Contacts of the helix formed by residues 240 - 246 (chain A) in PDB entry 2AYN
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 SER 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 2.5 37.5 + - - +
212A GLN* 4.3 3.3 - - - -
214A LEU 4.1 3.4 - - - -
216A ALA* 3.9 8.1 - - - +
239A LYS* 1.3 87.9 + - - +
241A LEU* 1.3 64.8 + - - +
242A ILE 4.3 0.7 - - - -
243A ASP* 3.0 44.3 + - - +
244A GLN* 3.3 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 4.1 10.5 - - + +
128A LEU* 5.2 4.3 - - + -
131A ALA* 3.1 35.9 - - + -
214A LEU* 3.1 36.7 + - + +
215A GLU 3.7 12.1 - - - +
216A ALA* 3.8 8.6 - - - +
217A ILE* 4.2 15.5 - - + -
240A SER* 1.3 67.8 - - - +
242A ILE* 1.3 61.7 + - + +
244A GLN* 2.7 40.7 + - - +
245A PHE* 3.2 31.8 + - + -
246A PHE* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.1 15.0 - - + -
207A MET* 4.1 19.3 - - + +
210A LEU* 3.6 25.4 - - + +
211A GLN* 3.2 37.5 - - + +
214A LEU* 4.4 4.5 - - + -
240A SER 3.3 0.2 - - - -
241A LEU* 1.3 76.5 - - + +
243A ASP* 1.3 56.7 + - - +
244A GLN 2.7 10.4 + - - -
245A PHE 3.0 1.6 + - - -
246A PHE* 2.9 61.5 + - + +
272A LEU* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 3.7 21.0 + - - +
239A LYS* 5.3 4.1 + - - +
240A SER* 3.0 40.1 + - - +
242A ILE* 1.3 78.4 - - - +
244A GLN* 1.3 57.0 + - + +
247A GLY* 3.3 18.6 + - - +
270A ASN* 6.2 0.5 - - - +
272A LEU* 3.8 19.3 - - - +
318A ARG* 3.1 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA* 3.2 15.6 - - + +
217A ILE* 3.1 36.2 + - - +
240A SER 3.5 11.4 - - - +
241A LEU* 2.7 21.2 + - - +
243A ASP* 1.3 82.1 - - + +
245A PHE* 1.3 67.4 + - + +
318A ARG* 3.3 22.4 + - - +
321A ALA 4.8 0.2 + - - -
410A GLY 3.0 26.8 + - - +
411A SER* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 5.8 0.2 - - + -
127A GLU* 3.3 36.3 - - + -
217A ILE* 4.1 18.4 - - + -
241A LEU* 3.2 27.8 + - + -
242A ILE 3.0 3.2 + - - -
244A GLN* 1.3 92.7 - - + +
246A PHE* 1.3 74.6 + - + +
247A GLY 3.7 0.2 - - - -
320A PRO* 3.6 5.0 - - - +
321A ALA* 3.8 13.9 - - + +
322A TYR* 2.9 62.9 + + + +
405A PHE* 4.2 14.1 - + - -
411A SER* 4.3 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.2 30.3 - - + -
128A LEU* 4.6 15.0 - - + -
203A TRP* 6.0 1.6 - + - -
207A MET* 3.5 25.1 - - + -
241A LEU* 5.0 2.0 - - + -
242A ILE* 2.9 60.2 + - + +
245A PHE* 1.3 93.1 - - + +
247A GLY* 1.3 69.2 + - - +
248A VAL* 3.6 2.6 + - - +
272A LEU* 3.4 33.3 - - + +
320A PRO* 3.5 9.5 - - - +
322A TYR* 3.5 30.0 - - + +
324A THR* 4.1 8.3 + - - -
478A LEU* 5.7 4.0 - - + -
----------------------------------------------------------
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