Contacts of the strand formed by residues 211 - 219 (chain B) in PDB entry 4LEY
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 GLU 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B TYR* 3.9 16.8 + - - +
205B LYS* 3.7 26.4 + - + +
209B PRO 3.6 1.2 - - - -
210B ASN* 1.3 90.1 + - - +
212B PHE* 1.3 68.0 + - - +
213B ASP* 5.5 2.9 - - - +
305B SER* 3.2 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 4.1 12.6 - - + -
168B ALA* 4.3 7.6 - - - -
171B VAL* 3.7 29.6 - - + -
200B TYR* 3.4 51.6 - + - -
201B TYR* 3.6 22.0 - + + +
209B PRO* 3.3 28.7 - - + -
211B GLU* 1.3 77.6 - - - +
213B ASP* 1.3 66.9 + - - +
214B VAL* 4.1 2.2 - - + -
304B ILE* 3.5 24.5 - - + -
305B SER 2.9 9.2 + - - +
306B VAL* 3.4 15.9 - - + +
307B ASP* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ASN* 3.7 1.4 - - - -
197B THR* 2.9 56.2 + - - +
198B GLY* 3.9 14.3 - - - -
199B SER 4.9 0.7 + - - -
200B TYR* 5.8 0.4 - - - +
201B TYR* 3.8 5.0 - - - -
211B GLU* 5.5 2.5 - - - +
212B PHE* 1.3 78.5 + - - +
214B VAL* 1.3 65.3 + - - +
307B ASP* 3.5 23.7 - - - +
309B ILE* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 5.5 0.9 - - + -
175B VAL* 4.2 22.0 - - + -
194B GLN* 3.6 34.3 - - + +
195B LEU 3.9 2.0 - - - +
196B ASN* 3.6 13.5 - - - +
201B TYR* 4.6 10.1 - - - +
212B PHE* 4.9 2.2 - - + -
213B ASP* 1.3 80.2 - - - +
215B MET* 1.3 65.5 + - - +
216B PHE* 3.7 17.6 + - + -
306B VAL* 4.4 12.1 - - + -
307B ASP 3.0 11.1 + - - +
308B ILE* 3.5 9.4 - - + -
309B ILE* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU 3.2 6.1 - - - +
194B GLN* 3.3 3.3 - - - +
195B LEU* 2.9 57.5 + - + +
197B THR* 3.9 30.5 - - - +
214B VAL* 1.3 72.5 - - - +
216B PHE* 1.3 62.7 + - - +
217B LYS* 3.6 3.0 + - + +
309B ILE* 3.6 23.3 - - + +
311B ALA* 3.6 27.1 - - + -
346B TYR* 4.2 27.1 - - + -
348B VAL* 5.0 2.5 - - + -
366B SER* 4.6 9.4 - - - +
368B SER* 4.0 18.2 - - - -
369B HIS 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 4.2 13.9 - - + -
178B LEU* 4.1 12.1 - - + -
179B LEU* 3.7 50.0 - - + -
182B MET* 4.3 8.7 - - + -
192B VAL* 3.8 27.3 - - + +
193B GLU 3.3 4.9 - - - -
194B GLN* 4.4 3.4 - - + -
214B VAL* 3.7 23.3 + - + -
215B MET* 1.3 76.6 - - - +
217B LYS* 1.3 61.0 + - - +
266B PHE* 3.9 31.2 - + + -
308B ILE* 4.0 22.2 - - + -
309B ILE 2.9 9.9 + - - +
310B LEU* 3.8 4.2 - - - +
311B ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 4.4 0.7 - - - +
192B VAL* 3.3 3.0 - - - +
193B GLU* 2.8 72.8 + - - +
194B GLN 4.3 10.1 - - - -
195B LEU* 4.2 19.7 - - + -
215B MET* 3.6 4.2 - - + +
216B PHE* 1.3 73.7 - - - +
218B LEU* 1.3 60.6 + - - +
219B GLU 4.2 0.2 - - - -
311B ALA* 3.3 12.3 - - + +
313B GLU* 2.5 31.3 + - + +
346B TYR* 3.5 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU 4.0 17.3 - - - +
189B PHE* 4.3 12.1 - - + +
190B LYS 3.7 15.7 - - - +
191B GLY* 3.8 4.9 - - - +
192B VAL* 3.7 33.7 - - + +
216B PHE 5.2 0.2 - - - +
217B LYS* 1.3 75.3 - - - +
219B GLU* 1.3 76.2 + - - +
220B VAL* 3.3 11.2 - - + +
248B LEU* 4.4 13.5 - - + -
262B MET* 4.1 25.4 - - + -
310B LEU* 5.5 1.8 - - + -
311B ALA 2.9 13.5 + - - +
312B LEU* 3.4 2.1 - - - -
313B GLU* 2.9 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 5.2 2.2 + - - -
217B LYS 4.2 0.4 - - - -
218B LEU* 1.3 82.3 - - - +
220B VAL* 1.3 63.7 + - - +
221B PRO* 3.3 30.3 - - + +
248B LEU* 5.9 0.3 - - - +
313B GLU* 3.3 36.3 + - + +
314B SER* 5.3 0.7 - - - -
315B LYS* 3.5 39.3 + - + +
----------------------------------------------------------
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