Contacts of the helix formed by residues 208 - 216 (chain D) in PDB entry 5TWV
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 208 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TRP* 4.7 12.1 - - + +
66D LEU* 6.1 1.1 - - - -
205D LYS 5.2 3.1 - - - +
206D PRO 3.4 6.8 + - - +
207D PRO* 1.3 75.2 - - - +
209D ASP* 1.3 66.0 + - - +
210D LEU* 4.2 6.5 - - + +
211D GLN* 3.7 22.9 + - + +
212D ASP* 3.6 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PRO 4.3 0.4 + - - -
208D GLU* 1.3 73.0 - - - +
210D LEU* 1.3 59.1 + - - +
212D ASP* 3.3 8.9 + - - +
213D LEU* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TRP* 6.4 2.7 - - + -
208D GLU* 3.3 6.0 - - + +
209D ASP* 1.3 77.2 - - - +
211D GLN* 1.3 60.1 + - - +
213D LEU* 3.1 11.0 + - - +
214D GLY* 2.9 24.6 + - - -
222D VAL* 5.0 15.9 - - + -
224D LEU* 5.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN* 6.2 3.6 - - - -
63D SER* 5.6 7.5 - - - +
64D THR* 6.2 0.9 - - - -
65D TRP* 5.3 16.7 - - + +
208D GLU* 3.7 21.8 + - + +
209D ASP 3.4 0.6 - - - -
210D LEU* 1.3 77.4 - - - +
212D ASP* 1.3 53.1 + - - +
214D GLY* 2.9 4.5 + - - +
215D VAL* 2.6 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D GLU 3.6 9.6 + - - +
209D ASP* 3.3 10.9 + - - +
210D LEU 3.2 0.2 - - - -
211D GLN* 1.3 75.5 - - - +
213D LEU* 1.3 68.1 + - - +
215D VAL* 3.6 12.2 + - - +
216D ARG* 3.9 10.6 + - - +
331E SER* 5.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ASP 3.0 12.8 + - - +
210D LEU* 3.1 13.2 + - - +
212D ASP* 1.3 78.1 - - - +
214D GLY* 1.3 58.3 + - - +
216D ARG* 3.9 3.8 + - - +
217D PHE* 3.2 21.2 + - - +
220D PRO 6.0 0.4 - - - +
260D LEU* 4.9 21.9 - - + +
263D TYR* 6.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D SER* 4.9 10.4 - - - -
210D LEU 2.9 12.8 + - - -
211D GLN* 2.9 5.3 + - - -
213D LEU* 1.3 75.0 - - - +
215D VAL* 1.3 58.0 + - - +
216D ARG 3.2 2.7 - - - -
217D PHE* 2.9 34.5 + - - +
220D PRO* 4.5 21.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
47C LYS* 4.2 15.8 - - + +
48C ASN* 4.4 19.5 - - + +
63D SER* 5.0 7.8 - - - -
211D GLN* 2.6 18.5 + - + +
212D ASP* 4.1 9.4 - - - +
213D LEU 3.6 0.6 - - - -
214D GLY* 1.3 72.6 - - - +
216D ARG* 1.3 61.2 + - - +
217D PHE 3.6 1.4 + - - +
329E ASP* 3.3 28.2 - - - +
331E SER* 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D ASP 3.9 10.2 + - - +
213D LEU 4.1 3.1 - - - +
214D GLY 3.2 0.4 - - - -
215D VAL* 1.3 78.3 - - + +
217D PHE* 1.3 56.5 + - - +
218D LEU 3.9 1.4 + - - -
258D ARG* 5.0 2.1 - - - +
329E ASP* 5.4 4.5 - - - +
332E LYS* 5.8 8.5 - - - +
----------------------------------------------------------
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