Contacts of the helix formed by residues 410 - 418 (chain B) in PDB entry 4YVF
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 THR 410 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 6.4 0.2 - - - +
408B LYS 4.6 4.5 - - - +
409B LEU* 1.3 75.8 - - - +
411B GLU* 1.3 58.9 + - - +
412B LYS* 3.4 9.6 + - - +
413B GLN* 2.9 46.7 + - - +
414B ALA* 2.8 26.9 + - - +
421B CYS* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU 4.0 0.4 + - - -
410B THR* 1.3 73.2 - - - +
412B LYS* 1.3 54.3 + - - +
414B ALA* 3.3 6.9 + - + +
415B GLN* 2.8 67.4 + - + +
421B CYS* 4.4 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 3.8 15.9 - - + -
280A ASP* 3.3 31.3 + - - +
410B THR* 3.7 8.0 - - - +
411B GLU* 1.3 78.9 - - - +
413B GLN* 1.3 56.6 + - - +
415B GLN* 3.8 9.3 - - - +
416B TYR* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A CYS* 3.8 8.3 - - - -
279A ILE* 2.9 33.0 + - + +
280A ASP* 3.2 25.7 + - + +
281A ILE* 4.3 0.4 - - - +
501A NAI 3.8 16.9 + - - -
407B THR* 5.6 1.6 - - - +
408B LYS 4.1 2.4 - - - +
409B LEU* 3.5 21.3 - - + +
410B THR* 2.9 50.1 + - - +
412B LYS* 1.3 73.7 - - - +
414B ALA* 1.3 55.7 + - - +
416B TYR* 3.1 7.1 + - - +
417B LEU* 2.7 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 4.2 15.6 - - + +
410B THR 2.8 19.7 + - - +
411B GLU* 3.7 3.8 - - - +
413B GLN* 1.3 72.8 - - - +
415B GLN* 1.3 54.3 + - + +
417B LEU* 3.1 2.2 + - - +
418B GLY 2.7 30.8 + - - -
419B MET 3.0 29.5 + - - +
421B CYS* 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLU* 2.8 57.6 + - + +
412B LYS* 3.9 7.2 - - - +
414B ALA* 1.3 72.3 - - + +
416B TYR* 1.3 65.6 + - - +
418B GLY* 3.3 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLY 3.8 19.7 - - - -
278A CYS* 4.2 0.7 - - - -
279A ILE* 3.4 50.7 - - + -
301A HIS* 3.2 32.4 + - - -
304A VAL* 3.7 6.5 - - + +
412B LYS 2.9 19.8 + - - +
413B GLN* 3.1 4.2 + - - +
415B GLN* 1.3 78.6 - - - +
417B LEU* 1.3 73.2 + - + +
418B GLY* 3.4 0.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
276A THR 5.2 2.0 - - - +
277A GLY 3.7 24.2 - - - +
278A CYS* 3.6 22.2 - - + -
501A NAI 4.1 9.9 - - + +
409B LEU* 3.6 39.5 - - + -
413B GLN 2.7 17.1 + - - +
414B ALA 3.8 0.2 - - - +
416B TYR* 1.3 80.3 - - + +
418B GLY* 1.3 62.2 + - - +
419B MET* 3.5 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ALA 2.7 12.3 + - - -
415B GLN* 3.3 8.4 + - - -
416B TYR 3.2 4.8 + - - -
417B LEU* 1.3 76.2 - - - +
419B MET* 1.3 57.4 + - - +
----------------------------------------------------------
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