Contacts of the helix formed by residues 186 - 200 (chain B) in PDB entry 4K9P
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 186 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A SER* 3.2 35.5 + - - +
184A ARG* 4.6 10.1 - - + -
320A ALA* 4.3 17.4 - - + +
184B ARG* 3.5 3.5 + - - +
185B LEU* 1.3 73.9 - - - +
187B ASP* 1.3 64.8 + - - +
188B GLN* 3.0 15.1 + - - +
189B ASP* 2.7 50.3 + - - +
190B LEU* 2.8 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 2.9 17.1 + - - +
184B ARG* 2.5 44.3 + - - +
186B ASN* 1.3 72.9 - - - +
188B GLN* 1.3 65.0 + - - +
190B LEU* 3.6 3.4 - - - +
191B ASP* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASN* 3.0 9.5 + - - +
187B ASP* 1.3 80.4 - - - +
189B ASP* 1.3 71.9 + - - +
191B ASP* 3.4 7.6 + - - +
192B ILE* 3.4 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A HIS* 6.6 0.4 - - - -
180A SER* 4.6 4.1 + - - -
182A SER* 4.2 7.1 + - - -
185B LEU* 3.4 33.0 - - + +
186B ASN* 2.7 28.6 + - - +
188B GLN* 1.3 86.4 - - - +
190B LEU* 1.3 63.3 + - - +
192B ILE* 3.4 18.7 + - + +
193B LEU* 3.1 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 3.2 30.5 - - - +
185B LEU* 3.5 15.1 - - + +
186B ASN 2.8 18.7 + - - +
187B ASP* 3.6 5.8 - - - +
188B GLN 3.2 0.2 - - - -
189B ASP* 1.3 75.7 - - - +
191B ASP* 1.3 61.9 + - - +
193B LEU* 3.2 11.4 + - + +
194B VAL* 2.9 32.6 + - + +
321B MET* 4.5 13.9 - - + -
324B ALA* 4.2 13.5 - - + -
325B LEU* 4.0 26.0 - - + -
328B LEU* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 2.9 25.7 + - - +
188B GLN* 3.7 6.8 - - - +
190B LEU* 1.3 77.3 - - - +
192B ILE* 1.3 57.4 + - + +
194B VAL* 3.6 7.4 - - - +
195B LYS* 2.9 38.4 + - + +
328B LEU* 4.9 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN* 3.4 23.0 + - + +
189B ASP* 3.4 22.4 + - - +
190B LEU 3.2 0.4 - - - -
191B ASP* 1.3 79.0 - - + +
193B LEU* 1.3 63.2 + - - +
195B LYS* 3.3 12.6 + - + +
196B ALA* 3.1 21.0 + - + +
294B ARG* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.7 3.8 - - + -
189B ASP 3.1 12.7 + - - +
190B LEU* 3.6 10.5 - - + +
192B ILE* 1.3 78.6 - - - +
194B VAL* 1.3 63.7 + - - +
196B ALA* 3.2 5.7 + - - +
197B LEU* 3.2 32.0 + - + +
271B LEU* 4.9 2.7 - - + -
296B ILE* 3.8 38.4 - - + -
298B VAL* 5.1 2.5 - - + -
314B ILE* 3.8 25.1 - - + -
321B MET* 4.1 9.4 - - + -
325B LEU* 3.9 34.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
190B LEU* 2.9 18.3 + - + +
191B ASP* 3.2 13.2 + - - +
193B LEU* 1.3 74.8 - - - +
195B LYS* 1.3 58.0 + - + +
197B LEU* 3.3 8.4 + - - +
198B ASN* 3.0 46.4 + - - +
325B LEU* 3.8 22.2 - - + -
328B LEU* 3.9 45.3 - - + +
329B VAL* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASP* 2.9 19.7 + - - +
192B ILE* 3.5 14.8 - - + +
193B LEU 3.3 0.2 - - - -
194B VAL* 1.3 76.9 - - + +
196B ALA* 1.3 52.4 + - - +
198B ASN* 3.4 9.1 + - + +
199B SER* 2.3 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 3.1 14.0 + - + +
193B LEU* 3.4 12.3 - - - +
195B LYS* 1.3 77.8 - - - +
197B LEU* 1.3 62.7 + - - +
199B SER* 3.3 5.8 + - - -
200B ALA* 3.0 24.9 + - - +
269B VAL* 4.5 8.5 - - + +
294B ARG* 3.8 26.0 - - - +
296B ILE* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.2 27.5 + - + +
194B VAL* 3.7 5.4 - - - +
196B ALA* 1.3 78.0 - - - +
198B ASN* 1.3 63.5 + - - +
200B ALA* 3.5 18.3 + - - +
203B PRO* 5.0 6.1 - - + +
223B LEU* 4.8 1.6 - - + -
227B LEU* 3.8 27.9 - - + +
269B VAL* 4.4 16.8 - - + -
271B LEU* 4.3 37.9 - - + -
296B ILE* 5.1 1.3 - - + -
325B LEU* 4.0 21.5 - - + -
329B VAL* 3.9 26.9 - - + -
334B ARG* 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 3.0 39.5 + - - +
195B LYS* 3.7 8.7 - - + +
197B LEU* 1.3 79.0 - - - +
199B SER* 1.3 59.9 + - - +
200B ALA 3.6 4.9 + - - +
227B LEU* 4.7 2.9 - - - +
328B LEU 4.8 1.2 + - - -
329B VAL* 3.8 9.7 - - - +
330B GLU* 2.9 63.1 + - - +
334B ARG* 5.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS 2.3 31.1 + - - -
196B ALA* 3.3 9.4 + - - -
198B ASN* 1.3 73.9 - - - +
200B ALA* 1.3 65.7 + - - +
201B SER* 3.3 4.5 + - - -
268B ASP* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA 3.0 9.4 + - - +
197B LEU* 3.6 15.1 - - - +
198B ASN 3.3 4.6 - - - +
199B SER* 1.3 78.6 - - - +
201B SER* 1.3 59.4 + - - +
202B ASN 3.4 0.2 - - - -
203B PRO* 4.0 13.9 - - + -
268B ASP* 3.4 11.4 - - - +
269B VAL* 3.6 34.1 - - + -
334B ARG* 3.2 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