Contacts of the helix formed by residues 198 - 213 (chain B) in PDB entry 3H8E
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 HIS 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PRO 4.2 9.4 - - - +
195B ASN 4.4 7.0 + - - +
196B LEU* 3.1 26.1 + - - -
197B CYS* 1.3 76.6 - - - +
199B PRO* 1.3 78.6 - - + +
200B SER* 3.3 36.9 - - - -
201B PHE* 3.1 23.6 + + + +
202B LEU* 3.1 15.1 + - - +
243B GLN* 2.8 51.9 + - + -
321B GLU* 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS* 1.3 89.4 - - + +
200B SER* 1.3 57.4 + - - +
202B LEU* 3.2 9.6 + - + +
203B ALA* 3.0 26.2 + - - +
243B GLN* 4.9 2.7 - - + +
244B PRO 3.3 24.7 - - - +
246B ARG* 3.8 16.7 - - + +
248B ILE* 4.4 0.3 - - - +
268B GLY 5.0 2.5 - - - +
269B ILE 6.1 0.9 - - - -
291B MET* 6.3 0.4 - - - -
319B CYS* 3.8 22.0 - - + -
320B ALA* 3.7 36.3 - - - +
321B GLU* 4.2 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS* 3.3 18.9 - - - -
199B PRO* 1.3 76.0 - - - +
201B PHE* 1.3 62.9 + - - +
203B ALA* 3.2 9.8 + - - +
204B GLU* 2.9 28.1 + - - +
243B GLN* 4.2 1.0 + - - -
244B PRO* 3.9 14.4 - - - +
246B ARG* 3.6 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 6.1 0.4 - - - -
189B LEU* 3.9 11.0 - - + -
192B LEU* 3.6 33.2 - - + -
196B LEU* 3.3 27.1 - - + +
197B CYS* 3.8 20.2 - - - -
198B HIS* 3.1 19.6 + - + +
200B SER* 1.3 79.3 - - - +
202B LEU* 1.4 61.5 + - + +
204B GLU* 3.2 11.4 + - + +
205B GLN* 2.9 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.1 15.9 - - + -
197B CYS* 3.9 10.8 - - - -
198B HIS 3.1 17.2 + - - +
199B PRO* 3.2 8.9 + - + +
201B PHE* 1.4 81.7 - - + +
203B ALA* 1.3 56.8 + - - +
205B GLN* 3.2 6.0 + - + +
206B ALA* 3.0 24.3 + - - +
248B ILE* 3.6 13.0 - - + -
268B GLY 4.8 2.2 - - - +
291B MET* 2.6 57.7 - - + -
294B ALA* 4.9 5.8 - - + -
298B PHE* 3.4 23.2 - - + -
319B CYS* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO 3.0 13.6 + - - +
200B SER* 3.2 13.4 + - - +
202B LEU* 1.3 76.1 - - - +
204B GLU* 1.3 59.2 + - - +
206B ALA* 3.2 4.1 + - - +
207B LYS* 2.9 37.3 + - - +
220B VAL* 3.7 31.2 - - + +
246B ARG* 4.3 7.2 - - + +
248B ILE* 3.5 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B SER* 2.9 19.0 + - - +
201B PHE* 3.2 13.6 + - + +
203B ALA* 1.3 74.7 - - - +
205B GLN* 1.4 64.8 + - - +
207B LYS* 2.9 36.4 + - - +
208B GLU* 2.9 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.0 23.2 - - + -
189B LEU* 4.1 12.4 - - + +
201B PHE* 2.9 55.9 + - + +
202B LEU* 3.4 10.1 - - - +
204B GLU* 1.4 75.6 - - - +
206B ALA* 1.3 57.4 + - - +
208B GLU* 3.4 22.8 + - - +
209B LEU* 3.0 27.9 + - - +
298B PHE* 4.0 14.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU 3.0 11.0 + - - +
203B ALA 3.2 8.0 + - - +
205B GLN* 1.3 73.0 - - - +
207B LYS* 1.3 63.0 + - - +
209B LEU* 3.2 5.2 + - - +
210B GLY 2.9 23.9 + - - -
218B VAL* 3.4 16.8 - - + +
248B ILE* 3.4 33.7 - - + -
250B LEU* 4.0 6.3 - - + -
298B PHE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ALA* 2.9 22.5 + - - +
204B GLU* 2.9 44.2 + - - +
206B ALA* 1.3 78.0 - - - +
208B GLU* 1.3 62.0 + - + +
210B GLY* 3.3 2.4 + - - -
211B LYS* 3.0 32.0 + - + +
218B VAL* 4.3 12.1 - - + +
220B VAL* 4.1 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 2.9 30.4 + - + +
205B GLN* 3.6 26.4 + - - +
207B LYS* 1.3 74.1 - - + +
209B LEU* 1.3 64.0 + - - +
211B LYS* 3.3 28.1 + - - +
212B ALA* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.9 6.3 - - + -
205B GLN 3.0 17.7 + - - +
206B ALA* 3.2 6.0 + - - +
208B GLU* 1.3 76.8 - - - +
210B GLY* 1.3 60.9 + - - +
212B ALA* 3.1 13.8 + - + +
213B HIS* 3.1 45.8 + - + +
216B LEU* 3.9 10.3 - - + -
250B LEU* 4.3 3.1 - - + -
298B PHE* 4.2 23.6 - - + +
301B LEU* 3.9 31.6 - - + -
302B ARG* 3.9 32.3 - - + +
305B LEU* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA 2.9 10.7 + - - -
207B LYS 3.3 4.2 + - - -
209B LEU* 1.3 73.6 - - - +
211B LYS* 1.3 61.7 + - - +
212B ALA 3.3 0.2 + - - -
213B HIS 3.3 19.1 - - - +
216B LEU* 3.8 19.1 - - - +
218B VAL* 3.7 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LYS* 3.0 19.3 + - + +
208B GLU* 3.3 33.5 + - - +
210B GLY* 1.3 76.8 - - - +
212B ALA* 1.3 62.1 + - - +
213B HIS 3.3 2.1 + - - -
214B LYS* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU 3.2 9.5 + - - +
209B LEU* 3.1 13.4 + - + +
211B LYS* 1.3 78.3 - - - +
213B HIS* 1.3 77.1 + - + +
214B LYS* 4.4 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.1 48.1 + - + +
210B GLY 3.3 13.0 - - - +
211B LYS 3.3 3.9 - - - -
212B ALA* 1.3 95.7 + - + +
214B LYS* 1.3 66.5 + - - +
215B ALA 4.8 0.7 - - - +
216B LEU* 3.3 25.6 + - + +
302B ARG* 5.7 2.6 + - - -
305B LEU* 3.8 41.6 + - + +
----------------------------------------------------------
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