Contacts of the strand formed by residues 216 - 220 (chain g) in PDB entry 5OA3
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 216 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208g ALA* 6.3 1.1 - - + -
209g SER 3.8 4.5 - - - +
214g GLY 3.9 0.8 + - - -
215g GLN* 1.3 71.3 - - - +
217g MET* 1.3 61.9 + - - +
218g LEU 4.0 0.7 + - - -
228g TYR 4.1 0.2 - - - +
229g THR* 3.8 2.4 - - - -
230g LEU* 2.9 58.4 + - + +
236g ILE* 3.6 23.3 - - + +
239g LEU* 4.8 14.1 - - + -
248g LEU* 5.2 4.7 - - + -
250g ALA* 5.2 5.4 - - + -
259g TRP* 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 217 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D PRO* 5.6 3.1 - - + -
190g GLY* 4.0 19.7 - - - +
191g HIS* 3.1 28.3 - - + +
208g ALA* 3.6 3.0 - - - -
209g SER 2.9 35.4 + - - +
213g ASP* 4.2 6.5 - - - +
215g GLN* 3.6 37.2 - - + +
216g ALA* 1.3 72.1 - - - +
218g LEU* 1.3 60.5 + - - +
219g TRP* 3.2 32.0 - - + +
226g HIS* 4.4 7.9 - - + -
228g TYR 3.8 1.3 - - - +
229g THR* 3.3 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206g LEU* 4.4 9.9 - - + -
207g CYS 3.6 14.4 - - - +
208g ALA* 4.1 6.7 - - + -
216g ALA 4.0 2.1 + - - +
217g MET* 1.3 71.7 - - - +
219g TRP* 1.3 63.8 + - - +
226g HIS* 4.4 1.4 + - - -
227g LEU* 3.1 20.6 + - + +
228g TYR* 2.9 66.7 + - + +
230g LEU* 6.0 3.6 - - + -
241g PHE* 3.4 31.6 - - + -
246g TYR* 5.9 0.2 - - - +
248g LEU* 4.1 10.1 - - + -
261g LEU* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 219 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D PRO* 3.4 26.0 - - + -
223D ILE 4.5 8.5 - - - -
224D SER* 4.8 0.2 - - - -
174g VAL* 5.2 3.8 - - + +
188g HIS* 4.2 44.0 - + + +
189g ILE 4.4 2.7 - - - -
190g GLY* 4.0 25.6 - - - -
191g HIS* 4.5 4.8 - + - -
205g SER 3.4 3.1 - - - +
206g LEU* 3.7 2.4 - - - -
207g CYS* 2.9 53.6 + - - +
209g SER* 3.4 14.6 + - - -
217g MET* 3.2 39.4 - - + +
218g LEU* 1.3 74.6 - - - +
220g ASP* 1.3 63.0 + - - +
221g LEU 3.9 0.6 + - - -
225g LYS 4.2 2.7 - - - +
226g HIS* 3.6 44.4 - + + -
227g LEU* 4.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188g HIS* 4.8 3.9 + - - -
205g SER* 2.8 32.0 - - - +
206g LEU* 4.5 5.4 - - - +
219g TRP* 1.3 72.2 - - - +
221g LEU* 1.3 61.9 + - - +
222g ASN* 3.6 3.3 - - - +
223g GLU* 3.3 39.4 + - + +
224g GLY* 3.0 26.0 + - - -
225g LYS* 3.1 25.1 + - + +
227g LEU* 4.0 22.1 - - + +
----------------------------------------------------------
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