Contacts of the strand formed by residues 177 - 181 (chain F) in PDB entry 2I2X
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 MET 177 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F THR 3.7 1.0 + - - -
126F VAL* 3.2 23.6 - - + +
127F VAL 3.0 21.8 + - - -
147F LEU* 6.0 0.7 - - - -
175F PRO* 3.2 10.2 - - - +
176F ILE* 1.3 84.2 - - + +
178F LEU* 1.3 71.6 + - - +
179F THR* 4.5 5.8 - - + -
205F ILE* 4.6 4.9 - - - -
206F PRO* 3.6 20.6 - - + +
208F ALA* 4.0 10.8 - - + -
234F ALA 4.3 2.5 - - - +
237F ILE* 3.5 56.1 - - + +
238F ALA* 3.7 16.6 - - + -
241F ILE* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F VAL* 3.2 38.8 - - + +
129F HIS* 3.7 20.6 - - - +
166F VAL* 3.9 13.2 - - + -
170F VAL* 4.2 10.3 - - + -
175F PRO* 5.6 0.2 - - + -
177F MET* 1.3 77.9 - - - +
179F THR* 1.3 65.3 + - - +
194F VAL* 3.9 17.0 - - + -
198F LEU* 3.9 28.5 - - + -
205F ILE* 4.7 11.4 - - + +
206F PRO 3.5 6.2 + - - +
207F PHE* 3.3 19.9 - - + -
208F ALA 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F VAL* 4.4 15.3 - - + -
127F VAL 2.7 10.9 + - - -
128F CYS* 3.1 25.6 - - - +
129F HIS* 2.8 35.2 + - - +
143F VAL* 4.1 14.9 - - + +
147F LEU* 4.7 3.6 - - + -
177F MET* 4.5 6.1 - - + -
178F LEU* 1.3 77.9 - - - +
180F GLY* 1.3 59.3 + - - +
181F THR* 5.6 0.9 + - - -
207F PHE* 4.0 1.6 - - - -
208F ALA* 3.1 13.9 - - + -
234F ALA* 4.8 3.8 - - + -
500F B13 3.4 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F HIS* 3.3 21.5 - - - -
179F THR* 1.3 73.9 - - - +
181F THR* 1.3 62.2 - - - -
191F PHE* 3.4 15.5 - - - -
207F PHE* 3.7 5.8 - - - -
208F ALA 3.0 7.4 + - - -
210F GLY 2.9 24.6 + - - -
500F B13 3.1 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F HIS 3.1 11.6 + - - -
130F VAL* 3.4 10.0 - - + +
131F ALA 3.0 22.7 + - - -
136F HIS 4.1 8.7 - - - +
139F GLY* 4.3 1.3 - - - -
140F LYS* 3.6 33.9 + - + +
179F THR* 5.6 0.9 + - - -
180F GLY* 1.3 73.6 - - - -
182F ALA* 1.3 60.0 + - - +
183F LEU* 3.5 26.5 - - + -
191F PHE* 3.6 2.3 - - - -
210F GLY 3.4 4.0 - - - +
500F B13 2.6 34.1 + - + +
----------------------------------------------------------
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