Contacts of the helix formed by residues 203 - 212 (chain C) in PDB entry 5D4D
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 203 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ARG* 4.0 19.9 + - - +
201C GLY 3.9 2.3 + - - +
202C TYR* 1.3 73.9 - - - +
204C GLN* 1.3 85.6 + - - +
205C GLU* 3.2 10.1 + - + +
206C THR* 3.0 26.5 + - - +
207C LEU* 3.2 13.0 + - - +
227C PHE* 3.6 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ASP* 1.3 84.0 + - - +
205C GLU* 1.3 55.1 + - - +
207C LEU* 3.6 2.0 + - - +
208C ALA* 2.9 28.5 + - + +
222C MET* 3.3 42.1 - - + +
223C ASP 6.3 0.4 - - - -
224C GLU* 5.8 2.2 - - - -
227C PHE* 3.3 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ASP* 3.2 7.7 + - + +
204C GLN* 1.3 75.8 - - - +
206C THR* 1.3 61.7 + - - +
208C ALA* 3.4 6.8 + - + +
209C ARG* 2.9 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TYR* 4.5 22.8 - - + -
203C ASP* 3.5 25.3 + - - +
205C GLU* 1.3 78.3 - - - +
207C LEU* 1.3 59.5 + - + +
209C ARG* 3.2 38.7 + - - +
210C GLU* 2.9 37.3 + - - +
304C LEU* 5.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C VAL* 5.2 1.3 - - + -
197C LEU* 3.9 28.5 - - + -
202C TYR* 3.9 27.8 - - + -
203C ASP 3.2 9.8 + - - +
204C GLN 4.0 5.6 - - - +
206C THR* 1.3 76.0 - - - +
208C ALA* 1.3 60.6 + - - +
210C GLU* 4.5 0.7 - - - +
211C LEU* 2.9 38.8 + - + +
212C GLY 3.7 0.3 + - - -
218C VAL* 3.7 4.0 - - - +
221C LEU* 3.9 20.9 - - + -
222C MET* 4.3 7.0 - - + -
227C PHE* 3.8 26.5 - - + -
304C LEU* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C GLN* 2.9 21.6 + - + +
205C GLU* 3.6 9.0 - - + +
207C LEU* 1.3 75.7 - - - +
209C ARG* 1.3 63.4 + - - +
212C GLY* 3.2 21.8 - - - -
218C VAL* 4.4 11.6 - - + +
222C MET* 5.0 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C GLU* 2.9 36.3 + - + +
206C THR* 3.2 32.1 + - - +
208C ALA* 1.3 79.6 - - - +
210C GLU* 1.3 96.2 + - - +
212C GLY* 3.9 3.5 + - - -
213C ALA* 4.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C THR* 2.9 25.4 + - - +
207C LEU 4.4 0.9 - - - +
209C ARG* 1.3 117.0 + - - +
211C LEU* 1.3 77.0 + - + +
212C GLY 3.3 0.8 + - - -
213C ALA* 4.2 5.7 + - - +
214C TYR* 3.9 12.6 - - - -
304C LEU* 3.9 27.4 - - + +
308C ARG* 4.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 2.9 25.8 + - + +
210C GLU* 1.3 81.1 - - + +
212C GLY* 1.3 62.5 + - - +
213C ALA 3.2 2.8 + - - -
214C TYR* 3.5 22.3 + - + +
218C VAL* 3.4 19.9 + - + +
221C LEU* 3.7 22.2 - - + -
304C LEU* 3.6 26.9 - - + -
307C LEU* 3.9 7.0 - - + -
308C ARG* 3.8 40.6 - - + +
311C PHE* 3.7 29.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU 3.7 1.0 + - - -
208C ALA* 3.2 24.8 + - - -
209C ARG 4.5 0.2 - - - -
210C GLU 3.3 1.0 - - - -
211C LEU* 1.3 74.6 - - - +
213C ALA* 1.3 62.3 + - - +
214C TYR 2.9 13.5 + - - +
215C GLY* 4.4 2.8 + - - -
218C VAL* 3.8 16.1 - - - +
----------------------------------------------------------
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