Contacts of the helix formed by residues 314 - 322 (chain X) in PDB entry 2AE0
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 314 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X TYR* 3.4 12.7 - - - -
103X THR 3.0 14.9 + - - -
105X VAL* 4.3 13.5 - - - -
313X ILE* 1.3 77.8 - - - +
315X PRO* 1.3 72.6 - - - +
316X GLU 3.4 2.2 - - - -
317X ALA* 3.3 2.6 + - - +
318X GLY 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 315 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X TYR* 5.3 1.3 - - + -
105X VAL* 5.4 7.0 - - + +
314X GLY* 1.3 82.2 - - - +
316X GLU* 1.3 67.1 + - + +
318X GLY* 3.1 3.5 + - - +
319X HIS* 2.9 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313X ILE 6.0 0.2 - - - +
314X GLY 3.4 0.8 - - - -
315X PRO* 1.3 84.3 - - + +
317X ALA* 1.3 62.4 + - - +
319X HIS* 3.2 24.9 + - - +
320X ARG* 3.2 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X TYR* 3.8 5.2 - - + -
311X GLN* 3.4 24.1 - - - +
312X GLY* 3.5 34.8 - - - +
313X ILE 3.8 6.6 + - - +
314X GLY 3.3 9.3 + - - +
316X GLU* 1.3 77.7 - - - +
318X GLY* 1.3 62.7 + - - +
320X ARG* 3.3 16.5 + - - +
321X ALA* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 318 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X TYR* 3.5 34.3 - - - -
209X GLN* 3.9 9.7 + - - -
212X ARG* 6.1 0.2 - - - -
314X GLY 3.0 10.3 + - - -
315X PRO* 3.1 6.0 + - - -
317X ALA* 1.3 78.0 - - - +
319X HIS* 1.3 61.5 + - - +
321X ALA* 3.4 14.6 + - - +
322X GLY 4.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 319 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X LEU* 4.9 5.2 - - - +
279X ASP 5.2 5.9 - - - +
282X GLY* 5.7 2.3 - - - -
315X PRO* 2.9 30.0 + - + +
316X GLU* 3.2 31.6 + - - +
318X GLY* 1.3 78.0 - - - +
320X ARG* 1.3 62.0 + - + +
321X ALA 3.5 0.3 + - - -
322X GLY* 3.8 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255X ARG* 3.4 43.6 - - - +
278X LEU* 3.8 16.1 - - - +
311X GLN* 2.9 64.6 + - - +
316X GLU* 3.2 35.1 + - - +
317X ALA* 3.5 14.6 - - - +
318X GLY 3.3 0.4 - - - -
319X HIS* 1.3 76.3 - - + +
321X ALA* 1.3 65.9 + - - +
322X GLY 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99X THR* 4.3 0.9 - - - -
100X GLY* 3.3 43.2 + - - +
101X TYR 4.0 2.9 - - - +
102X TYR* 4.1 10.1 - - + -
209X GLN* 3.7 14.8 - - - +
278X LEU* 4.5 2.1 - - - +
311X GLN* 3.9 10.7 - - + +
317X ALA 3.0 12.5 + - - +
318X GLY 3.5 12.1 - - - +
319X HIS 3.3 0.6 - - - -
320X ARG* 1.3 78.9 - - - +
322X GLY* 1.3 62.7 + - - +
324X TYR 5.6 0.9 - - - +
326X HIS* 5.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209X GLN* 2.9 29.0 + - - +
278X LEU* 3.7 21.3 - - - -
282X GLY* 5.0 3.4 - - - -
318X GLY 4.0 3.2 + - - -
319X HIS 3.8 7.6 + - - -
320X ARG 3.3 3.0 - - - -
321X ALA* 1.3 81.3 - - - +
323X TRP* 1.3 66.8 + - - -
324X TYR 3.9 1.8 - - - -
326X HIS* 5.1 2.2 - - - -
----------------------------------------------------------
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