Contacts of the helix formed by residues 413 - 424 (chain C) in PDB entry 5H2U
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 PRO 413 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C VAL* 4.1 16.6 - - + -
290C LEU* 4.3 10.8 - - + -
381C PHE* 3.9 17.0 - - + -
411C GLU 3.4 8.7 - - - +
412C CYS* 1.4 84.8 - - - +
414C PRO* 1.4 68.9 - - + +
415C SER* 3.2 4.3 - - - +
416C VAL* 2.8 41.3 + - + +
417C HIS 3.1 8.5 + - - -
444C PHE* 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C CYS* 4.5 6.7 - - - -
412C CYS 3.4 6.2 - - - +
413C PRO* 1.4 84.2 - - + +
415C SER* 1.3 56.9 + - - +
417C HIS* 3.3 8.9 + - + +
418C LYS* 3.1 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C PRO* 4.9 3.4 - - - -
414C PRO* 1.3 80.5 - - - +
416C VAL* 1.3 61.5 + - - +
418C LYS* 3.7 6.8 + - - +
419C LEU* 3.3 20.8 + - - +
440C ARG* 2.6 36.4 + - - +
444C PHE* 3.4 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 3.8 26.5 - - + -
377C LEU* 4.9 5.4 - - + -
381C PHE* 3.9 20.9 - - + -
412C CYS* 3.9 15.3 - - - -
413C PRO* 2.8 21.9 + - + +
415C SER* 1.3 73.8 - - - +
417C HIS* 1.3 61.9 + - - +
419C LEU* 3.2 10.0 - - + +
420C MET* 3.0 32.1 + - + +
441C LEU* 4.7 13.9 - - + -
444C PHE* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C MET 3.0 24.7 + - - -
407C PRO* 4.2 2.7 - - + -
408C CYS* 3.4 55.2 + - + +
412C CYS* 3.7 5.1 - - - -
413C PRO 3.1 5.6 + - - +
414C PRO* 3.3 7.8 + - + +
416C VAL* 1.3 74.9 - - - +
418C LYS* 1.3 63.0 + - - +
420C MET* 3.1 32.2 + - + +
421C LEU* 2.9 55.4 + - + +
424C TRP* 4.4 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C PRO* 3.1 31.7 + - + +
415C SER* 4.1 7.2 - - - +
416C VAL 3.3 0.2 - - - -
417C HIS* 1.3 80.3 - - - +
419C LEU* 1.3 61.2 + - - +
421C LEU* 3.4 22.7 - - + +
422C THR* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C PHE* 4.7 2.2 - - + -
377C LEU* 3.8 24.7 - - + -
415C SER 3.3 12.1 + - - +
416C VAL* 3.2 11.2 + - + +
418C LYS* 1.3 75.1 - - - +
420C MET* 1.3 65.2 + - - +
422C THR* 2.7 25.9 + - - +
423C CYS* 3.3 8.5 + - - -
437C LEU* 3.6 26.2 - - + -
440C ARG* 3.7 32.1 - - + +
441C LEU* 3.8 31.4 - - + -
444C PHE* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 420 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C GLY* 3.9 3.4 - - - +
377C LEU* 3.5 39.0 - - + +
378C HIS* 3.8 29.2 - - + +
381C PHE* 5.0 0.2 - - - -
409C PRO* 4.4 4.5 - - + -
412C CYS* 3.9 21.1 - - - -
416C VAL* 3.0 20.5 + - - +
417C HIS* 3.3 23.1 - - + +
419C LEU* 1.3 75.8 - - - +
421C LEU* 1.3 57.4 + - - +
423C CYS* 3.0 30.6 + - - +
424C TRP* 3.2 45.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C ARG* 4.3 18.6 + - + -
406C MET 4.4 0.9 - - - +
417C HIS* 2.9 51.3 + - + +
418C LYS* 3.4 27.4 - - + +
419C LEU 3.3 0.2 - - - -
420C MET* 1.3 77.2 - - - +
422C THR* 1.3 60.3 + - + +
424C TRP* 3.2 39.8 + - + +
425C CYS* 3.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C LYS 3.2 15.3 + - - +
419C LEU* 2.7 22.3 + - - +
421C LEU* 1.3 73.3 - - + +
423C CYS* 1.3 63.4 + - - +
424C TRP 3.2 1.0 + - - -
425C CYS* 3.6 9.6 + - - +
430C GLN 4.3 3.9 - - - +
431C ARG* 3.4 12.3 - - - +
432C PRO* 3.2 34.0 - - - +
437C LEU* 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C VAL* 3.5 36.8 - - - +
371C TRP* 3.3 12.0 - - - -
373C PHE* 4.2 10.1 - - - -
374C GLY* 4.0 14.6 - - - -
419C LEU* 3.3 20.0 + - - -
420C MET* 3.0 14.2 + - - +
422C THR* 1.3 76.3 - - - +
424C TRP* 1.3 58.6 - - + +
425C CYS 3.4 0.9 - - - -
431C ARG* 3.1 22.7 + - - -
432C PRO* 4.5 0.4 - - - -
437C LEU* 3.8 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 424 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C TRP* 3.2 54.9 + + + -
374C GLY* 3.3 25.9 - - - -
375C ILE* 3.4 24.3 - - + +
388C TYR* 5.4 2.7 - - - -
405C ARG* 2.8 51.7 + - + +
406C MET* 4.0 37.7 - - + -
417C HIS* 4.4 0.2 - - - -
420C MET* 3.4 37.7 - - + -
421C LEU* 3.2 40.3 + - + +
422C THR 3.2 1.2 - - - -
423C CYS* 1.3 81.9 - - - +
425C CYS* 1.3 58.5 + - - +
----------------------------------------------------------
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