Contacts of the strand formed by residues 243 - 253 (chain B) in PDB entry 3V56
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 ASN 243 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE 3.6 2.7 - - - -
234A GLN* 3.4 4.2 - - - +
235A ASN* 2.8 40.0 + - - +
499A SO4 3.0 21.8 + - - -
200B LEU* 3.6 4.2 - - - +
201B TYR* 2.8 39.9 + - - +
234B GLN* 3.9 17.0 - - + +
235B ASN 2.9 28.3 + - - -
236B MET* 3.6 20.0 - - - +
237B PRO* 4.2 1.0 - - - +
242B ASN* 1.3 70.9 - - - +
244B SER* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ARG 4.6 1.3 - - - -
232A CYS* 3.4 16.7 - - - -
233A ILE 2.9 33.7 + - - -
234A GLN* 3.4 14.9 - - - +
245A CYS* 3.9 2.9 - - - -
198B GLN* 4.0 21.7 + - - -
199B VAL 3.3 10.3 - - - -
200B LEU* 3.8 14.5 - - - +
234B GLN* 4.1 4.6 + - - +
243B ASN* 1.3 74.5 - - - +
245B CYS* 1.3 63.2 + - - +
276B VAL* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLN* 3.2 23.4 - - - +
199B VAL 2.9 8.8 + - - -
201B TYR* 4.2 15.0 - - + -
210B HIS* 3.2 10.6 - - + -
232B CYS* 2.0 48.5 - - + -
233B ILE 4.0 2.7 - - - -
234B GLN* 3.7 28.5 - - + -
243B ASN 4.1 0.2 + - - -
244B SER* 1.3 75.1 - - - +
246B TYR* 1.3 60.1 + - - +
244C SER* 3.9 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 4.4 1.4 - - - -
246A TYR* 3.5 34.1 - + + +
248A ALA* 3.4 39.3 + - - +
194B PHE* 4.0 9.9 - - - -
196B TYR* 3.4 27.5 - - + +
197B GLY 3.4 13.0 - - - -
198B GLN* 3.7 22.7 - - + +
232B CYS* 3.5 9.7 - - - -
244B SER 4.2 0.4 - - - -
245B CYS* 1.3 75.3 - - - +
247B SER* 1.3 61.2 + - - +
248B ALA* 3.6 20.8 - - + +
278B PHE* 4.3 3.4 - + - -
198C GLN* 4.0 0.5 - - - +
246C TYR* 3.4 53.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 3.6 0.7 - - - -
197B GLY 3.1 31.3 + - - +
210B HIS* 5.0 4.7 - - - -
212B ILE* 3.8 8.6 - - - +
230B PHE* 3.9 14.0 - - - +
231B ARG 4.2 2.8 + - - -
232B CYS* 3.9 16.5 - - - -
246B TYR* 1.3 79.4 - - - +
248B ALA* 1.3 62.4 + - - +
198C GLN* 2.6 33.4 + - - -
246C TYR* 4.4 1.6 - - - -
278C PHE* 3.8 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 3.6 24.7 - - + -
195B ILE 3.1 15.5 - - - +
196B TYR* 3.7 3.6 - - + -
230B PHE* 4.4 7.4 - - - -
246B TYR* 3.6 18.6 - - + +
247B SER* 1.3 78.3 + - - +
249B GLY* 1.3 58.5 + - - +
196C TYR* 4.4 0.3 - - - -
246C TYR* 3.1 18.8 - - - +
278C PHE* 3.1 26.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE 3.6 0.2 - - - +
194B PHE* 3.5 7.9 - - - -
195B ILE 2.9 31.0 + - - +
230B PHE* 3.5 21.4 - - - -
248B ALA* 1.3 75.7 - - - +
250B ILE* 1.3 66.0 + - - -
148C GLN* 4.0 4.0 - - - -
196C TYR* 4.1 12.8 - - - -
278C PHE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 4.3 7.6 - - + -
193B PHE 3.2 14.8 - - - +
194B PHE* 4.3 11.0 - - + -
230B PHE* 3.7 3.7 - - - -
249B GLY* 1.3 77.7 - - - +
251B ALA* 1.3 65.8 + - - +
284B LEU* 3.9 24.2 - - + -
146C CYS* 4.0 23.1 - - + -
148C GLN* 3.0 28.4 + - - +
172C PHE* 3.5 24.8 - - + -
196C TYR* 3.4 34.8 - - + +
281C ALA 4.6 0.7 - - - +
282C LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 4.6 1.3 - - - -
193B PHE 2.9 28.7 + - - +
195B ILE* 3.8 20.2 - - + -
229B LEU* 4.0 23.3 - - + -
230B PHE* 4.4 3.4 - - + -
250B ILE* 1.3 78.9 - - - +
252B LYS* 1.4 62.9 + - - +
253B LEU* 3.4 18.7 + - + +
172C PHE* 4.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 3.4 10.5 - - - +
192B TYR* 3.9 34.5 - - + +
214B ARG* 3.9 17.3 + - - -
251B ALA* 1.4 68.9 - - - +
253B LEU* 1.3 64.8 + - - +
172C PHE* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 5.7 0.2 - - + -
187B VAL* 3.8 25.8 - - + -
190B THR* 3.4 6.0 - - - +
191B GLY 2.9 31.5 + - - +
193B PHE* 3.7 28.3 - - + -
195B ILE* 3.9 9.0 - - + -
214B ARG* 3.7 31.9 - - + -
229B LEU* 4.3 1.3 - - + -
251B ALA* 3.4 25.5 + - + +
252B LYS* 1.3 77.5 - - - +
254B GLU* 1.4 62.1 + - - +
257B ASP* 3.7 6.7 - - + +
259B LEU* 3.8 29.6 - - + -
----------------------------------------------------------
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