Contacts of the strand formed by residues 223 - 231 (chain B) in PDB entry 5O67
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 ASP 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 3.8 21.5 - - + -
100B SER* 6.2 1.6 - - - -
213B LYS* 3.6 29.8 + - - +
215B LEU 3.5 6.1 - - - +
216B ASP* 3.7 4.0 - - - +
217B GLU* 3.0 32.9 + - - +
222B PRO* 1.3 69.2 - - - +
224B ALA* 1.3 59.7 + - - +
225B VAL* 4.9 3.6 - - + +
272B SER* 3.7 1.6 + - - +
273B MET* 3.3 5.7 - - - -
274B VAL* 3.0 47.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
213B LYS* 3.4 5.9 - - - +
214B PHE* 3.1 54.2 + - + -
215B LEU* 3.1 28.6 + - + -
222B PRO* 3.5 5.6 + - + +
223B ASP* 1.3 72.1 - - - +
225B VAL* 1.3 66.7 + - - +
271B LEU* 4.6 1.6 - - + -
272B SER 3.4 8.3 - - - +
273B MET* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B SER* 5.0 8.3 - - - +
101B GLY 5.8 0.7 - - - +
102B PHE* 4.1 24.5 - - + -
211B ALA* 4.0 18.4 - - + -
212B TYR 3.5 8.7 - - - +
213B LYS* 4.0 25.4 - - + -
214B PHE* 3.8 2.6 - - - -
223B ASP* 4.9 4.3 - - + -
224B ALA* 1.3 84.0 - - - +
226B VAL* 1.3 70.8 + - - +
227B SER* 4.9 2.8 + - - -
270B GLY 3.9 0.9 - - - +
271B LEU* 3.5 3.7 - - - -
272B SER* 3.2 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA* 3.5 0.7 - - - +
212B TYR* 3.0 52.3 + - + +
214B PHE* 3.8 23.3 - - + -
225B VAL* 1.3 74.3 - - - +
227B SER* 1.3 69.0 + - - +
228B VAL* 6.3 0.7 - - + -
269B PRO* 6.4 1.6 - - + -
270B GLY 3.5 9.6 - - - +
271B LEU* 4.6 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE 3.2 16.4 - - - -
211B ALA* 3.4 14.1 - - - +
225B VAL* 4.9 3.8 + - - -
226B VAL* 1.3 82.8 - - - +
228B VAL* 1.3 70.2 + - - +
268B THR 5.3 0.3 + - - -
269B PRO* 3.2 5.0 - - - +
270B GLY* 2.9 40.6 + - - +
501B LDA 5.0 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLY* 3.5 1.9 - - - -
210B ILE* 3.0 46.3 + - + +
226B VAL* 6.3 0.7 - - + -
227B SER* 1.3 85.1 - - - +
229B ARG* 1.3 64.2 + - - +
230B VAL* 4.4 16.6 - - + -
267B ILE* 4.5 12.3 - - + -
268B THR 3.4 11.0 - - - +
269B PRO* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 2.4 33.3 + - - -
169B ASN* 5.2 0.6 - - - +
207B ASN* 3.1 29.5 + - + +
208B PHE 3.4 7.9 + - - +
209B GLY* 3.8 20.9 - - - +
228B VAL* 1.3 75.6 + - - +
230B VAL* 1.3 67.0 + - - +
231B LYS* 5.3 3.8 - - + +
266B SER 3.8 1.4 - - - +
267B ILE* 3.6 2.3 - - - -
268B THR* 2.9 45.7 + - + +
501B LDA 5.6 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASN* 3.3 4.2 - - - +
208B PHE* 2.8 67.9 + - + +
210B ILE* 6.3 0.2 - - + -
228B VAL* 4.4 14.1 - - + -
229B ARG* 1.3 75.9 - - - +
231B LYS* 1.3 63.5 + - - +
265B TRP* 3.9 26.9 - - + -
266B SER 3.4 4.0 - - - +
267B ILE* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASP* 3.1 35.6 + - + +
207B ASN* 3.8 18.6 - - + +
229B ARG* 5.5 4.3 - - + -
230B VAL* 1.3 75.5 - - - +
232B ALA* 1.3 62.2 + - - +
262B ASN* 2.6 44.5 + - - +
264B VAL* 3.4 18.8 + - - +
265B TRP* 3.4 13.2 - - - -
266B SER* 3.0 49.1 + - - +
----------------------------------------------------------
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