Contacts of the helix formed by residues 241 - 255 (chain B) in PDB entry 3OYG
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 LYS 241 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER* 3.9 0.9 - - - -
238B ARG* 3.0 30.9 + - + +
240B THR* 1.3 82.7 - - + +
242B TRP* 1.3 60.4 + - - +
243B TYR 3.4 2.7 - - - -
244B ASP* 3.4 23.5 + - - +
245B LEU* 3.7 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.8 30.7 - - + +
134B PRO* 2.7 24.9 + - + -
136B SER* 3.5 11.4 - - - -
139B TYR* 3.4 37.5 - - + -
140B LEU* 4.2 1.3 - - - -
141B TYR 3.8 18.8 - - - -
142B VAL* 3.8 20.6 - - + -
157B PRO* 4.4 5.2 - - + -
231B LEU* 5.5 11.4 - - + -
234B LEU 6.3 0.2 - - - -
235B LEU* 5.1 17.5 - - + +
238B ARG 4.2 3.1 + - - +
239B PRO 3.3 23.8 - - - +
240B THR 3.3 1.2 - - - -
241B LYS* 1.3 74.9 - - - +
243B TYR* 1.3 85.8 + - - +
245B LEU* 2.9 22.9 + - + +
246B LEU* 3.2 30.8 + - + +
249B VAL* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER* 3.1 25.2 + - - +
137B GLN* 3.7 23.8 - - + -
139B TYR* 3.4 44.1 + + + -
157B PRO* 3.9 25.7 - - + +
242B TRP* 1.3 88.9 - - + +
244B ASP* 1.3 78.7 + - - +
246B LEU* 3.5 17.2 + - + +
247B PRO* 4.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLN* 4.3 16.4 + - - -
241B LYS* 3.4 16.0 + - + +
242B TRP 3.2 0.6 - - - -
243B TYR* 1.3 94.0 - - - +
245B LEU* 1.3 63.5 + - + +
246B LEU 3.4 0.2 - - - -
247B PRO* 3.2 18.8 - - - +
248B VAL* 5.2 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.6 18.8 - - + +
238B ARG* 3.8 47.8 - - + +
241B LYS* 3.9 17.7 - - + +
242B TRP* 2.9 14.3 + - + +
244B ASP* 1.3 81.7 - - + +
246B LEU* 1.3 66.0 + - - +
247B PRO 3.3 1.3 - - - -
248B VAL* 3.1 27.2 + - + +
249B VAL* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 4.5 15.0 - - + -
155B LEU* 3.9 30.5 - - + +
156B TYR 4.9 0.7 - - - -
157B PRO* 3.7 41.5 - - + -
231B LEU* 4.6 13.9 - - + -
242B TRP* 3.2 28.1 + - + +
243B TYR* 3.7 11.4 - - + +
245B LEU* 1.3 75.9 - - - +
247B PRO* 1.3 71.1 - - + +
249B VAL* 3.3 5.9 + - + +
250B GLN* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 3.7 26.5 - - + +
174A THR* 5.3 2.9 - - - +
175A SER* 3.4 32.9 - - - +
243B TYR 4.1 2.9 - - - +
244B ASP 3.2 20.0 - - - +
245B LEU 3.5 0.2 - - - -
246B LEU* 1.3 93.3 - - + +
248B VAL* 1.3 61.8 + - - +
250B GLN* 3.2 4.4 + - - +
251B LEU* 3.1 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 5.6 6.3 - - + -
244B ASP 5.2 0.4 + - - +
245B LEU* 3.1 43.2 + - + +
247B PRO* 1.3 76.1 - - - +
249B VAL* 1.3 69.2 + - + +
251B LEU* 3.2 11.6 + - + +
252B ALA* 3.0 22.7 + - + +
278B PHE* 4.2 23.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
155B LEU* 3.9 13.5 - - + -
227B ILE* 5.7 0.9 - - + -
230B LEU* 4.2 20.0 - - + +
231B LEU* 4.4 25.8 - - + -
234B LEU* 4.9 15.5 - - + -
242B TRP 5.9 0.2 - - - +
245B LEU* 3.0 32.5 + - + +
246B LEU* 3.6 10.3 - - + +
248B VAL* 1.3 78.8 - - + +
250B GLN* 1.3 57.2 + - - +
252B ALA* 3.4 6.5 + - - +
253B LEU* 3.0 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 3.7 36.5 + - - +
176A ILE* 4.9 1.7 - - - +
152B PHE* 5.9 0.2 - - - -
153B THR* 3.6 11.2 - - + +
154B TRP* 3.3 16.1 - - - +
155B LEU* 3.1 56.6 + - + +
246B LEU* 3.0 25.1 + - - +
247B PRO 3.6 5.8 - - - +
248B VAL 3.2 0.2 - - - -
249B VAL* 1.3 72.3 - - - +
251B LEU* 1.3 61.1 + - - +
253B LEU* 3.3 5.9 + - - +
254B ASN* 2.8 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.5 28.3 - - - +
175A SER 4.0 7.6 - - - +
176A ILE 4.1 3.4 - - - +
177A ALA* 3.9 20.9 - - - -
178A ILE* 4.0 18.6 - - + +
247B PRO* 3.1 22.7 + - + +
248B VAL* 3.2 14.8 + - + +
250B GLN* 1.3 75.6 - - - +
252B ALA* 1.3 57.1 + - - +
254B ASN* 4.8 1.6 - - - -
255B ASN* 2.6 46.9 + - - +
276B THR* 4.1 16.4 - - + +
278B PHE* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.2 16.6 - - + -
248B VAL* 3.0 13.3 + - + +
249B VAL* 3.4 10.3 - - - +
251B LEU* 1.3 72.2 - - - +
253B LEU* 1.3 62.1 + - - +
255B ASN 3.0 12.5 + - - -
256B THR* 2.7 25.4 + - - +
278B PHE* 4.1 29.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
153B THR* 4.3 22.7 - - + +
155B LEU* 4.4 5.2 - - + -
223B LYS* 3.1 32.2 + - + +
226B ASP* 4.2 20.9 - - + +
227B ILE* 3.6 34.8 - - + +
230B LEU* 3.8 19.5 - - + -
249B VAL* 3.0 37.4 + - + +
250B GLN* 3.3 5.6 + - - +
252B ALA* 1.3 75.4 - - - +
254B ASN* 1.3 62.2 + - - +
256B THR* 3.4 13.0 + - + +
265B PRO* 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER 4.8 3.4 + - - -
176A ILE 5.2 2.7 + - - +
151B GLY 4.0 1.7 - - - +
152B PHE* 3.2 43.7 - - + -
153B THR* 2.6 52.0 + - - +
250B GLN* 2.8 30.8 + - - +
251B LEU* 4.2 2.9 - - - +
253B LEU* 1.3 73.3 - - - +
255B ASN* 1.3 62.4 + - - +
256B THR 3.4 1.3 - - - -
264B THR* 3.5 1.0 - - - -
265B PRO* 3.2 13.0 - - - +
266B HIS* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE 5.6 1.0 + - - -
251B LEU* 2.6 40.2 + - - +
252B ALA 3.0 4.0 + - - +
254B ASN* 1.3 82.6 - - - +
256B THR* 1.3 59.6 - - - +
257B TYR 3.8 1.0 + - - -
264B THR* 3.7 15.5 + - + +
266B HIS* 3.6 13.9 + - - +
274B SER* 2.8 31.0 + - - -
276B THR* 3.4 34.9 + - - +
277B PRO* 4.9 1.5 - - + +
278B PHE* 4.1 26.1 + - + +
----------------------------------------------------------
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