Contacts of the helix formed by residues 185 - 205 (chain B) in PDB entry 4K2S
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 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 5.2 0.5 - - - +
157B ILE* 3.6 32.2 - - - +
184B TRP* 1.3 83.8 - - - +
186B THR* 1.3 62.7 + - - +
187B GLU* 3.7 9.1 + - - +
188B LYS* 3.3 30.0 + - - +
189B TYR* 3.2 20.6 + - - +
397B LEU* 5.6 0.2 - - - -
398B GLU* 4.0 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B TRP* 2.8 32.3 + - - +
185B SER* 1.3 72.1 + - - +
187B GLU* 1.3 71.0 + - - +
189B TYR* 3.1 3.6 + - - +
190B LEU* 2.9 46.0 + - + +
217B ARG 3.6 12.0 + - - -
218B LEU* 3.7 9.6 - - + +
222B GLU* 3.5 30.0 + - - +
397B LEU* 5.2 2.8 - - - +
403B TRP* 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 3.4 7.8 + - - +
186B THR* 1.3 89.3 + - + +
188B LYS* 1.3 64.0 + - + +
190B LEU* 3.4 9.5 + - + +
191B ASN* 3.3 32.1 + - - +
222B GLU* 4.6 9.9 - - - +
225B ARG* 4.8 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.7 16.2 - - + +
155B PRO 3.8 17.3 - - - +
156B GLY* 4.4 13.7 - - - -
157B ILE* 4.0 13.9 - - + -
185B SER* 3.3 19.6 + - - +
187B GLU* 1.3 79.4 - - + +
189B TYR* 1.3 62.3 + - - +
191B ASN* 3.5 6.4 + - - +
192B HIS* 3.1 24.1 + - - +
398B GLU* 3.9 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.8 25.4 - - + +
160B THR* 5.0 2.9 - - - -
184B TRP* 3.4 40.2 - + + -
185B SER 3.2 6.8 + - - +
186B THR 3.1 6.6 + - - +
188B LYS* 1.3 78.8 - - - +
190B LEU* 1.3 67.3 + - + +
192B HIS* 4.5 0.4 - + - +
193B ALA* 2.9 47.2 + - + +
212B HIS* 2.6 41.8 + + - -
213B ASP 5.7 0.2 - - - -
214B VAL* 3.7 22.6 - - + +
218B LEU* 4.2 18.2 - - + -
226B LEU* 3.7 18.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
186B THR* 2.9 41.3 + - + +
187B GLU* 3.8 6.7 - - + +
188B LYS 3.3 0.4 - - - -
189B TYR* 1.3 82.6 - - + +
191B ASN* 1.3 57.8 + - - +
194B PRO* 3.2 25.3 - - - +
218B LEU* 3.9 29.2 - - + -
222B GLU* 4.0 24.2 - - + +
225B ARG* 3.6 42.6 + - - +
226B LEU* 3.9 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.3 18.2 + - - +
188B LYS* 3.9 5.7 - - - +
189B TYR 3.2 0.6 - - - -
190B LEU* 1.3 78.4 - - - +
192B HIS* 1.3 61.1 + - - +
194B PRO* 4.1 6.6 - - - +
195B LYS* 2.8 29.2 + - - +
225B ARG* 2.9 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 4.0 29.0 + - + +
152B SER* 3.8 15.7 + - - -
153B GLY 3.1 25.2 + - - -
154B VAL* 4.2 10.1 - - + -
155B PRO* 3.4 33.4 - - + +
188B LYS 3.1 18.1 + - - +
189B TYR* 3.2 2.7 + - - +
191B ASN* 1.3 80.5 - - - +
193B ALA* 1.3 70.8 + - - +
195B LYS* 2.9 36.4 + - + +
196B LEU* 3.7 2.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TYR* 2.9 44.0 + - + +
192B HIS* 1.3 81.1 - - - +
194B PRO* 1.4 68.2 - - + +
196B LEU* 3.0 19.9 + - - +
197B PHE* 3.3 30.3 - - + -
212B HIS* 4.7 1.8 - - + +
226B LEU* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU 3.2 22.4 - - - +
191B ASN 4.1 5.4 - - - +
192B HIS 3.6 2.7 - - - -
193B ALA* 1.4 92.3 - - + +
195B LYS* 1.3 56.4 + - + +
197B PHE* 3.3 11.4 + - + -
198B ALA* 3.0 29.3 + - - +
226B LEU* 4.1 10.5 - - + -
229B ALA* 4.1 25.8 - - + +
230B VAL* 4.3 3.4 - - + -
233B TYR* 3.5 20.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
130B ILE* 3.7 16.1 - - + +
191B ASN* 2.8 31.5 + - - +
