Contacts of the helix formed by residues 382 - 390 (chain C) in PDB entry 3A4Y
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 GLY 382 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C TYR* 4.4 1.1 - - - -
192C ARG 4.2 5.6 - - - -
193C PRO* 4.3 1.8 - - - -
194C HIS* 3.3 31.2 + - - -
381C ALA* 1.3 74.9 - - - +
383C GLN* 1.3 58.2 + - - -
384C ASP* 3.1 10.5 - - - -
385C GLU* 2.7 33.3 + - - +
386C LEU* 2.8 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C TYR 3.0 24.7 + - - +
190C GLY* 2.9 28.2 - - - +
191C ASP* 3.3 13.3 + - - +
192C ARG* 3.4 20.1 + - - +
193C PRO* 4.1 12.9 - - - +
382C GLY* 1.3 69.2 - - - -
384C ASP* 1.3 63.7 + - - +
386C LEU* 3.2 7.9 + - - +
387C LEU* 2.9 42.6 + - + +
408C ALA* 4.8 1.7 - - - +
409C LEU* 4.7 2.1 + - + -
412C LEU* 3.1 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 5.2 5.4 - - - +
193C PRO* 3.6 26.7 - - + +
194C HIS* 4.7 2.1 + - - -
382C GLY* 3.2 12.0 - - - +
383C GLN* 1.3 77.1 - - - +
385C GLU* 1.3 82.3 + - - +
387C LEU* 3.2 16.0 + - + +
388C ASP* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLY 3.2 10.4 - - - +
165C ASN* 2.6 28.5 + - - -
166C ARG* 2.9 38.5 + - - +
167C GLU* 4.1 8.5 + - - +
174C PRO* 5.6 0.2 - - - +
194C HIS* 4.7 0.9 - - - -
381C ALA* 3.4 11.7 - - + +
382C GLY 2.7 22.7 + - - +
384C ASP* 1.3 91.5 + - - +
386C LEU* 1.3 56.0 + - - +
388C ASP* 2.9 16.0 + - - +
389C TRP* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LEU* 5.8 4.7 - - + -
186C GLU* 3.4 28.7 - - + +
187C GLY* 3.5 14.4 - - - -
188C THR 4.9 0.2 - - - +
190C GLY* 4.4 6.5 - - - +
381C ALA* 2.9 35.2 - - + +
382C GLY 2.8 28.6 + - - +
383C GLN 3.6 5.2 - - - +
385C GLU* 1.3 71.7 - - - +
387C LEU* 1.3 67.1 + - - +
389C TRP* 4.4 4.5 - - - +
390C LEU* 2.9 40.8 + - + +
409C LEU* 3.3 34.3 - - + -
413C LEU* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C GLN* 2.9 49.4 + - + +
384C ASP* 3.3 15.9 - - + +
386C LEU* 1.3 76.6 - - + +
388C ASP* 1.3 59.1 + - - +
390C LEU 3.8 0.2 - - - -
391C GLN* 2.9 23.8 + - - +
409C LEU* 5.0 6.5 - - + +
412C LEU* 3.9 31.0 - - + +
413C LEU* 4.0 23.3 - - + -
416C ARG* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 5.2 10.1 + - - +
176C LEU* 4.9 8.3 - - + +
384C ASP* 3.1 17.6 + - - +
385C GLU* 2.9 15.4 + - - +
387C LEU* 1.3 77.5 - - - +
389C TRP* 1.3 60.4 + - - +
391C GLN* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 5.4 0.3 + - - -
147C PHE* 3.7 26.0 - + - -
158C VAL* 3.8 18.4 - - + -
160C SER* 3.3 37.9 - - - -
163C LEU* 3.4 33.0 - - + +
174C PRO* 5.0 5.4 - - + -
175C SER 2.8 26.2 + - - -
176C LEU* 4.3 13.5 - - + +
177C PRO* 3.5 50.9 - - + +
183C VAL* 4.2 19.3 - - + -
185C ALA* 4.4 0.4 - - + -
385C GLU 2.8 17.7 + - - +
386C LEU* 3.9 6.7 - - - +
388C ASP* 1.3 73.8 - - - +
390C LEU* 1.3 82.3 + - + +
391C GLN 4.1 3.8 - - - +
393C GLU* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO* 6.1 0.2 - - + -
183C VAL* 3.4 33.9 - - + -
185C ALA* 3.9 20.2 - - + -
186C GLU 5.4 1.3 - - - +
386C LEU* 2.9 41.3 + - + +
387C LEU 4.5 1.1 - - - +
389C TRP* 1.3 92.0 - - + +
391C GLN* 1.3 68.4 + - - +
393C GLU* 2.9 17.1 + - + +
396C VAL* 4.2 17.3 - - + -
409C LEU* 5.9 3.6 - - + -
413C LEU* 4.5 21.1 - - + -
416C ARG* 4.0 0.4 - - - -
418C GLN* 2.8 22.5 + - - +
----------------------------------------------------------
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