Contacts of the strand formed by residues 190 - 200 (chain B) in PDB entry 4D1Q
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 ASN 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN* 5.8 3.8 - - - +
181B LEU* 4.4 9.7 - - - +
182B TRP 3.6 8.7 + - - +
183B THR* 3.4 25.5 - - - +
188B LYS 4.0 1.1 + - - +
189B ARG* 1.3 74.3 - - - +
191B PHE* 1.3 61.4 + - - +
213B SER* 3.6 1.7 - - - -
214B LEU* 2.9 43.4 + - + +
215B ASP 4.4 12.8 + - - +
216B PHE* 4.9 1.8 - - + -
219B SER* 3.6 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP 3.8 0.3 - - - +
181B LEU* 3.2 11.0 - - - +
182B TRP* 2.8 71.8 + + + +
184B ASP* 3.7 20.9 - - + -
189B ARG* 3.7 33.7 - - + -
190B ASN* 1.3 73.6 + - - +
192B LEU* 1.3 60.5 + - - +
193B GLY 4.1 0.4 + - - -
211B LEU* 3.1 41.3 - - + -
212B LYS 3.5 17.3 - - - -
213B SER* 3.8 4.3 - - - -
214B LEU* 5.2 1.6 - - - -
582B ILE* 4.3 8.3 - - + -
591B GLN* 4.3 25.6 - - + -
594B VAL* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 4.3 8.1 - - + -
180B ASP 3.4 13.9 - - - +
181B LEU* 3.3 25.6 - - + -
191B PHE* 1.3 73.9 - - - +
193B GLY* 1.3 68.2 + - - +
194B VAL* 4.2 11.2 - - + -
210B GLY 3.5 1.9 - - - +
211B LEU* 3.4 4.4 - - - -
212B LYS 2.8 32.8 + - - +
214B LEU* 4.3 10.8 - - + -
224B ILE* 3.6 34.8 - - + +
227B LYS* 4.1 10.1 - - + +
228B LEU* 3.8 24.7 - - + +
231B ILE* 3.7 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR 4.3 0.2 - - - -
179B ILE* 3.2 22.5 - - - -
180B ASP 3.2 12.1 + - - -
192B LEU* 1.3 73.2 - - - +
194B VAL* 1.3 67.7 + - - +
195B THR* 4.3 0.7 - - - -
210B GLY 3.4 7.2 - - - -
211B LEU* 4.0 7.3 - - - +
571B SER* 4.1 6.2 + - - -
574B THR* 5.1 6.5 - - - -
575B PHE* 4.0 19.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 4.9 2.2 - - + -
178B THR 3.4 5.6 - - - +
179B ILE* 3.6 19.3 - - + -
192B LEU* 4.2 7.2 - - + -
193B GLY* 1.3 80.9 - - - +
195B THR* 1.3 60.8 + - - +
208B ILE* 3.6 3.7 - - - +
209B LEU* 2.7 59.0 + - + -
210B GLY 2.9 11.3 + - - +
228B LEU* 3.8 14.1 - - + -
231B ILE* 4.0 25.8 - - + -
232B PHE* 4.1 17.0 - - + -
574B THR* 5.7 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 2.9 30.4 - - - +
178B THR* 2.5 37.0 + - - -
194B VAL* 1.3 75.4 - - - +
196B LEU* 1.3 58.9 + - - +
197B HIS* 3.3 9.0 - - + +
206B ASP* 4.2 4.7 - - - +
207B LEU 3.1 20.0 - - - +
208B ILE* 4.2 15.0 - - + -
209B LEU* 4.8 0.4 - - - -
570B ALA* 3.6 20.6 - - + -
571B SER* 3.2 10.4 + - - -
574B THR* 4.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.1 29.8 - - + -
170B VAL* 5.0 3.4 - - + -
175B ALA* 4.8 11.9 - - + -
176B SER 3.4 12.6 - - - +
177B ALA* 3.9 7.0 - - + -
195B THR* 1.3 73.2 - - - +
197B HIS* 1.3 68.0 + - - +
198B TYR* 3.9 28.9 - - + -
205B ARG* 3.5 2.1 - - - +
207B LEU* 2.6 43.1 + - + +
209B LEU* 3.9 19.7 - - + +
232B PHE* 3.7 33.2 - - + -
243B ILE* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 3.4 1.0 - - - +
176B SER* 2.6 49.4 + - - +
177B ALA* 4.0 3.4 - - - -
178B THR* 3.1 22.1 + - - -
195B THR* 3.3 14.7 - - + -
196B LEU* 1.3 80.1 + - - +
198B TYR* 1.3 64.3 + - - +
204B LEU* 5.8 2.2 - - + -
205B ARG* 3.0 17.2 + - - +
206B ASP* 3.7 18.6 - - - -
377B CYS* 4.0 9.1 + - - +
563B SER* 3.8 19.1 - - - +
565B PRO* 3.5 26.2 - - + +
570B ALA* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 2.8 35.6 + - + +
166B ILE* 4.2 15.6 - - + +
169B ALA* 3.6 26.2 - - + -
174B GLY 3.2 17.7 - - - +
175B ALA* 4.0 4.7 - - + -
196B LEU* 3.9 29.4 - - + -
197B HIS* 1.3 74.6 - - - +
199B HIS* 1.3 68.0 + - - +
200B GLU* 4.1 6.7 - - + -
204B LEU* 3.6 3.0 - - - +
205B ARG* 2.7 58.2 + - + +
207B LEU* 5.5 5.4 - - + +
563B SER* 3.5 16.7 + - - -
607B PHE* 3.6 18.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 6.0 1.0 - - - +
174B GLY 4.2 3.2 + - - +
198B TYR* 1.3 81.6 - - - +
200B GLU* 1.3 64.2 + - - +
201B ASN 2.7 32.0 + - - -
203B GLU 3.4 17.2 + - - +
204B LEU* 4.3 3.4 - - + -
541B MET* 4.2 14.1 - - - -
545B ASN* 3.2 23.1 + - - -
559B LEU* 3.4 57.6 - - + +
560B SER* 6.1 0.2 - - - -
563B SER* 4.0 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 3.6 34.6 - - - +
198B TYR* 4.1 10.0 + - + -
199B HIS* 1.3 79.5 - - - +
201B ASN* 1.3 84.8 + - + +
203B GLU* 3.0 26.8 + - - +
205B ARG* 3.7 22.0 - - - +
----------------------------------------------------------
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