Contacts of the helix formed by residues 200 - 208 (chain B) in PDB entry 3NDR
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 ALA 200 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.2 5.4 - - + -
196B PRO 4.4 0.6 + - - +
197B HIS* 3.0 20.7 + - + +
199B GLU* 1.3 76.1 - - - +
201B PHE* 1.3 64.9 + - - +
202B GLY 3.2 2.9 - - - -
203B PHE* 3.1 11.8 + - + +
204B VAL* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 3.5 32.9 - - + +
187B ILE 3.8 4.3 - - - -
188B GLU* 3.5 40.2 - - + -
192B VAL* 3.7 11.7 - - + -
198B ASN* 3.1 43.7 - - - +
199B GLU 3.4 2.2 - - - -
200B ALA* 1.3 77.3 - - - +
202B GLY* 1.3 56.5 + - - +
204B VAL* 3.3 10.8 - - + +
205B GLU* 2.8 35.3 + - + +
213B LYS* 3.3 52.7 - - + +
214B GLY 4.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU 4.5 3.4 + - - -
200B ALA 3.2 0.6 - - - -
201B PHE* 1.3 79.0 - - - +
203B PHE* 1.3 61.0 + - - +
205B GLU* 3.6 8.9 + - - +
206B MSE 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A MSE 4.0 22.0 - - + -
207A LEU* 4.2 19.3 - - + -
199B GLU 5.3 0.6 + - - +
200B ALA* 3.1 14.1 + - + +
202B GLY* 1.3 75.4 - - - +
204B VAL* 1.3 70.7 + - + +
206B MSE 3.2 46.8 + - + +
207B LEU* 3.3 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.0 27.4 - - + -
200B ALA* 2.9 26.0 + - + +
201B PHE* 3.3 20.6 - - + +
203B PHE* 1.3 81.1 - - + +
205B GLU* 1.3 69.7 + - + +
207B LEU* 3.2 10.1 + - + +
208B GLN* 3.0 37.7 + - - +
245B MSE 4.2 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 2.8 23.1 + - + +
202B GLY* 3.6 9.2 - - - +
203B PHE 3.2 0.2 - - - -
204B VAL* 1.3 74.3 - - + +
206B MSE 1.3 66.9 + - - +
208B GLN* 3.3 23.9 + - - +
210B MSE 4.2 2.9 - - - +
211B LYS* 2.5 40.0 - - + +
212B GLY 3.3 22.8 - - - +
213B LYS* 3.6 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 4.0 26.5 - - + -
206A MSE 4.8 0.7 - - + -
202B GLY 3.2 9.4 + - - +
203B PHE* 3.2 58.1 + - + +
204B VAL 3.1 0.2 - - - -
205B GLU* 1.3 83.0 - - - +
207B LEU* 1.3 76.1 + - + +
208B GLN 3.2 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 4.2 18.2 - - + -
207A LEU* 4.6 18.2 - - + -
203B PHE* 3.3 41.8 + - + +
204B VAL* 3.2 8.7 + - + +
206B MSE 1.3 93.8 - - + +
208B GLN* 1.3 63.1 + - - +
209B ALA 3.9 0.3 + - - -
244B GLY 3.9 3.6 - - - +
245B MSE 3.9 38.6 - - + +
247B ARG* 5.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.9 6.8 + - - +
201B PHE* 6.0 0.3 - - - -
204B VAL* 3.0 36.9 + - - +
205B GLU* 3.5 16.2 - - - +
206B MSE 3.2 10.1 - - - +
207B LEU* 1.3 80.9 - - - +
209B ALA* 1.3 62.6 + - - +
210B MSE 2.9 22.4 + - - +
211B LYS* 4.1 1.1 - - - +
212B GLY 3.1 26.1 + - - +
214B GLY 4.8 3.1 + - - -
242B ASP 3.6 16.8 - - - +
243B ALA* 3.7 20.1 - - - +
245B MSE 3.9 12.7 - - + +
233D TRP* 3.8 9.1 + - - -
----------------------------------------------------------
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