Contacts of the helix formed by residues 209 - 214 (chain A) in PDB entry 5Y9F
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 ASP 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A HIS* 4.4 1.1 - - + -
169A TRP 2.6 15.5 + - - +
170A THR* 3.5 16.8 + - - +
208A MET* 1.3 71.6 - - - +
210A PHE* 1.3 57.1 + - - +
211A LYS* 3.2 12.0 + - - +
212A LEU* 3.2 46.3 + - + +
213A LEU* 2.9 30.7 + - + +
227A SER 3.9 0.2 - - - +
228A ILE* 3.4 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.8 20.2 - - + -
206A GLY 3.7 13.0 - - - -
208A MET* 3.3 49.4 - - + -
209A ASP* 1.3 73.2 - - - +
211A LYS* 1.3 60.4 + - - +
214A GLN* 3.2 56.7 + - - +
220A VAL* 3.6 26.0 - - + -
224A ILE* 3.2 31.9 - - + +
225A CYS 3.8 7.5 - - - +
227A SER 3.2 9.1 + - - +
229A CYS* 3.6 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 3.2 9.3 + - - +
210A PHE* 1.3 81.5 - - - +
212A LEU* 1.3 70.8 + - + +
214A GLN 4.0 9.4 - - - +
215A ASP* 4.6 4.2 - - - +
225A CYS 4.0 1.7 + - - -
226A GLN* 3.3 62.9 + - - +
227A SER* 3.7 3.5 + - - +
228A ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 3.7 13.7 - - - +
171A LYS* 3.4 46.6 + - + +
209A ASP* 3.2 37.1 + - + +
211A LYS* 1.3 97.6 - - + +
213A LEU* 1.3 59.9 + - - +
214A GLN 3.5 0.2 - - - -
215A ASP* 3.9 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 4.0 22.7 - - + +
170A THR 4.2 4.9 - - - -
171A LYS* 3.7 34.3 - - + +
186A PRO* 3.9 16.4 - - + -
188A LEU* 3.7 30.7 - - + -
208A MET* 3.6 27.8 - - + -
209A ASP 2.9 13.6 + - - +
212A LEU* 1.3 76.8 - - + +
214A GLN* 1.3 62.3 + - - +
215A ASP* 4.0 1.3 - - - -
342B LEU* 5.7 0.9 - - + -
344B VAL* 3.4 14.9 - - + +
345B CYS 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A MET* 4.0 7.1 - - + +
210A PHE* 3.2 55.6 + - - +
211A LYS 4.0 6.6 - - - +
212A LEU 3.5 0.4 - - - -
213A LEU* 1.3 84.1 - - - +
215A ASP* 1.3 62.1 + - - +
216A ASN 3.1 6.0 + - - +
217A LYS* 3.5 12.2 + - - +
218A SER 5.6 0.2 + - - -
219A GLU* 3.3 36.8 + - + +
220A VAL* 3.6 9.9 - - - +
225A CYS 5.2 1.3 - - - +
226A GLN* 4.4 5.4 + - - -
343B SER* 2.9 38.2 + - - +
345B CYS* 4.0 7.4 - - - +
----------------------------------------------------------
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