASN 2.8 29.6 + - - -
422Y SER* 3.1 41.3 + - - +
425Y GLU* 3.5 27.2 + - + -
426Y ALA* 4.4 3.6 - - + -
429Y MET* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384Y ARG* 5.8 1.6 - - - +
414Y ILE* 3.2 14.2 + - + +
415Y GLU* 3.3 16.4 + - + +
417Y TYR* 1.3 75.1 - - - +
419Y ALA* 1.3 61.9 + - + +
421Y ASN* 3.1 22.7 + - - +
422Y SER 5.2 0.4 - - - +
426Y ALA* 5.1 4.1 - - + +
450Y VAL* 5.4 15.9 - - + +
454Y ASP* 3.7 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384Y ARG* 4.6 13.0 - - + +
389Y VAL* 4.9 10.1 - - + -
415Y GLU 3.3 7.2 + - - +
416Y CYS* 3.2 11.7 + - - +
418Y LEU* 1.3 84.3 - - + +
420Y SER* 1.3 60.7 + - - +
421Y ASN* 3.4 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389Y VAL* 4.8 10.9 - - - +
393Y ILE* 4.3 19.3 - - - +
416Y CYS 3.0 13.2 + - - -
417Y TYR* 3.1 15.1 + - - -
419Y ALA* 1.3 74.8 - - - +
421Y ASN* 1.3 68.6 + - - +
422Y SER* 3.8 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 421 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Y TYR 2.8 6.6 + - - -
418Y LEU* 3.1 16.0 + - - +
419Y ALA 3.2 2.4 - - - +
420Y SER* 1.3 80.3 - - - +
422Y SER* 1.3 57.4 + - - +
423Y ILE* 3.2 27.0 + - - +
454Y ASP* 4.2 6.9 - - - +
----------------------------------------------------------
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