Contacts of the helix formed by residues 198 - 215 (chain B) in PDB entry 3A7H
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 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B HIS* 3.4 47.3 + - - +
140B LYS 4.9 1.8 - - - -
141B ILE* 4.3 9.2 - - - -
169B LEU* 3.8 10.1 - - - +
197B ASP* 1.3 81.1 + - - +
199B LYS* 1.3 75.4 + - - +
200B ALA 3.1 0.2 - - - -
201B ASP* 2.9 21.4 + - - +
202B ILE* 3.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 2.9 25.2 + - - +
198B SER* 1.3 84.9 + - - +
200B ALA* 1.3 59.2 + - - +
202B ILE* 3.0 21.8 + - + +
203B TRP 3.1 4.5 + - - -
259B PRO* 3.4 39.9 - - + +
260B SER* 4.9 6.7 + - - +
262B ARG* 2.7 51.6 + - + +
263B PRO* 3.5 15.2 + - - +
264B THR* 3.5 20.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
141B ILE* 4.7 5.2 - - + -
143B ARG* 5.9 3.1 - - + -
187B ALA* 3.9 5.7 - - + +
189B GLU* 3.6 15.4 + - - +
190B VAL* 3.7 30.1 - - + -
196B TYR* 4.0 9.2 - - + -
197B ASP 2.9 15.1 + - - +
199B LYS* 1.3 76.8 - - - +
201B ASP* 1.3 62.1 + - - +
203B TRP* 3.3 5.2 + - - +
204B SER* 3.0 25.9 + - - -
262B ARG* 3.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.9 12.5 - - + +
135B LEU* 5.3 0.2 - - - +
136B HIS* 2.9 28.5 + - + +
141B ILE* 3.5 8.8 - - - +
142B HIS* 2.8 31.4 + - - +
143B ARG* 2.7 31.0 + - - -
145B ILE* 3.8 9.5 - - + +
198B SER 2.9 10.2 + - - +
200B ALA* 1.3 76.4 - - - +
202B ILE* 1.3 61.5 + - - +
204B SER* 3.7 5.9 + - - +
205B LEU* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 5.4 0.7 - - + -
132B LEU* 4.7 6.7 - - + -
136B HIS* 3.9 20.6 - - + +
198B SER* 3.8 10.5 - - - +
199B LYS* 3.0 19.6 + - + +
201B ASP* 1.3 75.8 - - - +
203B TRP* 1.3 66.1 + - - +
205B LEU* 3.2 6.2 + - + +
206B GLY 3.1 17.0 + - - -
254B CYS* 3.4 16.7 - - - +
262B ARG* 3.9 17.3 - - + -
263B PRO* 3.5 28.5 - - + +
264B THR* 4.4 1.3 - - - -
265B ALA* 4.0 20.2 - - + +
268B LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE 5.2 0.4 + - - -
185B TRP 3.6 7.2 - - - -
186B MET 3.2 11.9 + - - -
187B ALA* 3.4 22.9 - - + -
188B PRO* 3.5 29.8 - - + -
199B LYS 3.1 2.4 + - - -
200B ALA 3.6 7.4 - - - +
201B ASP 3.3 0.2 - - - -
202B ILE* 1.3 79.9 - - - +
204B SER* 1.3 65.8 + - - +
206B GLY 2.9 11.4 + - - -
207B ILE* 3.1 26.5 + - + +
231B ILE* 3.9 16.5 - - + +
236B PRO* 3.8 19.7 - - + -
237B PRO* 3.8 18.4 - - + -
254B CYS 3.8 9.6 - - - -
255B LEU* 3.3 35.4 - - + +
256B ASN 3.6 28.7 - - - -
257B LYS* 4.1 9.6 - - + -
262B ARG* 3.6 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG* 5.2 5.4 + - - -
145B ILE* 3.7 32.3 + - - +
185B TRP* 2.6 27.6 + - - +
186B MET* 4.6 2.8 - - - -
187B ALA 4.6 0.3 + - - -
200B ALA 3.0 15.6 + - - -
201B ASP* 3.3 9.9 + - - -
202B ILE 3.3 0.2 - - - -
203B TRP* 1.3 77.1 - - - +
205B LEU* 1.3 53.0 + - - +
207B ILE* 3.3 5.3 + - - +
208B THR* 2.8 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.8 26.2 - - + +
128B ILE* 3.6 34.1 - - + -
129B LEU* 3.5 31.0 - - + -
132B LEU* 4.3 9.9 - - + -
145B ILE* 4.2 5.3 - - + +
201B ASP 2.8 14.6 + - - +
202B ILE* 3.4 9.9 - - + +
203B TRP 3.1 0.2 - - - -
204B SER* 1.3 77.7 - - - +
206B GLY* 1.3 56.8 + - - +
208B THR* 3.2 6.8 + - - -
209B ALA* 2.9 25.5 + - - +
250B PHE* 3.8 21.1 - - + -
254B CYS* 4.0 10.8 - - - -
268B LEU* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE 3.1 7.9 + - - -
203B TRP 2.9 6.7 + - - -
205B LEU* 1.3 77.6 - - - +
