Contacts of the strand formed by residues 222 - 229 (chain L) in PDB entry 3Q2K
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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K TYR* 3.8 15.2 - - - +
155K MET* 3.6 24.7 - - + -
234K MET* 3.6 20.6 - - + -
184L ALA* 5.0 1.3 - - - -
185L PHE* 5.1 0.7 - - - -
210L THR* 3.4 3.6 - - - -
211L ALA 2.9 27.1 + - - +
213L LEU* 4.0 6.2 - - + +
220L GLU* 3.6 6.1 - - - +
221L ASP* 1.3 92.1 + - - +
223L GLY* 1.3 60.8 + - - +
239L VAL 3.4 7.6 - - - +
240L THR* 2.9 20.7 + - - -
242L LEU* 3.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K MET* 3.5 3.9 - - - +
234K MET* 4.1 4.7 - - - -
185L PHE* 3.9 16.9 - - - -
209L TYR 3.1 13.9 - - - -
210L THR* 3.8 3.4 - - - -
222L THR* 1.3 79.0 - - - +
224L VAL* 1.3 61.6 + - - -
239L VAL* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K MET* 4.0 10.3 - - + -
226K ALA* 4.2 10.3 - - + +
234K MET* 4.0 6.8 - - + -
235K GLY* 3.4 48.9 - - - +
236K SER* 3.9 8.7 - - - -
185L PHE* 4.4 2.9 - - - -
207L TYR 4.2 0.2 - - - +
208L ALA* 3.2 4.0 - - - +
209L TYR* 2.9 35.8 + - + +
223L GLY* 1.3 78.8 - - - +
225L ALA* 1.3 70.4 + - - +
226L ALA* 5.6 0.2 - - - -
236L SER* 4.7 0.7 - - - -
237L ILE 3.5 7.0 - - - +
238L ASN* 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L PHE* 4.3 2.9 - - + -
206L VAL* 5.0 0.7 - - + -
207L TYR 3.3 8.7 - - - +
208L ALA* 4.0 11.7 - - + -
224L VAL* 1.3 78.6 - - - +
226L ALA* 1.3 60.4 + - - +
227L LEU* 3.8 10.1 - - + +
236L SER* 3.1 6.4 - - - -
237L ILE* 3.0 50.3 + - + -
335L ILE* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207K TYR* 4.6 4.9 - - + +
209K TYR* 3.7 22.0 - - + -
224K VAL* 4.3 14.6 - - + +
226K ALA* 4.3 22.5 - - + +
206L VAL* 3.4 2.9 - - - +
207L TYR* 2.7 35.8 + - + +
224L VAL 4.4 0.2 - - - -
225L ALA* 1.3 74.8 - - - +
227L LEU* 1.3 65.6 + - - +
235L GLY 3.6 7.2 - - - +
236L SER* 4.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209K TYR* 3.8 7.7 - - - -
156L VAL 5.3 0.2 - - - +
196L LEU* 3.8 35.9 - - + -
203L VAL* 4.7 9.2 - - + -
205L SER 3.9 4.0 - - - -
206L VAL* 3.7 22.9 - - + -
225L ALA* 3.8 14.4 - - + +
226L ALA* 1.3 84.6 - - - +
228L ARG* 1.3 59.9 + - - +
229L TRP* 3.9 28.0 - - + -
234L MET* 3.3 7.7 - - - +
235L GLY 2.7 35.2 + - - +
236L SER 3.9 23.6 - - - +
237L ILE* 4.0 2.7 - - + +
331L LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207K TYR* 5.6 0.2 + - - -
209K TYR* 3.5 48.1 - - + +
210K THR 5.1 8.3 + - - +
339K ALA 5.7 3.0 + - - -
203L VAL* 3.7 3.9 - - - +
204L GLU* 2.8 56.1 + - - +
205L SER* 3.2 14.5 + - - +
227L LEU* 1.3 74.9 - - - +
229L TRP* 1.3 76.9 + - - +
232L GLY* 4.7 7.0 - - - +
233L ALA 3.4 9.0 - - - +
234L MET* 4.4 10.7 - - + +
344L ARG* 3.8 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 229 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L VAL* 3.7 30.1 - - + -
196L LEU* 3.1 37.6 + - + -
200L VAL* 3.5 26.3 - - + +
201L GLY 3.0 32.5 + - - -
202L PRO 3.4 14.6 - - - -
203L VAL* 3.7 11.6 - - + +
204L GLU* 4.1 2.9 - - - +
227L LEU* 3.9 24.7 - - + -
228L ARG* 1.3 89.7 - - - +
230L ARG* 1.3 65.5 + - - +
231L HIS* 3.1 21.1 - - + +
232L GLY* 2.8 11.3 + - - -
233L ALA* 2.8 34.4 + - + +
234L MET 3.9 1.3 - - - -
235L GLY* 3.8 21.3 - - - -
----------------------------------------------------------
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