Contacts of the helix formed by residues 207 - 216 (chain B) in PDB entry 3UO9
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 ASN 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG 3.3 16.0 + - - +
175B LEU* 3.3 30.2 - - + +
177B GLU* 3.0 19.1 + - - +
178B CYS* 3.1 38.6 - - + +
204B VAL 3.0 8.4 + - - +
206B SER* 1.3 88.4 - - - +
208B ILE* 1.3 64.7 + - - +
209B VAL 3.4 2.8 + - - -
210B LEU* 3.4 7.9 + - + -
211B LEU* 3.2 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.0 26.9 - - + +
140B GLU* 3.7 46.7 - - + +
143B LEU* 3.7 28.9 - - + -
204B VAL* 3.1 14.3 + - + +
205B GLN 3.4 17.7 + - - +
206B SER 3.6 0.6 - - - -
207B ASN* 1.3 77.2 - - - +
209B VAL* 1.3 69.0 + - + +
211B LEU* 3.4 2.3 + - + -
212B THR* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 5.2 10.3 - - + -
207B ASN 3.4 0.4 - - - -
208B ILE* 1.3 85.9 - - + +
210B LEU* 1.3 62.3 + - - +
212B THR* 3.3 5.8 + - - -
213B GLN* 3.1 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 4.6 8.1 - - + -
174B ARG* 3.4 64.6 - - + +
175B LEU* 4.0 22.7 - - + -
207B ASN* 3.4 10.5 + - + +
209B VAL* 1.3 78.6 - - - +
211B LEU* 1.3 62.9 + - - +
213B GLN* 3.4 18.2 + - - +
214B ALA* 3.1 22.2 + - - +
219B PHE* 3.9 20.9 - - + -
269B ASP* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 4.0 13.9 - - + -
159B PHE* 4.3 11.2 - - + -
163B LEU* 3.5 33.4 - - + -
168B LEU* 5.4 0.7 - - + -
175B LEU* 3.8 20.0 - - + -
178B CYS* 4.4 7.2 - - - -
204B VAL* 3.7 40.8 - - + +
207B ASN* 3.2 24.7 + - + +
208B ILE* 3.8 3.8 - - - +
210B LEU* 1.3 75.5 - - - +
212B THR* 1.3 57.7 + - - +
214B ALA* 3.3 3.3 + - - +
215B PHE* 3.0 43.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.2 32.0 - - + +
143B LEU* 4.2 16.3 - - + +
208B ILE* 2.9 27.5 + - - +
209B VAL* 3.8 4.9 - - - -
211B LEU* 1.3 73.2 - - - +
213B GLN* 1.3 61.8 + - + +
215B PHE* 4.2 0.2 - - - +
216B ARG* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 3.1 32.0 + - + +
210B LEU* 3.6 23.9 - - - +
212B THR* 1.3 78.5 - - + +
214B ALA* 1.3 59.8 + - - +
217B ARG 3.5 1.4 + - - -
218B LYS* 3.0 50.6 + - + +
219B PHE* 3.8 16.9 + - + -
269B ASP* 5.3 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.9 2.2 - - + -
166B THR* 3.6 31.5 - - + +
168B LEU* 3.9 9.0 - - + -
210B LEU 3.1 11.0 + - - +
211B LEU* 3.5 11.0 - - - +
213B GLN* 1.3 78.4 - - - +
215B PHE* 1.3 62.3 + - + +
217B ARG* 3.6 12.3 + - - +
219B PHE* 3.4 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.7 26.9 - - + -
146B THR* 5.4 2.0 - - - +
147B ILE* 3.7 28.9 - - + -
159B PHE* 4.0 12.6 - + - -
162B ALA* 3.6 31.9 - - + -
163B LEU* 3.6 43.7 - - + -
166B THR* 4.7 5.2 - - + -
211B LEU* 3.0 32.6 + - + +
212B THR 4.2 0.4 - - - +
214B ALA* 1.3 75.8 - - + +
216B ARG* 1.3 69.0 + - - +
217B ARG* 3.2 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 5.5 3.0 - - - +
146B THR* 4.2 29.5 + - - +
212B THR* 2.8 29.5 + - + +
215B PHE* 1.3 86.1 + - - +
217B ARG* 1.3 67.8 + - - +
218B LYS* 3.1 30.3 + - + +
----------------------------------------------------------
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