Contacts of the strand formed by residues 179 - 185 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F VAL* 3.8 29.6 - - + +
144F PHE* 4.1 1.8 - - - -
145F PHE* 3.6 47.0 - - + +
164F ALA* 3.6 0.5 - - - -
165F LEU* 2.8 44.7 + - + +
177F ALA* 3.9 2.9 - - - +
178F ALA* 1.3 76.3 - - - +
180F ALA* 1.3 61.4 + - - +
200F GLN* 3.7 22.7 - - + +
201F GLY 4.1 0.2 - - - -
202F ARG* 3.4 42.2 - - + +
204F LEU* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E PHE* 3.1 21.2 - - + -
145F PHE* 3.9 3.6 - - - -
163F LEU 3.6 10.5 - - - +
164F ALA* 4.6 2.2 - - + -
177F ALA* 4.2 15.9 - - + +
179F LEU* 1.3 77.1 - - - +
181F LEU* 1.3 62.1 + - - +
200F GLN* 2.9 26.1 + - - +
202F ARG* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E PHE* 3.7 16.8 - - + -
145F PHE* 3.8 31.4 - - + +
147F LEU* 4.4 14.4 - - + -
162F SER* 3.2 2.6 - - - -
163F LEU* 3.1 34.6 + - + +
180F ALA* 1.3 73.9 - - - +
182F THR* 1.3 89.9 + - - +
183F VAL* 4.1 2.2 - - + -
198F GLY* 3.3 44.0 - - - +
199F PHE* 3.8 6.7 - - - +
200F GLN* 4.0 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ARG* 5.8 6.1 - - + -
195E SER* 4.6 8.4 + - - +
197E PHE* 3.5 35.5 - - - +
160F SER* 3.3 27.4 - - - +
161F VAL 3.4 7.6 - - - +
162F SER* 3.6 13.7 + - - +
181F LEU* 1.3 90.1 + - - +
183F VAL* 1.3 69.3 + - - +
184F ASP 4.5 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LEU* 3.9 20.4 - - + +
149F LEU* 3.6 19.1 - - + -
160F SER* 3.5 2.3 - - - -
161F VAL* 2.9 33.2 + - - +
181F LEU* 4.1 3.4 - - + -
182F THR* 1.3 82.1 - - - +
184F ASP* 1.3 63.0 + - - +
185F LEU* 4.5 0.9 - - - +
196F ALA* 3.4 34.3 - - + +
197F PHE 3.6 23.6 - - - +
198F GLY* 3.8 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ARG* 5.2 14.1 - - + -
159F GLY 3.7 7.0 - - - +
160F SER* 4.6 3.1 - - - +
182F THR* 4.3 1.0 + - - +
183F VAL* 1.3 73.4 - - - +
185F LEU* 1.3 63.5 + - - +
186F PRO* 3.6 6.5 - - + +
196F ALA* 3.6 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 4.6 3.6 - - + -
149F LEU* 3.6 31.6 - - + -
158F SER* 3.7 8.9 - - - +
159F GLY 2.8 36.2 + - - +
160F SER* 4.2 9.0 - - - +
161F VAL* 3.8 23.3 - - + -
183F VAL 4.5 0.4 - - - +
184F ASP* 1.3 77.9 - - - +
186F PRO* 1.3 70.3 - - - +
187F PRO* 3.7 1.9 - - - +
196F ALA* 4.4 1.3 - - + -
218F THR* 5.8 0.9 - - - +
219F GLU 5.8 0.7 - - - +
223F ARG* 6.4 1.3 - - - -
226F TRP* 3.7 57.2 - - + +
----------------------------------------------------------
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