Contacts of the strand formed by residues 246 - 253 (chain B) in PDB entry 3H8E
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 ARG 246 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.8 33.1 - - + +
200B SER* 3.6 23.0 + - - +
203B ALA* 4.3 5.5 - - + +
220B VAL* 3.6 24.1 - - + +
221B LEU 3.4 7.6 - - - +
222B ASP* 3.6 24.5 - - - +
223B GLU* 3.8 2.2 - - - +
226B ILE* 4.2 0.2 - - - -
234B PHE* 3.6 4.7 - - - -
244B PRO* 3.5 25.1 - - - +
245B PRO* 1.3 98.2 + - - +
247B LEU* 1.3 60.1 + - - +
248B ILE* 4.2 15.5 - - + -
317B LEU 3.4 1.2 - - - +
319B CYS* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 3.7 0.5 - - - -
221B LEU* 2.8 67.2 + - + +
226B ILE* 3.8 4.6 - - + +
231B MET* 3.7 33.9 - - + -
234B PHE* 4.1 12.8 - - + -
246B ARG* 1.3 72.3 - - - +
248B ILE* 1.3 63.3 + - - +
249B VAL* 4.8 4.0 - - + -
316B LEU* 4.4 5.8 - - + -
317B LEU 3.4 20.4 - - - +
318B ALA* 4.4 1.3 - - - -
359B THR* 4.0 31.4 - - + +
362B TYR* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO 4.4 2.2 - - - +
202B LEU* 3.6 18.4 - - + +
203B ALA* 3.5 36.3 - - + +
206B ALA* 3.4 17.0 - - + -
218B VAL* 4.5 2.7 - - + -
219B GLU 3.8 6.5 - - - +
220B VAL* 4.6 5.6 - - + +
246B ARG* 4.2 11.0 - - + +
247B LEU* 1.3 78.2 - - - +
249B VAL* 1.3 59.8 + - - +
250B LEU* 3.0 27.1 - - + +
315B CYS 3.4 1.4 - - - +
316B LEU* 3.3 5.5 - - - -
317B LEU* 2.8 50.3 + - + +
319B CYS* 3.9 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LYS 3.8 0.7 - - - +
218B VAL* 3.3 4.7 - - - -
219B GLU* 2.8 47.0 + - + +
221B LEU* 3.9 24.9 - - + -
247B LEU* 4.6 4.3 - - + +
248B ILE* 1.3 75.0 - - - +
250B LEU* 1.3 70.8 + - - +
251B ASN* 4.8 6.3 - - + +
314B VAL* 4.3 6.7 - - + -
315B CYS 3.3 3.4 - - - +
316B LEU* 3.8 25.8 - - + -
362B TYR* 4.0 15.9 - - + +
366B PHE* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA* 4.0 6.7 - - + -
209B LEU* 4.3 6.3 - - + -
216B LEU* 4.0 6.6 - - + +
217B LYS 3.5 3.6 - - - -
218B VAL* 3.8 13.9 - - + -
248B ILE* 3.0 39.7 - - + +
249B VAL* 1.3 77.3 - - - +
251B ASN* 1.4 60.4 + - - +
252B TYR 4.0 0.4 - - - -
298B PHE* 4.0 28.0 - - + -
301B LEU* 3.5 33.8 - - + +
313B LEU 3.6 2.9 - - - +
314B VAL* 3.5 1.4 - - - -
315B CYS* 2.8 46.8 + - + +
317B LEU* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA 3.4 2.4 - - - +
216B LEU* 3.4 5.0 - - - +
217B LYS* 2.7 49.0 + - + +
249B VAL* 4.1 8.7 - - + +
250B LEU* 1.4 73.1 - - - +
252B TYR* 1.3 59.8 + - - +
253B GLN* 2.9 36.6 + - - +
313B LEU 3.7 2.2 - - - -
314B VAL* 3.8 22.8 - - + +
366B PHE* 4.2 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 3.4 31.0 - - + -
216B LEU* 3.9 12.7 - - + +
250B LEU 3.9 0.2 + - - -
251B ASN* 1.3 75.0 + - - +
253B GLN* 1.3 58.6 - - - +
254B GLY* 3.7 9.7 - - - -
301B LEU* 4.1 11.4 - - + -
304B VAL* 3.6 26.5 - - + -
305B LEU* 3.7 29.6 - - + -
308B GLN* 3.3 22.4 + - + +
309B LEU 2.7 29.4 + - - -
311B VAL 3.2 15.9 - - - -
312B ASN* 3.4 2.4 - - - -
313B LEU* 2.8 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 3.0 23.5 + - + +
251B ASN* 2.9 35.3 + - - +
252B TYR* 1.3 68.6 + - - +
254B GLY* 1.3 61.7 + - - +
255B GLY 3.4 6.5 + - - +
256B LYS 5.1 0.7 - - - +
257B LYS* 5.0 16.8 + - - +
261B PRO* 5.3 1.8 - - - +
312B ASN* 3.3 33.9 + - - +
314B VAL* 4.9 4.6 - - - +
----------------------------------------------------------
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