Contacts of the strand formed by residues 222 - 227 (chain B) in PDB entry 3IO6
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 THR 222 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 4.5 1.9 - - - +
121B LEU* 4.1 8.8 - - - +
145B SER* 3.1 22.0 + - - -
146B ALA 3.4 8.3 + - - -
148B MET* 3.5 19.5 + - + +
213B ALA 4.7 2.0 - - - +
216B ALA* 3.2 23.2 + - + +
217B PHE* 3.5 30.9 - - + +
220B GLY* 4.4 3.8 - - - -
221B GLU* 1.3 76.4 - - - +
223B ALA* 1.3 65.1 + - - +
224B MET 3.3 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.2 3.1 - - - +
118B ASN* 2.7 33.0 + - - +
121B LEU* 4.1 19.4 - - + +
122B LEU* 4.0 23.9 - - + +
139B LEU* 3.9 17.9 - - + -
145B SER 2.9 15.9 + - - +
146B ALA 3.5 9.0 - - - +
217B PHE* 3.5 1.5 - - - -
222B THR* 1.3 72.9 + - - +
224B MET* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.0 21.3 - - + -
116B ILE 3.3 7.2 - - - +
117B TYR* 3.8 15.9 - - + -
122B LEU* 3.9 12.8 - - + -
126B PRO* 3.6 39.3 - - + -
132B ILE* 4.3 12.6 - - + -
135B LEU* 4.3 2.2 - - + -
146B ALA* 2.7 37.9 + - + +
147B LEU* 3.8 20.4 - - + -
148B MET 3.1 21.3 + - - -
217B PHE* 4.1 4.0 - - - -
222B THR* 3.3 9.4 + - - +
223B ALA* 1.3 82.4 - - - +
225B THR* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.9 1.3 - - - +
116B ILE* 2.8 51.9 + - + +
147B LEU* 3.9 5.4 - - - -
148B MET 3.3 18.7 + - - -
149B PHE* 4.2 2.9 - - - +
213B ALA* 4.5 8.8 + - - +
214B GLU* 5.7 1.5 - - - -
217B PHE* 3.6 38.4 - - + -
222B THR* 5.3 0.2 - - - -
224B MET* 1.3 75.9 - - - +
226B ILE* 1.3 73.6 + - - +
227B ASN* 4.6 9.3 + - + +
235B ILE* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.1 24.5 - - + -
114B SER 3.6 10.5 - - - +
115B LEU* 4.6 6.3 - - + -
129B TRP* 3.7 28.7 - - + -
147B LEU* 4.3 7.4 - - + -
149B PHE* 3.6 47.7 - - + +
150B ASN 5.2 0.3 + - - -
156B PHE* 3.7 26.2 - - + +
159B PRO* 5.3 3.1 - - + -
225B THR* 1.3 79.2 + - - +
227B ASN* 1.3 68.7 + - - +
247B LEU* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 3.8 11.0 - - - -
114B SER* 3.2 26.4 + - - +
116B ILE* 3.7 25.3 - - + +
156B PHE* 4.0 3.0 - - - -
210B TYR* 3.3 32.4 + - - -
213B ALA* 6.1 2.2 - - - +
214B GLU* 5.0 10.5 - - - +
225B THR* 3.9 12.2 + - + +
226B ILE* 1.3 77.2 + - - +
228B GLY* 1.3 63.7 + - - +
230B TRP* 3.0 30.1 + - - -
231B ALA* 3.7 16.1 - - + +
232B TRP* 5.1 0.3 + - - -
235B ILE* 6.1 0.2 - - + -
----------------------------------------------------------
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