Contacts of the helix formed by residues 208 - 215 (chain D) in PDB entry 4NY0
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 208 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D TYR* 5.0 2.2 - - + +
156D MET* 4.5 5.8 - - + -
160D ALA* 3.6 40.2 - - + +
161D ASP* 3.1 20.6 - - - +
168D ALA* 4.1 20.9 - - + +
206D PHE 4.6 1.1 - - - +
207D PHE* 1.3 94.4 - - + +
209D LYS* 1.3 63.2 + - - +
210D SER* 4.0 2.7 - - - +
211D LEU* 3.1 27.6 + - + +
212D LEU* 3.3 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ASP* 3.4 8.0 + - - +
204D LYS* 6.0 4.0 - - + +
207D PHE 3.8 1.2 + - - -
208D PRO* 1.3 71.6 - - - +
210D SER* 1.3 65.2 + - - +
211D LEU 3.1 0.9 + - - -
212D LEU* 4.5 10.1 - - + +
213D ASP* 2.7 55.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ASP* 3.1 49.9 + - - -
165D GLN* 3.9 13.7 + - - +
208D PRO* 4.2 3.4 - - - -
209D LYS* 1.3 80.6 - - - +
211D LEU* 1.3 56.8 + - - +
213D ASP* 4.6 1.8 - - - +
214D SER* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLN* 3.3 42.4 - - + +
168D ALA* 4.2 17.0 - - + -
169D LEU* 4.0 21.1 - - + -
207D PHE* 3.8 32.1 - - + -
208D PRO* 3.1 17.5 + - + +
209D LYS 3.1 0.6 - - - -
210D SER* 1.3 75.7 - - - +
212D LEU* 1.3 66.8 + - + +
213D ASP 3.1 3.5 + - - -
214D SER* 3.7 2.5 + - - -
215D VAL* 3.6 30.6 + - + +
220D LEU* 4.4 15.5 - - + +
223D LEU* 5.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D LEU* 3.5 37.5 - - + +
204D LYS* 3.4 40.2 - - + +
207D PHE* 4.1 21.8 - - + +
208D PRO 3.3 12.0 + - - +
209D LYS* 3.4 9.6 + - + +
211D LEU* 1.3 76.6 - - + +
213D ASP* 1.3 65.5 + - - +
215D VAL 3.7 10.1 - - - +
220D LEU* 3.7 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D LYS* 2.7 54.4 + - - +
210D SER* 4.6 1.8 - - - +
211D LEU 3.1 0.6 - - - -
212D LEU* 1.3 84.4 - - - +
214D SER* 1.3 65.3 + - - +
215D VAL 3.3 8.8 + - - +
216D LYS* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLN* 3.7 16.2 + - - -
210D SER 2.9 20.6 + - - -
211D LEU* 3.7 4.5 + - - -
213D ASP* 1.3 79.2 - - - +
215D VAL* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLN* 4.5 12.1 - - - +
211D LEU* 3.6 16.2 + - + +
212D LEU 3.7 13.5 - - - +
213D ASP 3.3 8.7 - - - +
214D SER* 1.3 89.6 + - - +
216D LYS* 1.3 68.1 + - - +
219D THR* 3.6 32.1 - - + -
220D LEU* 3.8 20.7 - - + +
223D LEU* 3.9 18.4 - - + -
----------------------------------------------------------
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