Contacts of the helix formed by residues 205 - 216 (chain B) in PDB entry 1X1O
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 SER 205 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.3 0.5 - - - +
204B ARG* 1.3 81.1 - - - +
206B LEU* 1.3 64.2 + - - +
207B GLU* 3.4 22.9 + - - +
208B GLU* 3.2 28.4 + - - +
209B LEU 3.0 17.8 + - - -
225B PHE* 3.5 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B SER* 1.3 73.6 - - - +
207B GLU* 1.3 71.2 + - + +
209B LEU* 3.3 23.9 - - + +
210B GLU* 3.1 27.2 + - - +
225B PHE* 3.9 15.1 - - + -
229B ALA* 3.8 31.0 - - + +
232B GLU* 3.8 26.9 - - + -
233B ALA* 4.1 6.5 - - + +
236B ARG* 3.7 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B SER* 3.4 17.7 + - - +
206B LEU* 1.3 90.5 + - + +
208B GLU* 1.3 67.1 + - + +
210B GLU* 3.1 11.6 + - - +
211B GLU* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B VAL* 4.7 8.5 - - - +
182B VAL* 3.7 25.8 - - + +
202B GLU 4.5 0.9 - - - +
203B VAL* 3.4 13.3 - - + +
204B ARG* 2.7 53.9 + - - +
205B SER* 3.2 21.4 + - - +
207B GLU* 1.3 75.0 - - + +
209B LEU* 1.3 60.3 + - - +
211B GLU* 3.1 16.0 + - - +
212B ALA* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.0 12.7 - - + +
205B SER 3.0 12.5 + - - +
206B LEU* 3.3 22.9 - - + +
208B GLU* 1.3 76.6 - - - +
210B GLU* 1.3 63.3 + - - +
212B ALA* 3.2 3.6 + - - +
213B LEU* 3.0 31.4 + - + +
220B ILE* 3.8 33.7 - - + -
222B LEU* 4.4 9.2 - - + -
225B PHE* 5.0 1.3 - - + -
233B ALA* 3.6 40.8 - - + +
236B ARG* 4.7 10.5 - - + -
237B VAL* 4.0 16.4 - - + -
243B LEU* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU 3.1 15.5 + - - +
207B GLU* 3.1 11.2 + - - +
209B LEU* 1.3 83.7 - - - +
211B GLU* 1.3 57.0 + - - +
213B LEU* 3.4 17.4 + - - +
214B GLU* 2.9 30.6 + - - +
236B ARG* 3.6 38.2 - - - +
240B ARG* 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY* 4.3 2.1 - - - -
182B VAL* 3.3 22.4 + - + +
183B GLY* 3.0 26.1 + - - +
207B GLU* 3.0 19.1 + - - +
208B GLU* 3.1 16.5 + - - +
210B GLU* 1.3 75.7 - - + +
212B ALA* 1.3 53.5 + - - +
214B GLU* 3.2 6.8 + - - +
215B ALA* 2.7 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 3.7 8.5 - - + +
186B VAL* 4.6 1.6 - - - -
201B VAL* 3.8 24.2 - - + -
203B VAL* 3.9 9.0 - - + -
208B GLU 2.8 12.6 + - - +
209B LEU 3.4 8.7 - - - +
211B GLU* 1.3 77.1 - - - +
213B LEU* 1.3 62.4 + - - +
215B ALA* 3.3 4.2 + - - +
216B GLY 3.1 5.7 + - - -
217B ALA* 3.1 27.9 + - + +
220B ILE* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.0 23.5 + - + +
210B GLU* 3.8 25.1 - - - +
212B ALA* 1.3 76.1 - - - +
214B GLU* 1.3 62.1 + - - +
216B GLY* 3.4 11.0 + - - -
217B ALA 5.1 2.5 - - - +
220B ILE* 3.8 20.2 - - + -
236B ARG 5.0 0.7 - - - +
237B VAL* 4.2 23.1 - - + +
240B ARG* 3.7 41.2 + - + +
241B VAL* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 4.9 6.8 + - - +
210B GLU 2.9 17.8 + - - +
211B GLU* 3.6 7.2 - - - +
213B LEU* 1.3 79.0 - - - +
215B ALA* 1.3 59.8 + - - +
216B GLY 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLY* 3.9 17.0 - - - +
186B VAL* 3.5 34.3 - - + +
187B ARG* 3.9 26.5 - - + +
190B LYS* 4.2 6.4 - - - +
211B GLU 2.7 20.2 + - - +
212B ALA 3.3 1.7 + - - +
214B GLU* 1.3 72.7 - - - +
216B GLY* 1.3 59.8 + - - +
217B ALA 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 2.9 33.8 + - - +
212B ALA 3.1 3.4 + - - -
213B LEU 3.4 9.0 + - - -
214B GLU 3.2 4.2 - - - -
215B ALA* 1.3 79.6 - - - +
217B ALA* 1.3 68.7 + - - +
218B ASP* 3.6 1.4 - - - +
----------------------------------------------------------
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