Contacts of the strand formed by residues 209 - 221 (chain B) in PDB entry 6D6U
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 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 3.4 7.3 - - - -
164B ARG* 2.6 75.9 + - + +
202B ILE* 4.7 10.1 - - + -
203B VAL 4.1 4.9 - - - -
204B GLN* 4.4 26.0 + - + +
208B GLY* 1.3 70.7 - - - -
210B TYR* 1.3 60.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
100B PHE* 5.6 0.9 - + - -
102B HIS* 5.1 12.6 - + + -
159B SER* 4.5 14.4 - - - +
160B TYR* 4.8 13.2 - + - -
161B ALA* 4.0 20.6 + - - -
162B TYR 3.5 30.7 - - - +
163B THR* 4.0 9.0 - - + -
164B ARG* 4.5 5.9 - - - +
202B ILE* 3.4 19.1 - - - +
203B VAL* 3.1 26.2 + - + +
205B SER* 3.9 17.3 - - - -
207B THR* 2.6 34.8 + - + +
208B GLY 3.4 5.3 + - - -
209B GLU* 1.3 80.7 - - - +
211B VAL* 1.3 66.5 + - - +
212B VAL* 5.2 4.9 - - + -
115C MET* 4.1 9.2 - - - +
117C ARG* 4.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLY* 3.5 18.7 - - - -
159B SER* 3.7 12.4 + - - +
162B TYR 5.4 1.3 + - - +
163B THR 5.8 0.4 - - - +
164B ARG* 5.0 13.2 - - + +
167B VAL 3.8 22.2 - - - +
168B VAL* 4.5 5.8 - - + -
169B TYR* 4.1 30.0 - - + +
201B GLY 3.9 11.0 - - - +
202B ILE* 4.8 3.6 - - + +
210B TYR* 1.3 77.3 - - - +
212B VAL* 1.3 65.0 + - - +
213B MET* 3.7 22.8 + - + -
102J ARG* 4.5 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 3.5 29.2 - - + +
156B LYS* 4.1 20.4 - - + -
157B PHE 4.5 1.8 - - - -
158B GLY* 4.5 0.4 - - - -
201B GLY* 3.1 34.3 + - - +
203B VAL* 3.6 38.4 - - + +
210B TYR* 5.1 2.9 - - + -
211B VAL* 1.3 82.0 - - - +
213B MET* 1.3 74.3 + - - +
214B THR* 3.6 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 5.5 1.6 - - - +
155B LEU 3.7 1.2 - - - +
156B LYS* 3.2 5.9 - - - -
157B PHE* 3.1 69.9 + - + +
169B TYR* 3.8 38.1 - - + +
170B GLU* 4.9 1.6 - - - -
171B TRP* 3.9 22.0 - - + -
199B ASP 4.3 0.9 - - - -
200B SER* 3.0 33.9 - - - +
211B VAL* 3.7 22.9 + - + -
212B VAL* 1.3 93.0 - - - +
214B THR* 1.3 60.0 + - - +
102J ARG* 5.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO* 4.7 3.1 - - + -
155B LEU 3.7 2.5 - - - -
156B LYS* 3.5 29.9 - - + +
171B TRP* 4.3 2.8 - - - -
198B VAL* 3.6 2.8 - - - +
199B ASP* 2.9 45.0 + - - -
201B GLY 5.3 1.6 + - - -
212B VAL* 3.6 11.3 + - - +
213B MET* 1.3 75.5 - - - +
215B THR* 1.3 69.8 + - - +
216B HIS* 3.4 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.9 2.8 - - + +
154B PRO* 3.2 3.6 - - - +
155B LEU* 2.8 50.7 + - + +
157B PHE* 4.5 4.6 - - - -
171B TRP* 3.7 22.5 - - - -
179B VAL* 4.0 23.5 - - + +
196B GLN* 5.2 0.7 - - + -
197B THR 3.3 12.6 - - - +
198B VAL* 4.2 2.2 - - + +
214B THR* 1.3 77.3 + - - +
216B HIS* 1.3 67.8 + - - +
217B PHE* 4.0 24.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA* 4.7 19.3 - - + -
153B CYS 4.2 2.9 - - - -
154B PRO* 4.0 19.0 - - + +
195B GLY 4.0 0.2 - - - +
196B GLN* 3.8 3.1 - - - -
197B THR* 2.8 55.9 + - + +
199B ASP* 5.0 13.1 - - + +
214B THR* 3.4 29.5 + - + +
215B THR* 1.3 71.6 - - - +
217B PHE* 1.3 62.4 + - - +
218B HIS* 3.7 14.5 + + + +
28I TYR* 5.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 5.9 0.9 - - + -
47B VAL* 3.8 20.4 - - + -
50B PHE* 3.9 32.3 - + + -
60B TYR* 4.6 7.0 - - - -
62B ILE* 3.6 30.5 - - + -
152B ALA* 3.8 3.1 - - - -
153B CYS* 3.3 38.8 + - + +
155B LEU* 4.7 11.0 - - + -
179B VAL* 4.2 11.9 - - + -
181B VAL* 5.7 0.7 - - + -
193B LEU* 4.2 19.1 - - + -
195B GLY 4.0 1.3 - - - -
196B GLN* 3.6 33.9 - - + -
215B THR* 4.1 16.4 - - + -
216B HIS* 1.3 72.7 - - - +
218B HIS* 1.3 63.8 + - - +
219B LEU* 3.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS 4.0 10.4 + - - +
152B ALA* 4.5 13.6 - - + +
193B LEU* 3.5 12.6 - - - +
194B LEU* 3.6 22.2 + - + -
195B GLY* 3.2 31.7 + - - +
197B THR* 3.0 31.7 + - + +
216B HIS* 4.3 10.3 + - + -
217B PHE* 1.3 73.8 - - - +
219B LEU* 1.3 71.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.9 37.0 - - + -
53B VAL* 4.1 6.1 - - + -
150B ALA* 3.4 10.2 - - - +
151B HIS* 3.2 38.3 + - + +
153B CYS* 4.6 18.8 - - + -
188B LEU* 4.1 9.9 - - + -
191B TYR* 3.7 32.8 - - + -
192B ASP 4.3 3.6 - - - -
193B LEU* 4.0 21.5 - - + +
194B LEU* 5.1 5.1 - - - +
217B PHE 4.1 6.3 - - - +
218B HIS* 1.3 85.5 - - - +
220B LYS* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 5.7 4.9 - - - +
149B ASP 4.1 11.7 - - - +
150B ALA* 4.5 7.6 - - + +
151B HIS* 6.0 0.9 - - - -
191B TYR* 3.4 7.3 - - - -
192B ASP* 3.2 36.8 + - + +
194B LEU* 5.3 15.5 - - + -
219B LEU* 1.3 76.6 - - - +
221B ARG* 1.3 74.5 + - - +
222B LYS* 3.8 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 3.4 17.4 + - - -
143B LEU* 4.5 5.5 - - - +
146B PHE* 3.4 28.7 - - - -
147B PRO* 3.2 41.8 - - - +
148B MET* 5.5 2.4 - - - -
149B ASP* 3.6 22.1 + - - +
151B HIS* 4.4 5.9 + - - -
190B GLN* 2.8 36.0 + - + +
191B TYR* 2.8 42.3 + - + -
220B LYS* 1.3 87.6 - - - +
222B LYS* 1.3 71.7 + - - +
223B ILE* 3.6 3.6 + - - +
226B PHE* 3.9 14.0 - - + -
277B LEU* 5.3 0.8 - - - +
----------------------------------------------------------
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