Contacts of the helix formed by residues 418 - 422 (chain B) in PDB entry 2YWB
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 LEU 418 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 2.9 19.9 + - + +
416B TRP* 3.8 22.7 - - + +
417B GLY* 1.3 78.9 - - - +
419B TYR* 1.3 67.3 + - - +
420B GLU 3.4 0.9 - - - -
421B LYS* 2.9 35.0 + - + +
422B VAL* 3.5 10.7 + - - +
466B LEU* 4.4 11.7 - - + -
467B PRO* 4.1 25.8 - - + -
470B PHE* 3.6 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 4.7 6.1 + - - -
377B LEU 3.5 11.4 - - - -
378B ARG* 3.4 8.4 + - - +
379B HIS* 2.9 79.4 + + - +
410B THR* 4.1 21.3 - - + -
413B LEU* 3.1 25.5 + - + +
414B ARG* 3.6 58.9 + - + -
417B GLY* 3.4 1.0 - - - -
418B LEU* 1.3 78.3 - - - +
420B GLU* 1.3 90.9 + - + +
421B LYS 3.2 0.3 + - - -
422B VAL* 3.4 6.2 - - - +
425B ALA* 5.5 1.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
377B LEU* 2.8 51.6 - - + +
379B HIS* 4.8 2.7 - - - -
414B ARG* 4.5 4.5 + - - -
417B GLY 4.5 4.2 + - - +
418B LEU 3.4 0.4 - - - -
419B TYR* 1.3 96.2 - - + +
421B LYS* 1.3 62.4 + - + +
422B VAL 3.3 7.4 + - - +
421D LYS* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TRP 5.8 0.6 + - - -
417B GLY* 3.4 24.0 + - - +
418B LEU* 2.9 26.6 + - + +
420B GLU* 1.3 80.9 - - + +
422B VAL* 1.3 64.4 + - + +
454B THR* 3.9 2.4 - - - +
466B LEU* 6.4 0.4 - - + -
420D GLU 5.4 0.7 - - - -
421D LYS* 2.9 84.0 + - + +
422D VAL* 4.8 1.2 - - - +
423D ALA 5.6 0.2 - - - +
454D THR* 3.4 29.5 - - - +
455D THR 5.2 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B HIS* 3.2 32.2 + - - +
413B LEU* 5.1 3.8 - - + -
418B LEU 3.9 9.9 - - - +
419B TYR* 3.4 15.7 - - - +
420B GLU 3.9 5.8 - - - +
421B LYS* 1.3 85.2 - - + +
423B ALA* 1.3 59.5 + - - +
424B GLN 3.8 14.8 - - - +
425B ALA* 4.2 8.1 - - + -
452B ALA* 4.5 4.5 - - + -
453B VAL 3.6 9.6 - - - +
454B THR* 4.3 4.3 - - + -
464B ALA* 3.8 25.6 - - + -
466B LEU* 4.0 17.0 - - + -
421D LYS* 6.0 0.4 - - - -
----------------------------------------------------------
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