Contacts of the helix formed by residues 515 - 520 (chain L) in PDB entry 6Y5D
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 GLU 515 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161L GLY* 5.4 7.4 - - - -
164L LYS* 2.8 43.4 + - + +
165L LEU* 5.9 0.3 - - - +
511L GLU 3.1 1.4 + - - -
512L ARG 3.4 8.4 + - - +
513L ASN 5.6 0.7 - - - +
514L ASN* 1.3 82.2 - - - +
516L PHE* 1.3 72.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 516 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L LYS* 4.3 2.9 + - - -
165L LEU* 4.2 11.9 - - + -
416L LEU* 3.9 25.6 - - + -
461L GLY 6.0 0.7 - - - -
464L PHE* 3.3 39.0 - + - -
465L ASP* 5.1 3.8 - - + -
468L VAL* 4.2 8.1 - - + -
508L ILE 4.7 0.7 - - - -
511L GLU* 2.7 34.1 + - + +
512L ARG* 3.6 42.8 - - + -
515L GLU* 1.3 80.2 - - - +
517L PRO* 1.3 68.0 - - - +
518L VAL 3.2 2.7 - - - -
519L PHE* 3.1 40.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 517 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L LYS* 4.3 10.8 - - - +
423L ARG* 5.5 0.2 - - - +
510L TYR* 4.4 11.7 - - + +
511L GLU* 3.0 24.9 - - - +
514L ASN* 3.3 27.4 - - + +
515L GLU 3.5 0.8 - - - -
516L PHE* 1.3 84.8 - - - +
518L VAL* 1.3 55.7 + - - +
519L PHE 3.0 4.7 - - - -
520L ASP* 2.9 26.0 + - - +
521L GLU* 3.3 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 518 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416L LEU* 4.0 19.3 - - + -
419L GLN* 2.8 56.6 + - + -
420L LEU* 4.6 4.5 - - + -
423L ARG* 3.3 22.4 - - - +
511L GLU* 2.9 30.3 + - + +
516L PHE 4.7 0.4 - - - +
517L PRO* 1.3 76.9 - - - +
519L PHE* 1.3 68.8 + - + +
520L ASP 3.1 1.0 + - - -
521L GLU* 3.4 13.3 + - - -
522L PHE* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 519 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L LYS* 5.6 3.1 - - + -
165L LEU* 3.5 28.5 - - + -
168L VAL* 3.6 24.1 - - + +
171L LYS* 2.8 20.6 + - - -
412L LEU* 3.5 22.2 - - + -
415L TYR* 2.8 52.1 + + + -
416L LEU* 3.6 29.2 - - + -
419L GLN* 4.8 0.2 - - + -
464L PHE* 3.8 13.9 - + - -
515L GLU 5.2 0.4 - - - -
516L PHE* 3.1 39.5 + + + +
517L PRO 2.9 0.4 + - - -
518L VAL* 1.3 86.7 - - + +
520L ASP* 1.3 54.9 + - - +
522L PHE* 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 520 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L LYS* 3.0 38.4 + - - +
168L VAL* 4.4 10.0 - - - +
171L LYS* 4.2 11.8 + - - +
517L PRO* 2.9 10.5 + - - +
519L PHE* 1.3 83.0 - - - +
521L GLU* 1.3 63.9 + - + +
522L PHE* 3.2 4.4 + - - -
----------------------------------------------------------
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