192B HIS* 2.9 27.5 + - + +
194B PRO* 1.3 74.4 - - + +
196B LEU* 1.3 65.3 + - - +
198B ALA* 3.5 7.7 + - - +
199B ALA* 3.1 23.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
130B ILE* 3.7 25.6 - - + +
133B CYS* 4.1 22.7 - - + -
134B LEU* 5.2 0.4 - - + -
150B VAL* 3.8 34.1 - - + +
151B GLN* 4.0 0.4 - - - -
152B SER* 3.8 40.6 - - - +
192B HIS* 3.7 3.4 + - + +
193B ALA* 3.0 15.9 + - - +
195B LYS* 1.3 78.6 - - - +
197B PHE* 1.3 71.7 + - + +
199B ALA* 3.1 5.0 + - - +
200B VAL* 3.0 32.7 + - + +
212B HIS* 4.8 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 3.7 24.2 - - + -
193B ALA* 3.3 30.3 - - + -
194B PRO* 3.3 2.8 + - + -
196B LEU* 1.3 81.5 - - + +
198B ALA* 1.3 63.4 + - - +
200B VAL* 3.2 7.3 + - - +
201B ARG* 3.0 28.1 + - - +
210B VAL* 4.6 2.2 - - + -
212B HIS* 3.3 55.4 - + + -
226B LEU* 5.0 1.8 - - + -
230B VAL* 3.5 34.5 - - + -
233B TYR* 3.6 24.2 - - + -
235B LEU* 4.1 20.2 - - + -
238B LEU* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PRO 3.0 16.6 + - - +
195B LYS* 3.7 9.2 - - - +
196B LEU 3.2 0.2 - - - -
197B PHE* 1.3 76.7 - - - +
199B ALA* 1.3 56.3 + - - +
201B ARG* 3.4 3.0 + - - +
202B GLU* 2.9 28.9 + - - +
233B TYR* 3.6 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 3.5 28.5 - - + -
134B LEU* 3.9 13.5 - - + +
195B LYS 3.1 11.7 + - - +
196B LEU 3.5 8.5 - - - +
198B ALA* 1.3 73.2 - - - +
200B VAL* 1.3 66.5 + - - +
202B GLU* 3.4 7.5 + - - +
203B ARG* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.8 20.6 - - + -
137B VAL* 4.9 3.8 - - + -
150B VAL* 4.2 25.1 - - + -
196B LEU* 3.0 29.5 + - + +
197B PHE* 3.2 11.0 + - - +
199B ALA* 1.3 77.0 - - - +
201B ARG* 1.3 58.3 + - + +
204B PHE* 2.9 41.8 + - + +
205B GLY 4.0 0.6 + - - +
208B LEU* 4.4 9.0 - - + -
210B VAL* 3.9 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE 3.0 18.8 + - - +
198B ALA 3.9 3.6 - - - +
200B VAL* 1.3 76.7 - - + +
202B GLU* 1.3 64.8 + - - +
205B GLY* 3.0 45.9 + - - -
206B ASP* 3.7 27.2 + - - +
208B LEU* 2.8 32.1 + - - +
209B HIS* 4.9 0.4 - - - +
210B VAL* 3.6 27.4 - - + +
232B PRO 5.4 0.2 - - - +
233B TYR* 2.8 47.0 + - + +
234B HIS* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ALA 2.9 18.5 + - - +
199B ALA* 3.8 8.9 - - - +
200B VAL 3.4 0.2 - - - -
201B ARG* 1.3 79.2 - - - +
203B ARG* 1.3 73.4 + - - +
205B GLY 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLU* 2.9 40.0 + - - -
134B LEU* 3.5 29.1 - - + +
135B GLY* 5.0 1.0 - - - +
138B ALA* 6.1 0.9 - - - -
199B ALA 3.1 15.9 + - - +
202B GLU* 1.3 89.3 + - - +
204B PHE* 1.3 94.7 + - + +
205B GLY 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 3.2 39.9 - - + -
137B VAL* 3.5 27.6 - - + -
138B ALA* 3.4 32.1 - - + -
141B VAL* 4.7 10.5 - - + -
200B VAL* 2.9 25.5 + - + +
203B ARG* 1.3 102.5 - - + +
205B GLY* 1.3 63.1 + - - +
207B ASP* 5.0 1.9 + - - +
208B LEU* 3.9 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL 4.7 0.5 - - - +
201B ARG* 3.0 42.0 + - - -
202B GLU 4.7 0.4 - - - -
203B ARG 3.7 1.2 - - - -
204B PHE* 1.3 82.5 - - - +
206B ASP* 1.3 66.2 + - - -
207B ASP 3.6 1.3 + - - -
208B LEU* 4.5 2.3 + - - +
----------------------------------------------------------
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