207B ILE* 1.3 61.9 + - - +
209B ALA* 3.3 8.6 + - - +
210B ILE* 3.1 26.3 + - - +
251B VAL* 4.3 4.5 - - - +
254B CYS* 3.5 26.2 - - - +
255B LEU* 3.9 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE 3.5 22.7 - - - +
185B TRP* 3.2 26.9 - - + -
203B TRP* 3.1 40.1 + - + +
204B SER 3.3 7.2 + - - +
206B GLY* 1.3 74.6 - - - +
208B THR* 1.3 57.9 + - - +
210B ILE* 3.2 7.9 + - - +
211B GLU* 3.0 24.4 + - - +
217B PRO* 3.6 17.9 - - + -
218B PRO* 4.0 10.8 - - + +
237B PRO* 3.8 24.9 - - + -
255B LEU* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.9 1.6 - - + -
128B ILE* 4.4 22.7 - - + -
145B ILE* 3.5 8.9 + - + +
146B LYS* 3.4 21.5 - - - -
147B ALA* 3.9 23.3 - - - +
185B TRP* 3.6 1.6 - - - +
204B SER 2.8 18.5 + - - -
205B LEU* 3.4 13.2 - - + -
206B GLY 3.2 0.2 - - - -
207B ILE* 1.3 74.9 - - - +
209B ALA* 1.3 58.8 + - - +
211B GLU* 3.2 10.0 + - - +
212B LEU* 2.8 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.9 2.8 - - - +
125B LEU* 3.9 31.6 - - + +
205B LEU 2.9 13.6 + - - +
206B GLY* 3.5 10.8 - - - +
207B ILE 3.3 0.2 - - - -
208B THR* 1.3 76.0 - - - +
210B ILE* 1.3 64.6 + - - +
212B LEU* 3.3 4.6 + - - +
213B ALA* 3.1 22.3 + - - +
239B LEU* 6.0 0.2 - - - -
247B LEU* 5.0 3.7 - - + +
250B PHE* 4.3 8.5 - - + -
251B VAL* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY 3.1 10.1 + - - +
207B ILE* 3.5 7.6 - - - +
209B ALA* 1.3 75.5 - - - +
211B GLU* 1.3 52.9 + - - +
213B ALA* 3.0 7.4 + - - +
214B ARG* 2.7 55.0 + - - +
216B GLU 4.0 7.6 - - - +
217B PRO 4.8 0.2 - - - -
218B PRO* 3.8 35.9 - - + -
237B PRO* 4.2 2.9 - - + -
238B THR 4.2 16.4 - - - +
239B LEU* 4.5 9.4 - - + -
251B VAL* 3.7 20.0 - - + -
255B LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.6 17.3 - - - +
111B LEU* 3.4 5.8 - - + +
146B LYS* 3.9 0.5 - - - -
147B ALA* 2.9 46.3 + - + +
148B ALA 4.5 1.9 + - - -
185B TRP* 3.0 37.2 + - - +
207B ILE 3.0 13.1 + - - +
208B THR* 3.4 8.0 - - - +
210B ILE* 1.3 77.3 - - - +
212B LEU* 1.3 55.6 + - - +
215B GLY* 2.6 44.7 + - - +
216B GLU 3.6 20.2 + - - -
217B PRO* 4.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 4.1 26.2 - - + +
111B LEU* 3.6 26.0 - - + +
115B PRO* 5.8 0.2 - - - +
116B LEU* 3.9 23.1 + - + +
121B ILE* 3.8 29.4 - - + +
124B ILE* 4.1 20.2 - - + -
125B LEU* 3.8 36.8 - - + -
128B ILE* 4.8 0.4 - - + -
147B ALA* 4.3 11.7 - - + -
208B THR* 2.8 29.3 + - + +
209B ALA 3.9 3.6 - - - +
211B GLU* 1.3 73.2 - - - +
213B ALA* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS* 5.3 0.3 - - - -
115B PRO* 5.2 9.6 - - - +
116B LEU 5.5 1.7 - - - +
121B ILE* 3.7 18.2 - - + -
209B ALA 3.1 14.9 + - - +
210B ILE 3.0 4.9 + - - +
212B LEU* 1.3 78.3 - - - +
214B ARG* 1.3 61.7 + - - +
239B LEU* 4.2 17.0 - - + -
243B TYR* 3.0 41.5 + - + -
247B LEU* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS* 3.6 29.8 + - + +
210B ILE* 2.7 27.5 + - - +
213B ALA* 1.3 72.8 - - - +
215B GLY* 1.3 59.5 + - - +
216B GLU* 3.3 16.7 + - - +
218B PRO* 6.4 0.2 - - - +
239B LEU* 3.5 26.5 - - + +
240B GLU* 4.4 19.2 + - - +
243B TYR* 3.4 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.5 8.5 - - - +
111B LEU* 4.0 23.3 - - - +
211B GLU* 2.6 32.4 + - - +
212B LEU 4.4 0.6 - - - -
213B ALA 3.7 0.8 - - - -
214B ARG* 1.3 73.2 - - - +
216B GLU* 1.3 71.6 + - - +
----------------------------------------------------------
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