Contacts of the strand formed by residues 218 - 223 (chain B) in PDB entry 2AY6
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 LEU 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A MET* 3.6 38.4 - - + -
6A LEU* 4.7 5.6 - - + -
183B GLY* 5.0 1.8 - - - +
184B ASP 2.8 13.3 + - - +
185B MET* 3.2 28.5 - - + +
186B VAL 2.9 24.0 + - - -
212B LEU* 5.1 0.4 - - - -
216B GLY 3.6 3.1 + - - +
217B ALA* 1.3 69.9 - - - +
219B PRO* 1.3 67.4 - - - +
247B ILE* 5.8 0.2 - - - -
249B GLU* 3.3 48.5 - - + +
250B VAL* 3.8 10.1 - - - -
251B LEU* 4.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 3.5 9.4 - - + +
188B LEU* 4.3 9.9 - - + -
212B LEU* 3.8 23.8 - - + -
217B ALA 3.3 10.3 - - - +
218B LEU* 1.3 84.8 - - - +
220B LEU* 1.3 59.9 + - - +
221B ILE* 3.9 5.2 - - + -
243B ILE* 3.8 18.8 - - + -
247B ILE* 4.0 8.1 - - + -
249B GLU 3.6 15.7 - - - +
250B VAL* 3.8 19.0 - - + +
251B LEU* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 4.5 15.9 - - + -
115B ALA* 3.7 24.0 - - + -
116B LEU* 4.2 15.7 - - + -
185B MET* 3.7 34.5 - - + -
186B VAL 2.8 10.0 + - - +
187B LEU* 3.3 23.7 - - + +
188B LEU* 2.9 27.0 + - - +
218B LEU 3.7 0.6 + - - -
219B PRO* 1.3 71.7 - - - +
221B ILE* 1.3 66.8 + - - +
251B LEU* 3.3 30.3 - - + +
252B ILE 4.7 0.2 - - - +
253B ALA* 4.7 7.4 - - + +
270B LEU* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.3 19.7 - - + +
190B GLY* 3.8 19.3 - - - +
205B TRP* 4.6 12.8 - - + -
219B PRO* 4.6 7.2 - - + +
220B LEU* 1.3 77.6 - - - +
222B ASP* 1.3 64.8 + - - +
223B LEU* 3.7 2.4 + - + +
240B THR* 3.6 31.6 - - + +
243B ILE* 4.5 22.0 - - + -
250B VAL* 4.2 9.4 - - + -
251B LEU 2.9 15.3 + - - +
252B ILE* 4.0 21.1 - - + -
253B ALA* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.4 15.2 - - + +
143B HIS* 2.7 30.8 + - + +
187B LEU* 3.8 13.7 - - + -
188B LEU 2.8 15.5 + - - +
189B HIS* 3.6 9.3 - - + +
190B GLY 3.0 20.3 + - - -
191B CYS 4.7 2.1 + - - +
220B LEU 3.9 0.4 + - - -
221B ILE* 1.3 72.5 - - - +
223B LEU* 1.3 59.1 + - - +
224B ALA* 3.7 11.3 + - - +
253B ALA* 3.7 6.9 - - - +
413B PLP 3.3 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.7 35.2 - - + -
190B GLY* 4.6 10.1 - - - -
191B CYS* 4.2 20.4 - - - -
221B ILE* 3.7 3.8 + - + -
222B ASP* 1.3 70.7 + - - +
224B ALA* 1.3 60.2 + - - +
226B GLN* 3.6 44.5 + - + +
236B ASP 4.4 9.2 - - - +
237B ALA* 5.1 2.9 - - + -
240B THR* 4.7 9.4 - - - +
252B ILE* 4.3 12.3 - - + -
253B ALA 2.8 15.8 + - - +
254B ALA* 3.3 5.6 - - + +
255B SER 3.0 23.8 + - - +
----------------------------------------------------------
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