Contacts of the strand formed by residues 202 - 210 (chain E) in PDB entry 5LS6
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 ASP 202 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 5.4 0.2 - - - +
199E HIS* 3.2 35.5 + - + +
200E PRO 3.4 1.2 + - - -
201E ARG* 1.3 81.1 - - - +
203E PRO* 1.3 66.5 - - - +
204E ASN* 3.0 20.6 + - - -
205E LEU* 3.1 37.8 + - + +
274E ILE* 4.7 1.4 - - - +
278E TYR* 2.6 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 5.6 0.9 - - - +
104E HIS* 5.6 0.4 - - + -
153E THR* 2.9 37.1 + - - +
154E TYR* 3.4 56.2 - - + +
156E SER* 4.6 8.5 - - - +
198E PHE* 3.5 13.9 - - + -
199E HIS 4.5 3.8 - - - +
201E ARG 4.6 2.0 - - - +
202E ASP* 1.3 87.4 - - - +
204E ASN* 1.3 69.3 + - - +
220E ILE* 3.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E TYR 5.0 3.3 - - - +
155E ASP* 5.7 3.3 - - - -
156E SER* 5.6 3.3 + - - -
198E PHE* 4.5 0.9 - - - -
202E ASP* 3.0 13.3 + - - +
203E PRO* 1.3 91.5 - - - +
205E LEU* 1.3 60.5 + - - +
206E LEU 3.2 3.9 + - - -
218E TRP 2.9 13.7 - - - +
219E ASN* 3.3 18.6 - - - +
220E ILE* 3.0 42.2 + - + +
221E GLN* 3.4 33.3 + - - +
278E TYR* 4.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E PHE* 3.8 2.5 - - - -
199E HIS* 2.9 56.1 + - + +
202E ASP* 3.1 34.3 + - + +
203E PRO 3.7 0.2 - - - -
204E ASN* 1.3 72.5 - - - +
206E LEU* 1.3 59.2 + - - +
217E LEU* 4.4 11.9 - - + -
218E TRP 3.2 11.0 - - - +
219E ASN* 4.1 23.1 - - + +
226E VAL* 4.2 10.8 - - + -
244E TYR* 3.2 4.6 + - - -
274E ILE* 3.8 38.1 - - + -
278E TYR* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E ALA* 4.3 8.5 - - + -
172E ILE* 4.0 28.0 - - + -
174E ILE* 4.5 1.8 - - + -
186E TYR* 5.1 1.8 - - + -
196E LEU* 4.0 16.8 - - + -
197E LYS 3.1 33.7 - - - +
198E PHE* 3.7 34.3 - - + -
204E ASN 3.2 3.4 + - - +
205E LEU* 1.3 72.3 - - - +
207E LEU* 1.3 74.9 + - - +
217E LEU* 3.4 1.7 - - - -
218E TRP* 2.7 53.0 + - + +
220E ILE* 4.3 14.4 - - + -
244E TYR* 3.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLU 4.2 0.3 - - - +
196E LEU* 3.4 4.7 - - - -
197E LYS* 2.7 47.7 + - + +
206E LEU* 1.3 75.5 - - - +
208E SER* 1.3 65.7 + - - +
209E VAL* 4.0 7.4 - - + +
215E LEU* 3.8 18.8 - - + -
216E ARG 3.5 15.7 - - - +
217E LEU* 4.3 9.2 - - + +
229E PHE* 5.1 2.5 - - + -
242E ALA* 3.8 28.9 - - + -
244E TYR* 3.4 23.6 + - + +
251E ILE* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E ILE* 3.7 15.0 - - - -
189E HIS* 3.1 20.9 + - - -
193E ILE* 4.3 3.6 - - - -
195E GLU 3.9 0.2 - - - -
196E LEU* 3.5 23.8 - - - -
206E LEU* 4.1 1.2 + - - -
207E LEU* 1.3 72.0 - - - +
209E VAL* 1.3 65.8 + - - +
215E LEU* 3.2 3.8 - - - +
216E ARG* 2.7 35.9 + - - +
218E TRP* 3.0 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E HIS* 4.6 0.2 - - - -
193E ILE* 3.2 7.1 - - - +
194E ASN 2.9 22.9 + - - -
195E GLU* 3.2 35.6 + - + +
196E LEU* 6.0 0.2 - - - -
197E LYS* 6.4 1.1 - - + -
207E LEU* 4.0 8.3 - - + +
208E SER* 1.3 81.7 - - - +
210E SER* 1.3 60.9 + - - +
214E ALA 3.8 4.7 - - - -
215E LEU* 3.7 13.7 - - + -
239E VAL* 3.6 25.1 - - + +
240E LEU 3.9 9.2 - - - +
241E SER 4.2 4.9 - - - +
242E ALA* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E HIS* 3.2 33.6 - - - -
191E ASN 3.4 9.5 + - - -
192E ALA 2.8 15.9 + - - -
193E ILE* 4.5 0.4 - - - -
194E ASN* 4.2 2.0 - - - +
209E VAL* 1.3 75.1 - - - +
211E LYS* 1.3 66.7 + - - +
212E ASP* 2.8 22.2 + - - +
213E HIS 3.8 1.0 + - - -
214E ALA 3.1 6.3 + - - -
239E VAL* 2.6 41.8 + - - +
----------------------------------------------------------
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