Contacts of the helix formed by residues 185 - 200 (chain B) in PDB entry 3KHU
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 THR 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLN* 5.3 0.5 + - - -
183B ASP* 3.1 20.3 + - + +
184B GLU* 1.3 83.2 - - - +
186B PRO* 1.3 69.7 - - - +
187B GLU* 3.7 6.1 + - - +
188B GLY* 3.0 20.8 + - - -
189B GLN* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU 4.7 0.9 - - - +
185B THR* 1.3 87.7 - - - +
187B GLU* 1.3 62.0 + - + +
189B GLN* 3.5 5.5 + - + +
190B ARG* 3.1 52.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
123B TYR* 3.7 18.0 + - - -
153B ASN* 3.3 26.3 + - - +
155B GLN* 3.7 23.2 + - - +
185B THR* 3.3 6.0 + - - +
186B PRO* 1.3 77.1 - - + +
188B GLY* 1.3 66.4 - - - +
190B ARG* 3.0 32.7 + - - +
191B ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLN* 3.9 9.0 + - - -
157B LEU* 4.3 2.9 - - - +
183B ASP* 3.7 25.6 - - - -
185B THR* 3.0 18.1 + - - -
187B GLU* 1.3 76.7 - - - +
189B GLN* 1.3 55.3 + - - +
191B ALA* 3.2 6.6 + - - +
192B VAL* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY 4.3 4.2 + - - -
183B ASP 2.9 24.8 + - - +
184B GLU* 4.1 10.5 - - - +
185B THR 2.9 21.4 + - - +
186B PRO* 4.0 5.8 - - + +
188B GLY* 1.3 76.4 - - - +
190B ARG* 1.3 58.3 + - + +
192B VAL* 3.6 20.9 - - - +
193B GLN* 3.0 31.2 + - - +
210B THR* 5.2 5.7 + - - -
211B THR 5.2 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 6.1 4.9 - - - -
2B PHE* 5.2 9.5 - - + +
123B TYR* 4.7 6.7 - - - +
186B PRO* 3.1 45.5 + - - +
187B GLU* 3.0 43.1 + - - +
188B GLY 3.3 0.2 - - - -
189B GLN* 1.3 73.7 - - + +
191B ALA* 1.3 64.6 + - - +
193B GLN* 3.9 5.3 - - - +
194B ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 3.9 8.4 + - - +
125B ILE* 4.0 19.3 - - + +
155B GLN* 3.8 26.0 - - + -
157B LEU* 3.6 22.3 - - + +
187B GLU 3.1 12.5 + - - +
188B GLY* 3.2 8.5 + - - +
190B ARG* 1.3 77.7 - - - +
192B VAL* 1.3 61.8 + - - +
194B ALA* 3.2 4.9 + - - +
195B LEU* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.6 25.3 - - + +
180B ILE* 4.1 11.7 - - + +
181B GLY* 5.2 0.2 - - - -
182B GLY* 3.9 19.3 - - - +
188B GLY 3.0 19.2 + - - +
189B GLN* 3.6 22.9 - - - +
190B ARG 3.4 0.2 - - - -
191B ALA* 1.3 74.1 - - - +
193B GLN* 1.3 59.7 + - - +
195B LEU* 3.1 4.9 + - - +
196B CYS* 2.9 28.6 + - - -
210B THR* 3.6 36.6 - - + -
211B THR 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B SER* 3.9 34.4 - - - -
189B GLN 3.0 18.1 + - - +
190B ARG* 3.9 6.1 - - - +
192B VAL* 1.3 76.4 - - - +
194B ALA* 1.3 64.5 + - - +
196B CYS* 3.1 13.1 + - - +
197B ALA* 2.9 28.2 + - + +
200B GLU* 4.4 14.0 + - - +
205B ARG* 5.2 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 3.8 33.8 - - + +
4B ILE* 3.6 17.2 + - + +
125B ILE* 3.8 19.7 - - + -
190B ARG 3.1 15.3 + - - +
191B ALA 3.2 9.2 + - - +
193B GLN* 1.3 80.3 - - - +
195B LEU* 1.3 59.8 + - - +
197B ALA* 3.4 16.3 + - - +
198B VAL* 3.5 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.0 5.4 - - + +
84B LEU* 3.9 29.2 - - + -
86B PHE* 4.2 7.2 - - + -
125B ILE* 5.7 0.2 - - + -
127B THR* 4.1 9.6 - - + +
157B LEU* 4.0 21.1 - - + -
159B ASN* 4.0 26.0 - - + +
180B ILE* 3.9 22.7 - - + -
191B ALA 3.2 10.4 + - - +
192B VAL 3.1 7.9 + - - +
194B ALA* 1.3 73.8 - - - +
196B CYS* 1.3 67.4 + - - +
198B VAL* 3.2 21.9 + - + +
199B TYR* 3.3 26.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 3.8 14.5 - - - +
192B VAL* 2.9 23.1 + - - -
193B GLN* 3.4 15.5 - - - +
195B LEU* 1.3 77.0 - - - +
197B ALA* 1.3 51.8 + - - +
199B TYR* 2.9 6.6 + - - +
200B GLU* 2.8 48.3 + - - +
205B ARG* 4.6 10.1 - - - +
208B ILE* 3.8 16.8 - - + +
210B THR* 3.7 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE 5.5 3.4 - - - +
3B GLU* 6.5 1.6 - - + -
193B GLN* 2.9 16.6 + - + +
194B ALA* 3.5 13.9 - - - +
195B LEU 3.2 0.6 - - - -
196B CYS* 1.3 76.6 - - - +
198B VAL* 1.3 62.5 + - + +
200B GLU* 3.5 22.5 + - - +
201B HIS* 3.0 21.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.9 31.2 - - + -
7B ILE* 4.6 6.3 - - + -
23B ILE* 4.0 32.8 - - + -
27B CYS* 3.7 7.8 - - - -
30B ILE* 4.3 12.3 - - + -
194B ALA 3.5 14.3 + - - +
195B LEU* 3.4 17.3 - - + +
196B CYS 3.1 0.8 - - - -
197B ALA* 1.3 76.7 - - + +
199B TYR* 1.3 67.0 + - + +
201B HIS* 3.0 29.9 + - - +
202B TRP* 3.6 7.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 4.7 3.7 - - + +
23B ILE* 4.8 8.0 - - + +
86B PHE* 4.6 2.9 - + - -
129B LYS* 3.9 6.6 + - - -
159B ASN* 2.5 32.7 + - - -
161B GLN* 3.9 19.3 + - - -
172B LEU* 6.2 1.3 - - + -
178B VAL* 3.8 38.1 - - + -
180B ILE* 4.3 4.3 - - + -
195B LEU* 3.3 38.2 + - + -
196B CYS* 2.9 6.9 + - - +
198B VAL* 1.3 80.9 - - + +
200B GLU* 1.3 58.4 + - - +
201B HIS 3.1 1.5 + - - -
202B TRP* 3.2 38.3 + + - -
203B VAL* 2.8 31.6 + - + +
208B ILE* 4.0 17.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
193B GLN* 4.4 12.0 + - - -
196B CYS* 2.8 23.6 + - - +
197B ALA* 3.7 25.2 + - - +
198B VAL 3.2 0.8 - - - -
199B TYR* 1.3 71.8 - - - +
201B HIS* 1.3 60.7 + - - +
202B TRP* 3.1 1.5 + - - -
203B VAL 3.6 14.5 + - - +
205B ARG* 3.7 31.3 + - + +
208B ILE* 3.6 15.9 - - + -
----------------------------------------------------------
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