Contacts of the strand formed by residues 203 - 212 (chain B) in PDB entry 4AEJ
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 TRP 203 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 3.4 75.2 - - + +
150B HIS* 3.6 25.6 - - + -
151B CYS 3.4 26.5 - - - -
152B LYS* 3.7 27.1 - - + +
202B GLU* 1.3 81.1 + - - +
204B SER* 1.3 63.3 + - - +
234B GLU* 3.5 47.6 - - + -
235B PHE* 3.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 5.7 0.2 + - - -
150B HIS* 3.3 8.1 + - - +
151B CYS* 2.8 36.6 + - - -
195B GLY* 3.1 33.1 + - - -
202B GLU 5.1 1.6 - - - -
203B TRP* 1.3 77.3 - - - +
205B LYS* 1.3 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 3.7 23.6 - - + +
149B TYR 3.1 12.6 - - - +
150B HIS* 4.1 17.7 - - + +
151B CYS* 3.7 0.2 - - - -
193B GLU* 3.4 34.4 + - - +
194B ASP* 4.1 0.3 - - - -
195B GLY* 2.8 24.4 + - - -
196B CYS* 3.5 3.6 - - - -
204B SER* 1.3 84.7 + - - +
206B THR* 1.3 63.9 + - - +
207B VAL* 4.8 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 3.4 2.6 - - - +
149B TYR 2.9 30.8 + - - -
156B ALA* 3.5 15.6 - - + +
157B TYR* 4.3 1.6 - - + -
191B VAL* 3.8 13.0 - - + -
193B GLU 3.2 17.5 - - - +
194B ASP* 2.7 28.0 + - - +
196B CYS* 3.0 18.2 - - - +
205B LYS* 1.3 74.6 + - - +
207B VAL* 1.3 63.3 + - - +
208B PHE* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLN* 3.9 24.0 - - + +
147B ILE 3.6 7.4 - - - +
148B THR* 3.8 25.4 - - + +
191B VAL* 3.4 6.9 - - - +
192B LEU* 2.8 46.1 + - + -
193B GLU* 3.0 37.6 + - + +
205B LYS* 4.8 6.7 - - + +
206B THR* 1.3 75.9 - - - +
208B PHE* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLN* 3.1 7.8 - - - +
147B ILE* 2.8 55.2 + - + +
149B TYR* 3.9 9.9 - - + -
156B ALA* 3.4 23.6 - - + -
157B TYR* 4.2 2.2 - - + -
169B LEU* 3.5 30.3 - - + -
171B LEU* 4.3 8.3 - - + -
189B TYR* 3.5 49.1 - + + -
190B THR 3.5 3.8 - - - +
191B VAL* 3.9 14.1 - - + -
206B THR* 3.6 30.3 - - + -
207B VAL* 1.3 78.7 - - - +
209B GLU* 1.3 59.6 + - - +
223B ILE* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER* 4.8 2.0 + - - -
145B GLN 3.4 15.3 - - - +
146B GLN* 3.7 26.6 + - + +
171B LEU* 5.8 0.9 - - - -
189B TYR* 3.3 6.5 - - - +
190B THR* 2.8 49.8 + - - +
192B LEU* 4.1 20.0 - - + +
208B PHE* 1.3 76.4 - - - +
210B TYR* 1.3 71.4 + - - +
211B ARG* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER* 3.2 4.0 - - - -
145B GLN 3.1 31.8 + - - +
171B LEU* 5.5 1.5 - - + +
179B PHE* 3.6 60.3 - + + -
186B LYS 2.6 28.6 + - - -
187B PHE* 4.0 3.5 - - - -
188B THR 3.5 28.5 - - - -
189B TYR* 4.7 3.6 - - + +
209B GLU* 1.3 73.9 - - - +
211B ARG* 1.3 69.1 + - - +
212B THR* 3.4 32.9 - - + -
217B ARG* 3.2 24.0 + - + -
218B LEU* 4.0 13.2 - - + +
220B ILE* 5.1 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 5.2 5.7 + - - -
142B ARG* 5.6 12.0 - - + +
143B ALA 3.5 8.7 - - - +
144B SER* 3.9 21.6 + - - -
209B GLU* 3.0 39.1 + - + +
210B TYR* 1.3 85.7 - - - +
212B THR* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.3 6.6 - - - +
143B ALA 2.9 40.0 + - - +
210B TYR* 3.4 31.0 - - + -
211B ARG* 1.3 79.0 - - - +
213B ARG* 1.3 69.9 + - - +
214B LYS* 2.8 31.0 + - - +
215B ALA* 4.2 3.1 - - - +
217B ARG* 3.5 17.9 + - + -
218B LEU* 4.2 11.9 - - + -
----------------------------------------------------------
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