Contacts of the strand formed by residues 190 - 198 (chain E) in PDB entry 6DWZ
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 190 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E LEU* 6.0 1.8 - - + -
182E TRP 3.6 6.5 - - - +
183E THR* 3.6 12.3 - - + -
188E LYS 5.1 2.0 - - - +
189E ARG* 1.3 78.6 - - - +
191E PHE* 1.3 62.1 + - - +
213E SER* 3.8 0.3 - - - -
214E LEU* 3.1 46.0 + - + +
215E ASP 2.8 24.1 - - - +
216E PHE* 4.6 4.3 + - - -
217E GLU 3.8 13.5 + - - -
218E ARG 5.0 0.8 - - - -
219E SER* 3.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E LEU* 3.3 14.1 - - - +
182E TRP* 2.9 63.1 + + + +
184E ASP* 4.0 12.6 - - + -
189E ARG* 4.0 33.4 - - + -
190E ASN* 1.3 75.7 - - - +
192E LEU* 1.3 59.6 + - - +
193E GLY 4.0 0.6 + - - -
211E LEU* 3.6 39.3 - - + -
212E LYS 3.7 1.1 - - - -
213E SER* 3.5 36.8 - - - -
214E LEU* 5.0 0.9 - - - -
575E PHE* 5.3 0.2 - - - -
582E ILE* 4.7 10.1 - - + -
591E GLN* 4.5 18.8 - - + -
594E VAL* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ILE* 3.9 19.5 - - + -
180E ASP 3.2 20.2 - - - +
181E LEU* 4.2 11.0 - - + -
191E PHE* 1.3 71.3 - - - +
193E GLY* 1.3 73.4 + - - +
194E VAL* 4.1 9.6 - - + -
210E GLY 3.7 1.4 - - - +
211E LEU* 3.3 7.9 - - - -
212E LYS 3.0 33.6 + - - +
214E LEU* 4.5 11.2 - - + +
224E ILE* 3.9 34.8 - - + +
227E LYS* 4.0 14.4 - - + -
228E LEU* 4.2 15.5 - - + +
231E ILE* 3.8 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E THR 4.3 0.4 - - - -
179E ILE* 3.1 30.7 - - - +
180E ASP 3.1 14.3 + - - -
191E PHE 4.0 1.0 - - - -
192E LEU* 1.3 74.3 - - - +
194E VAL* 1.3 63.3 + - - -
210E GLY 3.8 1.8 - - - -
211E LEU* 3.7 16.7 - - - +
571E SER* 4.3 5.2 - - - -
574E THR* 5.3 4.5 - - - -
575E PHE* 3.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ALA* 4.7 2.0 - - + -
178E THR 3.4 2.9 - - - -
179E ILE* 4.1 16.6 - - + -
192E LEU* 4.1 12.8 - - + -
193E GLY* 1.3 79.2 - - - +
195E THR* 1.3 77.0 + - - +
208E ILE* 4.0 3.1 - - - +
209E LEU* 3.1 24.7 + - + -
210E GLY 3.1 12.1 + - - +
228E LEU* 4.3 24.5 - - + -
231E ILE* 3.5 28.9 - - + -
232E PHE* 4.5 18.6 - - + -
245E PHE* 5.5 0.2 - - + -
574E THR* 5.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ALA* 2.9 29.5 - - - +
178E THR* 2.9 21.7 + - - +
194E VAL* 1.3 80.4 - - - +
196E LEU* 1.3 61.4 + - - +
197E HIS* 3.1 23.5 + - - -
206E ASP* 4.6 4.0 - - - +
207E LEU 3.6 11.2 - - - -
208E ILE* 4.2 10.5 - - + -
209E LEU* 3.9 5.4 - - - +
570E ALA* 3.8 21.2 - - + +
571E SER* 4.4 3.8 - - - +
574E THR* 3.9 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E ILE* 4.0 36.3 - - + +
169E ALA* 5.1 1.1 - - + -
170E VAL* 5.4 4.5 - - + -
175E ALA* 4.4 16.4 - - + -
176E SER 3.1 15.7 - - - +
177E ALA* 4.0 6.1 - - + -
195E THR* 1.3 71.0 - - - +
197E HIS* 1.3 67.4 + - - +
198E TYR* 4.2 20.4 - - + -
205E ARG 3.8 1.4 - - - +
206E ASP* 3.7 0.9 - - - -
207E LEU* 2.8 37.0 + - + +
209E LEU* 3.5 19.0 - - + +
232E PHE* 3.7 34.8 - - + -
243E ILE* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ALA* 3.1 4.7 - - - +
176E SER* 2.4 60.2 + - - -
177E ALA* 4.4 1.6 - - - -
178E THR* 4.1 2.0 + - - -
195E THR* 3.1 24.2 + - - -
196E LEU* 1.3 78.8 - - - +
198E TYR* 1.3 61.9 + - - +
204E LEU* 5.1 6.4 - - + +
205E ARG 3.6 5.8 + - - +
206E ASP* 3.4 32.5 + - + +
377E CYS* 3.8 31.5 + - + -
563E SER 3.7 9.6 - - - +
565E PRO* 3.9 24.4 - - + +
570E ALA* 3.7 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E GLU* 3.4 18.9 + - + +
166E ILE* 4.0 23.6 - - + +
169E ALA* 3.3 32.5 - - + -
174E GLY 3.7 17.5 - - - +
175E ALA* 4.2 0.4 - - - -
196E LEU* 4.2 11.4 - - + -
197E HIS* 1.3 73.9 - - - +
199E HIS* 1.3 68.2 + - + +
200E GLU* 4.6 6.7 - - + +
204E LEU* 3.3 8.2 - - - +
205E ARG* 3.0 69.1 + - + +
207E LEU* 4.7 6.5 - - + +
563E SER* 4.1 8.0 + - - -
607E PHE* 3.3 29.3 - - - -
----------------------------------------------------------
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