Contacts of the strand formed by residues 187 - 196 (chain K) in PDB entry 6R8Y
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 GLY 187 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K GLN* 3.2 17.3 + - - -
184K ASP* 2.7 41.1 + - - +
185K PRO 3.3 1.4 + - - -
186K GLN* 1.3 78.2 - - - +
188K ARG* 1.3 59.4 + - - -
189K HIS* 3.6 2.9 + - - -
214K ALA* 6.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165K ILE* 4.2 24.8 - - - +
181K VAL* 4.6 4.0 - - + -
182K TYR 3.3 10.3 - - - +
183K GLN* 3.0 31.3 + - + +
187K GLY* 1.3 70.7 - - - -
189K HIS* 1.3 69.9 + - - +
211K ASN* 3.8 1.9 - - - +
212K VAL* 3.0 31.3 + - + +
213K GLU 3.4 18.4 - - - +
214K ALA* 2.9 29.6 + - - +
215K GLU* 3.1 28.5 + - - +
216K ALA* 2.4 38.0 + - - +
217K SER* 3.4 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K VAL* 3.3 4.7 - - - +
182K TYR* 2.9 53.4 + + + +
184K ASP* 2.8 43.3 + - - -
186K GLN* 4.0 18.1 - - + +
187K GLY* 3.6 6.3 + - - -
188K ARG* 1.3 80.1 + - - +
190K VAL* 1.3 61.1 + - - +
209K GLN* 3.3 24.8 + - - +
210K GLU 3.4 9.4 - - - +
211K ASN* 2.5 34.5 + - - -
212K VAL* 4.2 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K CYS* 3.7 24.7 - - - -
180K PHE 3.4 11.4 - - - +
181K VAL* 4.2 7.4 - - + -
189K HIS* 1.3 74.3 - - - +
191K LYS* 1.3 65.1 + - - +
207K TRP* 4.2 15.4 - - + -
208K LYS 4.6 0.3 - - - +
209K GLN* 3.3 7.6 - - - +
210K GLU* 2.9 46.8 + - + +
212K VAL* 3.5 20.4 - - + +
231K ILE* 4.1 16.8 - - + -
240K HIS* 4.5 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K GLU* 6.1 0.4 - - - +
161K GLU* 5.1 7.8 + - + -
179K CYS* 3.4 1.4 - - - -
180K PHE* 2.9 48.9 + - + +
182K TYR* 4.2 12.3 + - + -
190K VAL* 1.3 77.3 - - - +
192K THR* 1.3 86.7 + - - +
193K TYR* 2.7 40.5 + - + +
207K TRP* 5.1 3.8 - - - +
209K GLN* 3.5 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K LEU* 4.5 2.7 - - + -
177K THR* 4.5 1.3 - - - -
178K ILE 3.2 9.4 - - - +
179K CYS* 3.5 13.9 - - + -
180K PHE* 4.5 1.3 - - - -
191K LYS* 1.3 92.8 - - - +
193K TYR* 1.3 77.2 - - - +
205K GLY* 3.5 18.3 + - - -
206K PRO* 3.6 12.3 - - - +
207K TRP* 3.3 58.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159K LEU* 5.0 5.8 - - + -
160K GLU* 4.9 16.2 + - - +
161K GLU* 5.4 3.4 - - + +
177K THR* 3.4 5.8 - - - -
178K ILE* 2.9 42.5 + - + +
180K PHE* 3.4 40.2 - + - -
191K LYS* 2.7 38.7 + - - +
192K THR* 1.3 74.3 - - - +
194K GLU* 1.3 59.8 + - - +
202K PHE* 3.5 46.7 - + + -
203K ASN 3.5 16.4 - - - +
204K LYS* 4.9 2.0 - - - -
205K GLY* 4.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174K GLN* 3.4 19.3 + - - -
175K ALA* 3.9 20.5 - - + +
176K PRO 3.3 7.4 - - - +
177K THR* 3.6 18.4 + - + +
193K TYR* 1.3 76.5 - - - +
195K VAL* 1.3 60.2 + - - +
196K SER 4.0 0.2 - - - -
202K PHE* 3.2 9.2 - - - -
203K ASN* 2.9 48.0 + - + +
204K LYS 3.7 17.8 - - - +
205K GLY* 4.1 6.3 - - - -
206K PRO* 4.5 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K MET* 3.7 34.6 - - + +
140K PHE* 4.8 3.6 - - + -
142K VAL* 4.4 10.5 - - + -
155K PHE* 5.1 1.3 - - + -
157K ILE* 4.4 18.4 - - + -
169K PHE* 4.6 0.7 - - + -
175K ALA* 5.3 1.7 - - - +
176K PRO* 2.8 38.5 + - - +
178K ILE* 4.2 21.1 - - + -
193K TYR 4.3 1.3 - - - +
194K GLU* 1.3 77.0 - - - +
196K SER* 1.3 64.4 + - - +
197K LEU* 3.5 4.7 + - + +
201K GLU 3.9 2.7 - - - -
202K PHE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194K GLU 4.0 1.2 + - - -
195K VAL* 1.3 73.4 - - - +
197K LEU* 1.3 53.5 + - - +
198K ARG* 3.6 8.5 + - - +
199K GLU* 3.2 28.6 + - - +
200K LYS* 2.7 28.9 + - - -
201K GLU 2.9 22.6 + - - -
203K ASN* 3.3 29.5 + - - -
----------------------------------------------------------
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