Contacts of the strand formed by residues 224 - 228 (chain A) in PDB entry 2ILU
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 224 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.8 13.7 - - + -
145A VAL 3.7 2.0 + - - -
146A THR* 3.3 11.2 - - + +
147A THR 3.0 22.7 + - - -
222A VAL* 3.3 8.2 - - - +
223A ALA* 1.3 83.3 - - - +
225A VAL* 1.3 68.3 + - - +
226A SER* 4.1 2.9 + - - -
246A THR* 4.0 1.1 - - - -
247A LYS* 3.3 44.0 - - + +
248A VAL 4.4 0.2 - - - +
249A OCS 3.8 27.1 - - + +
468A GLU 3.7 19.7 - - - +
469A TYR* 3.5 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.0 22.0 - - - +
149A ILE* 3.8 27.4 - - + -
216A LEU 3.8 12.6 - - - +
217A ALA* 4.1 9.9 - - + -
222A VAL* 4.1 2.2 - - + +
224A MET* 1.3 72.3 - - - +
226A SER* 1.3 63.1 + - - +
227A MET 4.0 0.3 + - - -
237A ILE* 3.9 14.8 - - + -
241A ALA* 4.2 9.6 - - + -
246A THR* 4.2 3.1 - - + +
247A LYS 3.0 5.6 + - - +
248A VAL* 3.4 25.9 - - + +
249A OCS 3.0 20.6 + - - +
250A LEU* 4.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 6.4 0.2 - - - -
147A THR 2.7 16.0 + - - -
148A GLY* 3.2 3.8 - - - -
149A ILE* 2.9 25.1 + - - +
162A LYS* 3.0 31.5 + - - +
173A ILE* 6.4 0.4 - - - -
224A MET* 4.1 4.0 + - - -
225A VAL* 1.3 72.5 - - - +
227A MET* 1.3 61.0 + - - +
249A OCS 3.2 26.4 + - - +
469A TYR* 3.7 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.4 24.0 - - + +
162A LYS* 4.1 2.6 + - - +
225A VAL 4.0 0.6 + - - -
226A SER* 1.3 75.3 + - - +
228A THR* 1.3 70.3 + - - +
229A GLY* 3.2 35.2 - - - +
230A SER 3.9 2.0 - - - +
233A ALA* 3.7 26.7 - - + -
234A GLY* 4.3 5.8 - - - -
237A ILE* 3.1 34.1 - - + -
249A OCS 2.8 12.3 + - - +
250A LEU* 3.3 12.9 - - + -
251A GLU* 3.1 23.2 + - - +
252A LEU* 3.9 14.6 - - - -
482A NDP 3.8 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE 3.2 7.2 + - - +
150A LEU 4.1 0.3 - - - -
151A PRO* 3.0 35.8 - - + +
158A LEU* 4.0 25.1 - - + +
161A ARG* 5.6 0.7 - - - -
162A LYS* 2.9 26.2 + - - +
227A MET* 1.3 84.7 + - - +
229A GLY* 1.3 61.1 + - - +
251A GLU* 3.4 39.8 + - - +
482A NDP 4.3 0.9 - - - +
----------------------------------------------------------
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