Contacts of the helix formed by residues 408 - 422 (chain B) in PDB entry 3RU0
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 HIS 408 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA* 5.0 11.2 - - + -
215B VAL* 3.7 33.2 - - + +
216B PHE 2.9 26.4 + - - -
217B ASN* 3.7 26.9 - - + -
222B LEU* 4.3 4.0 - - + -
404B HIS* 3.6 33.1 + + + +
405B GLY 3.0 6.7 + - - +
406B ARG 3.8 5.5 - - - +
407B GLU* 1.3 79.3 - - - +
409B SER* 1.3 68.3 + - - +
410B LEU* 3.0 42.8 + - + +
411B ILE* 3.1 18.4 + - - +
412B GLU 4.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASN* 2.9 35.1 + - - -
407B GLU 3.8 1.2 + - - -
408B HIS* 1.3 72.7 + - - +
410B LEU* 1.3 63.8 + - - +
411B ILE 3.2 0.2 - - - -
412B GLU* 3.3 19.6 + - - +
413B ASP* 3.5 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA* 3.7 39.9 - - + +
189B GLU* 5.5 2.5 - - - +
371B VAL* 4.1 6.5 - - + -
374B MET* 3.9 21.1 - - + -
400B MET* 3.7 26.1 - - + +
404B HIS* 3.9 14.6 - - + +
408B HIS* 3.0 20.4 + - + +
409B SER* 1.3 76.1 + - - +
411B ILE* 1.3 59.4 + - - +
413B ASP* 3.3 20.8 + - + +
414B LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PHE* 4.3 21.8 - - + -
400B MET* 3.8 37.9 - - + +
401B ARG* 4.0 7.9 - - - +
404B HIS* 4.2 8.1 - - + -
405B GLY 3.4 24.0 - - - +
406B ARG* 4.4 13.5 - - + +
408B HIS* 3.1 12.0 + - - +
410B LEU* 1.3 75.3 - - - +
412B GLU* 1.3 59.8 + - - +
414B LEU* 3.4 8.1 + - + +
415B ILE* 3.0 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B HIS 4.2 1.2 + - - +
409B SER* 3.3 14.8 + - - +
411B ILE* 1.3 79.7 - - - +
413B ASP* 1.3 61.7 + - - +
415B ILE* 3.3 10.5 + - - +
416B LEU* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 4.2 11.9 - - + -
409B SER* 3.5 13.6 + - - +
410B LEU* 3.3 22.7 + - + +
411B ILE 3.3 0.4 - - - -
412B GLU* 1.3 77.0 - - - +
414B LEU* 1.3 64.8 + - - +
416B LEU* 3.3 8.9 + - - +
417B LEU* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 3.7 31.8 - - + +
393B LEU* 3.9 33.4 - - + +
396B ALA* 3.7 12.1 - - + +
397B PHE* 3.5 39.5 - - + +
400B MET* 3.9 18.6 - - + -
410B LEU 3.0 15.0 + - - +
411B ILE* 3.8 8.1 - - + +
412B GLU 3.4 0.2 - - - -
413B ASP* 1.3 76.8 - - - +
415B ILE* 1.3 58.3 + - + +
417B LEU* 3.3 6.2 + - + +
418B LEU* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PHE* 4.1 24.5 - - + -
411B ILE* 3.0 39.6 + - + +
412B GLU* 3.6 9.0 - - - +
413B ASP 3.3 0.2 - - - -
414B LEU* 1.3 74.3 - - - +
416B LEU* 1.3 63.2 + - - +
418B LEU* 3.3 11.9 + - + +
419B GLU* 3.0 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLU 3.0 13.5 + - - +
413B ASP* 3.4 12.3 - - - +
415B ILE* 1.3 75.9 - - - +
417B LEU* 1.3 56.4 + - + +
419B GLU* 3.4 7.4 + - - +
420B GLU* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET* 3.8 30.1 - - + -
378B LYS* 3.9 50.0 - - + -
381B LEU* 3.9 15.9 - - + +
393B LEU* 3.9 24.9 - - + +
413B ASP* 3.1 14.1 + - + +
414B LEU* 3.5 7.2 - - - +
416B LEU* 1.3 75.2 - - + +
418B LEU* 1.3 58.9 + - - +
420B GLU* 3.4 7.3 + - + +
421B CYS* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B MET* 3.8 19.1 - - - +
393B LEU* 3.7 37.0 - - + +
394B ARG* 3.9 9.6 - - + +
397B PHE* 4.1 29.4 - - + -
414B LEU* 3.0 24.6 + - + +
415B ILE* 3.3 17.2 + - + +
417B LEU* 1.3 73.0 - - - +
419B GLU* 1.3 65.0 + - - +
421B CYS* 3.3 8.0 + - - +
422B ASP* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ILE* 3.0 15.4 + - + +
416B LEU* 3.6 10.3 - - - +
418B LEU* 1.3 76.6 - - - +
420B GLU* 1.3 57.6 + - - +
421B CYS 3.1 0.2 - - - -
422B ASP* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 4.1 16.3 - - + +
386B PHE* 5.7 1.4 - - - -
416B LEU 2.9 18.1 + - - +
417B LEU* 3.7 10.1 - - + +
418B LEU 3.4 0.2 - - - -
419B GLU* 1.3 74.7 - - - +
421B CYS* 1.3 58.0 + - - +
422B ASP 3.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 3.9 22.0 - - + -
386B PHE* 3.6 38.9 - - - +
389B ALA* 4.1 7.0 - - - -
390B MET* 3.5 30.9 - - + +
393B LEU* 4.1 8.3 - - + -
417B LEU 3.0 16.8 + - - +
418B LEU 3.6 5.6 - - - +
419B GLU 3.1 0.4 - - - -
420B GLU* 1.3 77.1 - - - +
422B ASP* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B MET* 3.8 13.2 - - + -
418B LEU 3.1 13.7 + - - +
419B GLU* 3.1 19.1 + - - +
420B GLU 4.5 2.9 - - - +
421B CYS* 1.3 81.7 - - - +
----------------------------------------------------------
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