Contacts of the strand formed by residues 218 - 227 (chain B) in PDB entry 5B4N
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 SER 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY* 3.3 30.8 - - - -
213B ARG* 4.0 9.4 + - - -
216B CYS* 3.9 3.3 + - - -
217B GLY* 1.3 75.8 + - - -
219B LYS* 1.4 63.6 - - - +
243B THR* 3.7 0.7 - - - -
244B ILE* 2.7 50.5 + - - +
284B TRP* 3.9 3.0 - - - -
285B TYR 3.3 4.8 - - - -
286B GLY 3.1 23.6 + - - -
287B PRO* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR 6.1 0.2 - - - +
218B SER* 1.4 78.4 - - - +
220B TYR* 1.3 60.3 + - - +
241B PRO* 5.0 8.7 - - + +
242B ALA 3.2 8.5 - - - +
243B THR* 2.7 34.3 + - - +
244B ILE* 4.7 0.9 - - - -
275B GLY* 3.6 6.8 - - - -
276B VAL* 3.6 29.6 - - + +
284B TRP* 3.7 44.4 - - + +
285B TYR 2.8 12.7 + - - +
287B PRO* 3.3 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP* 2.5 36.5 + - - +
210B TYR* 3.4 56.3 - + + -
219B LYS* 1.3 75.9 - - - +
221B GLN* 1.3 66.9 + - - +
222B LEU* 3.3 33.5 - - + +
239B PRO* 6.3 0.4 - - + -
240B ASP 4.8 0.2 - - - +
241B PRO* 3.5 3.1 - - - +
242B ALA* 2.9 40.5 + - + +
244B ILE* 4.1 3.8 - - + -
255B ILE* 3.7 12.0 - - + +
273B HIS* 4.1 11.0 - - + -
274B GLY 3.4 12.6 - - - -
275B GLY* 4.5 0.4 - - - -
276B VAL* 4.1 2.9 - - - +
287B PRO* 3.9 20.2 - - + -
289B VAL* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ARG* 3.0 42.1 + - - +
220B TYR* 1.3 81.9 - - - +
222B LEU* 1.3 80.9 + - - +
223B THR* 4.3 2.9 - - - +
238B GLN* 3.1 21.8 - - - +
239B PRO 2.9 23.7 + - - +
240B ASP* 4.7 1.1 - - - -
241B PRO* 3.6 28.8 - - + +
273B HIS* 3.3 0.7 - - - +
274B GLY 2.8 22.4 + - - -
275B GLY 4.6 0.9 - - - +
276B VAL* 4.4 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 5.3 5.6 - - + +
207B LYS 5.8 0.2 - - - -
208B ASP* 4.2 4.0 - - + +
220B TYR* 3.3 31.2 - - + +
221B GLN* 1.3 88.7 + - - +
223B THR* 1.3 63.5 + - - +
224B VAL* 3.9 20.9 - - + -
237B PHE* 4.0 15.9 - - + -
238B GLN* 3.7 0.7 - - - -
239B PRO* 3.4 20.3 - - + +
255B ILE* 4.0 30.1 - - + +
271B PHE* 3.8 28.3 - - + -
272B GLU 3.3 17.3 - - - +
273B HIS* 3.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ARG* 3.7 14.1 + - - +
221B GLN* 4.1 2.8 + - - +
222B LEU* 1.3 75.9 + - - +
224B VAL* 1.3 62.8 + - - +
225B ARG* 3.6 35.2 - - + +
236B GLU* 4.2 4.3 - - - +
237B PHE 3.5 3.4 - - - -
238B GLN* 3.0 35.0 + - + +
270B ARG* 3.7 4.1 - - - +
272B GLU* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.7 32.5 - - + -
222B LEU* 3.9 26.5 - - + -
223B THR* 1.3 79.7 - - - +
225B ARG* 1.3 66.9 + - - +
236B GLU* 3.5 2.6 - - - +
237B PHE* 2.8 46.9 + - + +
259B PHE* 3.7 24.0 - - + -
269B VAL* 4.1 17.0 - - + -
270B ARG 3.1 9.0 - - - +
271B PHE* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B THR* 3.6 22.8 - - + +
224B VAL* 1.3 80.4 - - - +
226B LEU* 1.3 64.4 + - - +
227B LEU* 3.9 19.6 + - + +
233B VAL* 4.1 23.1 - - + +
235B ALA 3.5 6.5 - - - +
236B GLU* 2.6 33.4 + - + +
238B GLN* 4.2 7.7 - - - +
268B PHE 3.9 0.2 - - - +
269B VAL* 3.2 7.1 - - - +
270B ARG* 2.8 62.4 + - + +
272B GLU* 5.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 4.2 10.3 - - + -
225B ARG* 1.3 79.4 - - - +
227B LEU* 1.3 60.1 + - - +
233B VAL* 3.7 3.8 - - - -
234B LEU* 2.9 26.0 + - - -
235B ALA* 2.9 32.2 + - + +
259B PHE* 3.7 52.5 - - + -
262B TYR* 3.8 25.4 - - + -
266B VAL* 3.8 21.3 - - + -
268B PHE 3.6 2.9 - - - -
269B VAL* 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 5.1 6.1 - - + -
225B ARG* 3.9 26.0 - - + +
226B LEU* 1.3 81.7 - - - +
228B SER* 1.3 60.5 + - - +
231B GLU* 4.0 27.6 - - + +
232B ASP 3.3 10.8 - - - +
233B VAL* 4.0 16.6 - - + -
234B LEU* 4.2 3.8 - - - -
266B VAL* 3.7 0.8 - - - +
267B ARG 2.7 31.0 + - - -
268B PHE* 2.8 36.9 + - + +
270B ARG* 4.3 22.2 - - + -
----------------------------------------------------------
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