Contacts of the helix formed by residues 289 - 302 (chain A) in PDB entry 6O0Z
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 LEU 289 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 4.4 23.1 + - - +
195A LEU* 5.6 7.4 - - + -
288A ASP* 1.3 77.4 - - + +
290A PHE* 1.3 59.2 + - - +
292A ALA* 3.3 8.6 + - - +
293A ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A TYR* 4.7 16.6 + - - +
275A LEU* 6.3 2.9 - - + -
288A ASP* 3.3 4.5 - - + +
289A LEU* 1.3 75.7 - - - +
291A LEU* 1.3 58.9 + - - +
293A ALA* 3.3 7.5 + - - +
294A LYS* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP 3.3 23.3 + - - +
289A LEU 3.3 0.4 - - - -
290A PHE* 1.3 78.0 - - - +
292A ALA* 1.3 57.7 + - - +
294A LYS* 3.4 7.2 + - - +
295A ASN* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 5.4 3.4 - - - +
187A GLN* 4.8 6.7 - - + +
188A LEU* 4.6 17.6 - - + +
191A THR* 4.4 22.2 - - + +
288A ASP 3.1 12.7 + - - +
289A LEU 3.6 8.1 - - - +
290A PHE 3.3 0.2 - - - -
291A LEU* 1.3 74.9 - - - +
293A ALA* 1.3 59.7 + - - +
295A ASN* 3.4 6.8 + - - +
296A LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.8 5.3 - - + +
243A ALA 4.3 5.4 - - - +
244A LEU* 2.9 41.1 - - + +
271A TYR* 5.8 3.4 - - - +
289A LEU 2.9 16.5 + - - +
290A PHE* 3.6 8.3 - - - +
292A ALA* 1.3 75.6 - - - +
294A LYS* 1.3 57.8 + - - +
296A LEU* 3.3 2.6 + - - +
297A SER 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A TYR* 6.3 3.1 - - + -
290A PHE 2.9 17.6 + - - +
291A LEU* 3.7 7.9 - - - +
293A ALA* 1.3 77.3 - - - +
295A ASN* 1.3 56.5 + - - +
297A SER* 3.2 8.1 + - - -
298A ASP* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP* 5.4 12.8 - - + +
184A LEU* 5.2 13.0 - - + +
291A LEU 2.9 18.0 + - - +
292A ALA* 3.8 7.4 - - - +
294A LYS* 1.3 76.3 - - - +
296A LEU* 1.3 57.1 + - - +
298A ASP* 3.3 9.1 + - - +
299A ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 5.3 13.8 - - + +
185A PHE* 5.8 3.1 - - - -
188A LEU* 4.6 14.8 - - + -
244A LEU* 4.7 1.8 - - + -
245A SER* 3.9 13.5 - - - -
292A ALA 2.9 17.6 + - - +
293A ALA* 3.6 8.1 - - - +
295A ASN* 1.3 74.0 - - - +
297A SER* 1.3 59.7 + - - +
299A ALA* 3.3 7.5 + - - +
300A ILE* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 3.2 20.8 + - - -
245A SER* 4.0 14.2 - - - +
293A ALA 2.9 8.2 + - - -
294A LYS* 3.2 12.8 + - - -
296A LEU* 1.3 76.8 - - - +
298A ASP* 1.3 56.4 + - - +
300A ILE* 3.4 1.8 + - - +
301A LEU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.7 29.2 - - + -
175A ASN 4.8 8.5 - - - +
177A ASP* 5.5 6.7 - - + +
294A LYS 2.9 13.4 + - - +
295A ASN* 3.3 12.5 + - - +
297A SER* 1.3 76.3 - - - +
299A ALA* 1.3 55.8 + - - +
301A LEU* 3.3 4.0 + - - -
302A LEU* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP* 6.0 5.6 - - + +
180A ASP 3.4 26.9 - - - +
181A VAL* 4.0 16.8 - - + +
184A LEU* 5.4 1.8 - - + -
295A ASN 2.9 17.2 + - - +
296A LEU* 3.8 7.2 - - - +
297A SER 3.3 0.2 - - - -
298A ASP* 1.3 77.7 - - - +
300A ILE* 1.3 56.2 + - - +
302A LEU* 3.6 2.4 - - - -
303A SER* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LYS* 5.6 11.2 - - + -
245A SER* 3.9 25.8 - - - +
296A LEU 2.9 17.6 + - - +
297A SER* 3.9 3.6 - - - +
299A ALA* 1.3 77.2 - - - +
301A LEU* 1.3 58.9 + - - +
303A SER* 2.8 23.8 + - - -
304A ASP* 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 4.5 21.1 - - + -
174A LEU* 5.9 2.5 - - + -
297A SER 2.9 17.5 + - - +
298A ASP* 3.8 6.1 - - - +
300A ILE* 1.3 78.5 - - - +
302A LEU* 1.3 63.5 + - + +
304A ASP* 3.2 22.0 - - - +
305A ILE* 3.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.8 32.5 - - + -
175A ASN 5.5 3.4 - - - +
176A PRO* 4.9 16.6 - - + -
177A ASP 6.2 0.2 - - - +
298A ASP* 2.9 31.0 + - + +
299A ALA* 3.6 4.5 - - - +
301A LEU* 1.3 78.7 - - + +
303A SER* 1.3 63.7 + - - +
304A ASP 3.6 0.4 - - - -
305A ILE* 3.8 15.7 - - + -
306A LEU* 3.4 33.1 - - + +
316A PRO* 5.6 4.5 - - + -
411A PRO* 5.8 4.3 - - + -
414A ILE* 3.8 27.1 - - + -
----------------------------------------------------------
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