Contacts of the strand formed by residues 221 - 228 (chain B) in PDB entry 3ZZY
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 GLN 221 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 4.3 32.6 - - + +
188B VAL 6.0 0.2 - - - +
189B GLU* 5.6 5.1 - - - +
217B THR* 3.3 10.4 - - - +
218B LYS 3.0 26.7 + - - +
219B ASN* 3.3 26.9 - - - +
220B ASN* 1.3 79.6 - - - +
222B PHE* 1.3 64.8 + - - +
223B GLN* 3.3 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 3.5 4.5 - - - +
188B VAL* 3.1 58.0 + - + +
191B LEU* 3.8 32.9 - - + +
195B VAL* 3.3 39.0 - - + -
196B THR 5.5 0.7 - - - -
200B LEU* 4.6 9.6 - - + -
215B THR* 4.1 33.7 - - + -
216B PHE 3.9 2.7 - - - -
217B THR* 4.3 15.4 - - - +
221B GLN* 1.3 72.1 - - - +
223B GLN* 1.3 64.1 + - - +
224B ALA* 5.5 0.2 - - + -
271B LYS* 4.6 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE 3.1 9.4 - - - +
187B ILE* 4.0 23.6 - - + +
188B VAL* 6.2 0.7 - - - -
215B THR* 3.4 5.2 - - - -
216B PHE* 2.8 55.8 + - + +
218B LYS* 3.0 46.5 + - - +
219B ASN* 4.9 1.2 - - - +
221B GLN* 3.6 16.8 + - + +
222B PHE* 1.3 84.5 - - - +
224B ALA* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 3.6 3.1 - - - +
186B ILE* 2.8 45.2 + - + -
200B LEU* 4.0 17.3 - - + -
213B ILE* 4.7 2.7 - - + -
214B ILE 3.1 13.2 - - - +
215B THR* 3.9 15.3 - - + +
216B PHE* 4.4 4.6 - - - -
222B PHE* 5.5 1.3 - - + -
223B GLN* 1.3 79.1 - - - +
225B LEU* 1.3 67.8 + - - +
226B LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 4.3 3.6 - - + -
184B LEU 3.4 7.0 - - - +
185B ARG* 3.7 30.5 - - + -
213B ILE* 3.3 5.0 - - - +
214B ILE* 2.8 42.6 + - + +
216B PHE* 4.2 21.5 - - + -
224B ALA* 1.3 78.3 - - - +
226B LEU* 1.3 60.7 + - - +
258B SER* 4.2 12.6 - - - +
260B LEU* 4.1 20.2 - - + -
263B LEU* 3.7 21.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
182B PRO 3.7 0.7 - - - +
183B VAL* 3.3 2.6 - - - +
184B LEU* 2.8 40.1 + - + +
186B ILE* 4.1 17.5 - - + -
200B LEU* 4.5 3.4 - - + +
204B PHE* 3.6 38.1 - - + -
210B VAL* 3.9 17.5 - - + -
212B LYS 3.4 3.4 - - - -
213B ILE* 3.9 28.0 - - + -
224B ALA* 4.2 0.4 - - + -
225B LEU* 1.3 76.7 - - - +
227B GLN* 1.3 67.3 + - - +
228B TYR* 3.7 35.9 - - + -
263B LEU* 4.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO* 3.6 8.1 - - + +
183B VAL* 4.0 12.6 - - + +
210B VAL* 3.7 3.5 - - - +
211B LEU* 2.8 51.4 + - + +
212B LYS* 2.9 34.5 + - - +
226B LEU* 1.3 75.9 - - - +
228B TYR* 1.3 66.9 + - - +
261B THR 4.0 5.5 + - - -
262B SER* 3.3 31.7 + - - +
263B LEU* 3.2 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO* 2.9 27.2 + - - +
184B LEU* 3.9 8.1 - - + -
204B PHE* 2.6 49.1 + + + +
207B PHE* 3.9 3.9 - - + +
208B GLY 3.8 15.7 - - - -
209B THR 3.4 15.7 - - - -
210B VAL* 3.9 7.6 - - + -
211B LEU* 3.8 4.2 - - - +
226B LEU* 3.7 19.1 - - + -
227B GLN* 1.3 82.8 + - - +
229B ALA* 1.3 63.3 + - - +
230B ASP 3.2 17.5 - - - +
233B SER* 3.6 21.1 - - - -
234B ALA* 3.5 32.3 - - + +
237B ALA* 3.4 19.1 - - + +
----------------------------------------------------------
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