Contacts of the strand formed by residues 205 - 210 (chain K) 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 LEU 205 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198K PHE* 3.6 3.2 - - - -
199K HIS* 2.9 55.4 + - + +
202K ASP* 3.1 37.9 + - + +
203K PRO 3.4 1.0 - - - -
204K ASN* 1.3 77.4 - - - +
206K LEU* 1.3 57.6 + - - +
217K LEU* 4.2 10.8 - - + -
218K TRP 3.3 13.9 - - - +
219K ASN* 4.0 19.3 - - + -
226K VAL* 4.3 8.3 - - + -
244K TYR* 3.3 7.4 + - - -
274K ILE* 3.7 38.1 - - + -
278K TYR* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K ALA* 4.2 7.0 - - + -
172K ILE* 3.7 34.8 - - + -
174K ILE* 4.2 6.5 - - + -
186K TYR* 5.3 1.1 - - + -
196K LEU* 3.8 24.2 - - + -
197K LYS 3.3 22.4 - - - +
198K PHE* 3.7 33.6 - - + -
204K ASN 3.5 2.4 + - - -
205K LEU* 1.3 72.6 - - - +
207K LEU* 1.3 69.0 + - - +
217K LEU* 3.4 2.4 - - - -
218K TRP* 2.8 48.2 + - + +
220K ILE* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K GLU 4.1 0.3 - - - +
196K LEU* 3.4 3.5 - - - -
197K LYS* 2.9 38.0 + - + +
206K LEU* 1.3 73.5 - - - +
208K SER* 1.3 61.3 + - - +
209K VAL* 4.5 5.2 - - + +
215K LEU* 4.0 25.1 - - + -
216K ARG 3.3 21.1 - - - +
217K LEU* 4.2 4.0 - - + +
229K PHE* 4.5 5.8 - - + -
242K ALA* 4.1 14.4 - - + -
243K ASP 5.2 1.6 - - - -
244K TYR* 3.1 34.6 + - + +
251K ILE* 3.7 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K ILE* 3.8 11.0 - - - -
189K HIS* 2.9 30.5 + - - -
193K ILE* 4.2 6.5 - - - -
195K GLU 3.5 5.6 - - - -
196K LEU* 3.5 21.8 - - - -
206K LEU 4.1 0.6 - - - -
207K LEU* 1.3 73.1 - - - +
209K VAL* 1.3 66.7 + - - +
215K LEU* 3.2 4.5 - - - +
216K ARG 2.8 31.7 + - - +
218K TRP* 3.0 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K HIS* 4.5 0.2 - - - -
193K ILE* 3.4 7.2 - - - +
194K ASN 2.9 22.4 + - - -
195K GLU* 3.0 34.1 + - + +
207K LEU* 4.5 5.6 - - + +
208K SER* 1.3 78.8 - - - +
210K SER* 1.3 62.1 + - - +
214K ALA 3.8 4.9 - - - -
215K LEU* 3.4 28.0 - - + +
239K VAL* 3.6 27.1 - - + +
240K LEU 4.0 0.4 - - - -
241K SER* 4.0 15.3 - - - +
242K ALA* 3.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K HIS* 3.0 32.6 - - - -
191K ASN 3.4 7.1 + - - -
192K ALA 3.0 15.8 + - - -
193K ILE* 4.2 0.9 - - - +
194K ASN 4.3 0.9 - - - +
209K VAL* 1.3 76.3 - - - +
211K LYS* 1.3 65.2 + - - +
212K ASP* 2.8 24.3 + - - -
213K HIS 3.2 8.5 + - - -
214K ALA 3.2 6.7 + - - -
239K VAL* 3.0 31.0 + - - +
----------------------------------------------------------
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