Contacts of the strand formed by residues 206 - 211 (chain A) in PDB entry 1IJI
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 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.2 17.3 - - + -
181A VAL* 3.5 17.3 - - + +
183A ALA* 4.7 3.1 - - + -
196A LEU* 3.9 33.4 - - + +
199A TRP* 3.8 35.4 - - + +
200A LEU* 3.9 15.8 - - + +
203A TYR* 3.4 28.5 + - + +
204A PRO 3.5 1.2 - - - +
205A HIS* 1.3 79.4 - - - +
207A ALA* 1.3 75.0 + - - +
208A ILE* 4.4 10.1 - - + -
228A ALA* 3.8 14.9 - - - +
229A ASN* 4.5 2.4 + - - -
232A VAL* 5.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.3 12.8 - - + -
180A ILE* 4.1 11.2 - - + -
181A VAL 2.8 10.8 + - - +
182A VAL* 3.3 21.1 - - + -
183A ALA 2.9 24.4 + - - -
206A LEU* 1.3 76.4 - - - +
208A ILE* 1.3 67.1 + - - +
226A THR* 4.7 5.6 - - + -
227A LEU 3.5 7.2 - - - +
228A ALA* 4.2 8.7 - - + -
232A VAL* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 5.0 0.2 - - - -
183A ALA* 3.4 10.1 - - + +
185A GLU* 3.4 33.9 - - + +
196A LEU* 3.6 11.9 - - + +
197A ALA* 3.4 41.3 - - + +
200A LEU* 4.7 6.1 - - + -
206A LEU* 4.4 12.3 - - + -
207A ALA* 1.3 82.7 - - - +
209A LEU* 1.3 71.3 + - - +
210A ARG* 3.9 10.5 + - + +
225A PHE 3.7 0.2 - - - +
226A THR* 3.2 8.2 - - - +
227A LEU* 2.8 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 4.2 13.9 - - + +
87A GLY* 3.9 23.8 - - - -
88A ILE* 3.7 26.0 - - + +
91A LEU* 4.2 8.7 - - + -
151A TYR* 4.5 5.2 - - + -
182A VAL* 3.6 25.4 - - + -
183A ALA 2.9 7.7 + - - -
184A ASP* 3.8 33.2 - - + +
185A GLU* 2.8 32.6 + - - +
186A ALA 4.8 0.9 - - - -
208A ILE* 1.3 73.5 - - - +
210A ARG* 1.3 59.9 + - - +
225A PHE 3.6 2.7 - - - +
226A THR* 3.7 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.0 42.8 + - + +
70A TYR* 4.2 9.9 + - - -
71A ALA* 3.9 21.0 + - - +
84A ALA* 4.0 9.2 - - - +
185A GLU* 3.0 30.6 + - - +
186A ALA* 5.3 0.7 - - - -
188A ILE* 3.5 14.1 - - - +
189A GLU* 4.3 6.2 + - - -
195A SER* 2.9 31.5 + - - -
197A ALA* 3.7 15.0 - - - +
208A ILE* 4.0 3.6 - - + +
209A LEU* 1.3 81.5 - - - +
211A THR* 1.3 63.3 + - - +
224A GLY* 3.4 2.6 - - - -
225A PHE* 2.8 35.7 + - + +
227A LEU* 3.9 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 5.2 1.3 + - - -
84A ALA* 4.6 1.3 - - - -
185A GLU 5.2 0.4 + - - -
186A ALA* 3.5 37.0 - - + +
189A GLU* 4.4 10.2 + - - +
210A ARG* 1.3 77.8 - - - +
212A LEU* 1.3 76.7 + - - +
213A SER* 2.8 15.7 + - - +
214A LYS* 4.0 18.1 + - + +
215A ALA 5.7 0.5 + - - -
216A PHE* 4.0 9.7 + - - -
223A CYS 3.8 5.6 + - - -
224A GLY* 4.1 1.6 - - - -
225A PHE* 5.1 0.7 - - - -
500A PLP 2.7 33.9 + - - -
----------------------------------------------------------
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