Contacts of the strand formed by residues 227 - 232 (chain C) in PDB entry 1XSK
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 LYS 227 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLN* 3.8 15.9 + - - +
136C ASN* 3.8 33.0 - - - +
153C ARG* 4.2 17.7 - - + -
154C LEU 3.5 7.6 - - - +
155C ASP* 2.8 37.5 + - - +
156C LEU* 3.7 8.9 - - - +
219C GLU 3.5 3.1 - - - +
221C GLY 2.9 22.9 + - - -
224C LYS* 3.1 31.9 + - + +
225C VAL 3.3 2.2 + - - -
226C SER* 1.3 102.2 + - - +
228C VAL* 1.3 59.5 + - - +
229C GLN* 3.8 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ARG* 3.5 1.5 - - - -
154C LEU 3.0 31.3 + - - +
156C LEU* 3.5 28.5 - - + -
162C VAL* 3.8 21.1 - - + -
200C TYR* 3.6 42.2 - - + +
218C PHE* 4.3 11.7 - - + -
219C GLU 3.8 3.4 - - - -
220C VAL* 4.0 18.6 - - + +
227C LYS* 1.3 70.7 - - - +
229C GLN* 1.3 59.7 + - - +
230C PHE* 3.8 14.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 2.9 30.3 + - - +
3C ILE* 3.7 14.7 - - + +
151C PHE* 4.5 5.8 - - + -
152C GLU 3.2 11.4 - - - +
153C ARG* 3.0 30.5 + - + +
217C SER 3.6 0.9 + - - +
218C PHE* 3.2 4.5 - - - +
219C GLU* 2.8 58.9 + - + +
223C GLU* 2.9 34.2 + - + +
224C LYS* 5.8 2.5 - - + +
227C LYS* 3.8 1.9 - - + +
228C VAL* 1.3 73.9 - - - +
230C PHE* 1.3 67.3 + - - +
231C SER* 4.6 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C PHE* 3.3 4.2 - - - +
152C GLU* 3.0 58.2 + - + -
154C LEU* 4.1 22.7 - - + -
200C TYR* 4.3 9.9 - + - -
208C VAL* 4.4 0.9 - - + -
210C VAL* 3.7 33.7 - - + -
216C VAL* 4.0 7.9 - - + -
217C SER 3.3 6.1 - - - +
218C PHE* 3.9 25.1 - + + -
228C VAL* 3.8 20.6 - - + -
229C GLN* 1.3 76.7 - - - +
231C SER* 1.3 60.3 + - - +
237C LEU* 4.2 10.4 - - + +
239C TYR* 4.0 28.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.4 43.1 + - - +
3C ILE* 4.5 3.4 - - - -
149C TYR* 4.8 2.0 - - - -
150C MET 3.3 13.2 - - - -
151C PHE* 3.7 11.9 - - - -
215C CYS 4.4 0.2 - - - +
216C VAL* 3.7 3.5 - - - -
217C SER* 2.9 37.1 + - - -
229C GLN* 4.6 3.6 + - - -
230C PHE* 1.3 76.2 - - - +
232C VAL* 1.3 63.7 + - - +
237C LEU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C TYR* 3.4 7.8 - - - -
150C MET* 3.1 25.6 + - + +
210C VAL* 5.6 0.2 - - + -
212C HIS* 3.8 32.3 - - + +
214C GLN* 3.2 42.8 - - + +
215C CYS 3.8 10.5 - - - +
216C VAL* 4.7 5.6 - - + -
231C SER* 1.3 76.9 - - - +
233C GLU* 1.3 65.5 + - - +
234C SER* 3.0 17.9 + - - -
236C TYR 4.3 2.2 - - - +
237C LEU* 3.8 16.2 - - + -
----------------------------------------------------------
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