Contacts of the strand formed by residues 179 - 185 (chain B) in PDB entry 6CU0
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 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.8 28.3 - - + +
144B PHE* 4.1 3.1 - - - -
145B PHE* 3.7 45.1 - - + +
164B ALA* 3.6 0.9 - - - -
165B LEU* 2.8 44.5 + - + +
177B ALA* 3.8 3.3 - - - +
178B ALA* 1.3 76.5 - - - +
180B ALA* 1.3 63.5 + - - +
200B GLN* 3.7 21.8 - - + +
202B ARG* 3.4 43.7 - - + +
204B LEU* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 5.8 1.6 - - - +
197A PHE* 3.3 18.3 - - + -
145B PHE* 3.9 2.9 - - - -
163B LEU 3.6 10.5 - - - +
164B ALA* 4.6 2.7 - - + -
177B ALA* 4.3 15.9 - - + +
179B LEU* 1.3 76.5 - - - +
181B LEU* 1.3 61.8 + - - +
200B GLN* 2.9 29.7 + - - +
202B ARG* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.0 15.2 - - + -
145B PHE* 3.8 31.9 - - + +
147B LEU* 4.4 15.3 - - + -
162B SER* 3.2 2.6 - - - -
163B LEU* 3.1 34.7 + - + +
180B ALA* 1.3 73.5 - - - +
182B THR* 1.3 89.3 + - - +
183B VAL* 4.2 2.2 - - + -
198B GLY* 3.3 44.0 - - - +
199B PHE* 3.8 7.0 - - - +
200B GLN* 4.0 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER* 5.0 5.6 + - - +
197A PHE* 3.8 35.3 - - - +
160B SER* 3.3 27.1 - - - +
161B VAL 3.4 8.1 - - - +
162B SER* 3.6 12.8 + - - +
181B LEU* 1.3 90.2 + - - +
183B VAL* 1.3 69.3 + - - +
184B ASP* 4.3 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.9 20.6 - - + +
149B LEU* 3.6 18.4 - - + -
160B SER* 3.5 2.8 - - - -
161B VAL* 2.9 33.0 + - - +
181B LEU* 4.2 3.4 - - + -
182B THR* 1.3 79.4 - - - +
184B ASP* 1.3 65.2 + - - +
185B LEU* 3.7 1.0 + - - +
196B ALA* 3.4 34.3 - - + +
197B PHE 3.6 23.8 - - - +
198B GLY* 3.8 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 5.5 2.9 - - - +
193A ARG* 3.5 27.5 - - - +
195A SER 5.4 2.3 - - - +
159B GLY 3.7 8.1 - - - +
160B SER* 4.6 4.6 - - - +
182B THR* 4.6 10.6 - - - +
183B VAL* 1.3 76.8 - - - +
185B LEU* 1.3 63.2 + - - +
186B PRO* 3.6 6.7 - - + +
196B ALA* 3.6 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.6 3.1 - - + -
149B LEU* 3.6 31.6 - - + -
158B SER* 3.7 9.3 - - - +
159B GLY 2.8 35.8 + - - +
160B SER* 4.3 9.2 - - - +
161B VAL* 3.8 22.4 - - + -
183B VAL 4.5 0.7 - - - +
184B ASP* 1.3 76.0 - - - +
186B PRO* 1.3 70.9 - - - +
187B PRO* 3.7 1.7 - - - +
196B ALA* 4.3 1.8 - - + -
218B THR* 5.8 1.1 - - - +
219B GLU 5.7 0.9 - - - +
223B ARG* 6.4 1.8 - - - -
226B TRP* 3.7 57.7 - - + +
----------------------------------------------------------
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