Contacts of the helix formed by residues 209 - 215 (chain B) in PDB entry 1O9S
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 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 2.9 10.3 + - - -
208B PRO* 1.3 74.5 - - - +
210B PRO* 1.3 65.3 - - - +
211B TYR* 3.0 32.4 + - - +
212B GLU* 3.0 24.4 + - - +
213B SER* 2.9 27.2 + - - -
244B PHE* 3.4 13.3 - - + -
288B CYS 4.3 0.6 + - - -
289B ALA 3.3 21.1 + - - +
310B HIS* 2.7 32.3 + - - -
312B ARG* 4.5 5.4 + - - +
313B PHE* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.6 13.0 - - + +
153B THR* 5.1 1.1 - - - -
155B LEU* 4.3 4.3 - - + -
169B LEU* 3.6 40.6 - - + -
191B TYR* 3.5 31.6 - - + +
208B PRO 3.8 5.8 - - - +
209B ASP* 1.3 92.0 - - - +
211B TYR* 1.3 62.0 + - - +
213B SER* 3.4 17.4 + - - -
214B GLU* 3.4 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.3 54.9 - + + -
149B PRO* 4.2 12.5 - - + +
150B ASP* 3.8 17.1 + - + +
153B THR* 4.4 4.2 - - - +
209B ASP* 3.0 2.3 + - - +
210B PRO* 1.3 77.7 - - - +
212B GLU* 1.3 64.1 + - - +
214B GLU* 3.4 8.4 + - - -
215B ARG* 2.9 71.0 + - - +
240B THR* 4.5 4.3 - - - +
241B VAL* 2.8 49.4 + - + +
242B MET 4.5 4.5 - - - -
244B PHE* 3.7 20.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 3.0 19.7 + - - +
211B TYR* 1.3 76.0 - - - +
213B SER* 1.3 61.1 + - - +
215B ARG 2.9 0.9 + - - +
216B VAL* 2.9 53.1 + - + +
242B MET 3.8 16.6 - - - +
243B SER* 2.6 25.0 + - - -
244B PHE* 2.8 24.5 + - + +
288B CYS 4.7 0.5 - - - +
289B ALA 3.6 7.6 - - - +
290B SER* 3.3 21.6 - - - -
291B LEU* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PRO* 5.3 8.5 - - - -
209B ASP 2.9 14.8 + - - -
210B PRO* 3.5 15.7 - - - -
211B TYR 3.3 0.2 - - - -
212B GLU* 1.3 76.7 - - - +
214B GLU* 1.3 56.8 + - - +
216B VAL 4.7 2.2 - - - -
233B LYS* 2.7 36.5 + - - +
291B LEU* 6.4 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
153B THR* 3.5 21.0 + - - +
169B LEU* 5.8 3.8 - - - +
185B MET* 5.9 3.1 - - - +
210B PRO* 3.5 14.4 - - - +
211B TYR* 3.4 1.8 + - - -
212B GLU 3.1 1.0 - - - -
213B SER* 1.3 80.4 - - - +
215B ARG* 1.3 90.8 + - - +
216B VAL 4.0 0.2 - - - -
233B LYS* 3.7 17.6 - - - +
234B VAL* 4.2 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP* 2.5 38.0 + - - +
152B ARG* 6.0 0.4 - - - +
211B TYR* 2.9 76.5 + - - +
212B GLU 2.9 1.6 + - - -
214B GLU* 1.3 108.0 + - - +
216B VAL* 1.3 64.0 + - - +
232B SER* 3.3 4.9 - - - -
233B LYS* 2.8 24.8 + - - -
234B VAL* 4.3 16.2 + - + -
236B VAL* 5.1 3.0 - - + +
240B THR* 5.2 4.2 - - - +
241B VAL 3.9 7.2 - - - -
242B MET* 3.6 31.1 - - + +
----------------------------------------------------------
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