Contacts of the strand formed by residues 223 - 227 (chain B) in PDB entry 1N86
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 GLU 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PRO* 3.0 27.9 - - - +
221B THR* 3.2 23.5 + - - +
222B SER* 1.3 77.2 - - - +
224B MET* 1.3 66.3 + - - +
225B TYR* 3.3 25.4 + - + -
239B TYR* 3.7 14.1 - - - -
240B CYS 3.0 27.5 + - - +
285B TYR* 3.6 17.7 - - + +
286B CYS 3.5 16.3 + - - +
287B GLY* 3.6 8.1 - - - -
217C HIS* 3.3 23.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
201B CYS* 3.4 39.9 - - + +
202B ASN 6.0 0.2 - - - +
203B ILE* 5.3 7.6 - - + -
204B PRO* 3.4 15.3 - - - +
223B GLU* 1.3 94.2 + - - +
225B TYR* 1.3 74.4 + - - +
226B LEU* 5.6 0.2 - - - -
237B ARG* 3.3 40.8 - - + +
238B VAL 3.6 11.9 - - - +
239B TYR* 4.4 1.6 - - - +
276B VAL* 3.9 21.8 - - + -
277B ALA* 3.8 11.2 - - + +
286B CYS* 3.2 17.8 + - + +
141C ASP* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PRO* 4.3 14.6 - - + -
206B VAL* 3.5 34.3 - - + +
214B ILE* 3.6 36.6 - - + -
219B GLY* 3.9 11.6 - - - -
221B THR* 2.8 42.4 + - - -
223B GLU* 3.3 35.1 + - + +
224B MET* 1.3 85.8 - - - +
226B LEU* 1.3 61.0 + - - +
227B ILE* 4.1 1.1 + - + -
237B ARG* 3.7 0.3 - - - -
238B VAL* 3.0 32.6 + - - +
240B CYS* 3.7 25.1 - - + -
242B MET* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.6 46.0 - - + +
206B VAL 4.9 3.6 + - - +
207B SER* 2.7 41.0 + - - +
214B ILE* 4.5 0.2 - - - +
224B MET* 5.6 0.4 - - - -
225B TYR* 1.3 76.6 - - - +
227B ILE* 1.3 56.3 + - - +
235B PRO* 3.7 15.5 - - + +
236B TYR* 3.0 40.6 - - - +
237B ARG* 3.7 13.5 - - + +
145C ILE* 4.3 15.7 - - + -
168C PHE* 4.5 11.7 - - + -
179C LEU* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B SER* 4.8 0.9 - - - -
208B GLY 3.6 3.8 - - - +
209B LYS 3.6 10.1 - - - +
210B GLU* 3.3 36.6 - - + +
211B CYS 3.8 2.0 - - - +
214B ILE* 3.4 26.0 - - + -
225B TYR 4.1 0.4 - - - -
226B LEU* 1.3 74.6 - - - +
228B GLN* 1.3 62.9 + - - +
229B PRO* 4.3 0.2 - - - +
235B PRO* 2.9 26.4 - - - +
236B TYR* 3.0 52.4 + - + +
238B VAL* 3.6 24.0 - - + -
250B THR* 4.4 9.4 - - + -
302B LEU* 5.0 1.1 - - + -
----------------------------------------------------------
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