Contacts of the helix formed by residues 248 - 260 (chain A) in PDB entry 2AZT
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 CYS 248 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 5.2 0.4 - - - -
179A TYR* 4.8 0.2 - - - -
180A ASP* 3.5 20.9 - - - +
183A LEU* 3.8 29.4 - - - -
215A ALA* 6.2 0.7 - - - -
246A PRO 3.3 7.7 + - - -
247A HIS* 1.3 73.3 - - - +
249A LEU* 1.3 60.8 + - - +
250A ALA* 3.5 2.9 - - + +
251A SER* 3.3 16.1 + - - +
252A PHE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 5.0 4.1 - - - +
180A ASP* 2.8 20.8 + - - +
247A HIS 4.0 1.2 + - - -
248A CYS* 1.3 70.9 - - - +
250A ALA* 1.3 60.9 + - - +
252A PHE* 4.1 3.3 - - - +
253A THR* 2.7 36.4 + - - +
268A VAL* 4.0 10.5 - - + -
275A TYR* 3.8 32.1 - - + +
286A PHE* 3.5 49.4 - - + -
288A HIS* 3.9 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASP* 5.3 1.6 + - - -
248A CYS* 3.5 2.3 - - + +
249A LEU* 1.3 80.6 - - - +
251A SER* 1.3 61.9 + - - +
253A THR* 3.4 6.5 - - - -
254A GLU* 3.2 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 4.8 10.7 + - - -
247A HIS* 5.3 2.6 + - - -
248A CYS* 3.3 19.7 + - - +
250A ALA* 1.3 77.3 - - - +
252A PHE* 1.3 65.9 + - - +
254A GLU* 3.3 14.1 + - - +
255A LEU* 3.0 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.5 42.8 - + + -
159A LEU* 4.7 9.4 - - + -
174A ILE* 4.4 15.9 - - + -
175A ASP 4.3 10.5 - - - -
176A ASN* 2.9 31.4 - - + +
247A HIS* 3.7 30.5 - + + +
248A CYS 2.9 21.7 + - - +
249A LEU* 4.1 2.2 - - - +
251A SER* 1.3 70.5 + - - +
253A THR* 1.3 66.8 + - - +
255A LEU* 3.0 13.8 + - + +
256A LEU* 2.9 48.7 + - + +
288A HIS* 3.4 17.3 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 2.7 29.0 + - - +
250A ALA* 3.4 7.2 - - - -
252A PHE* 1.3 74.9 - - - +
254A GLU* 1.3 63.0 + - - +
256A LEU* 3.2 4.7 + - - +
257A GLN* 3.0 38.1 + - + +
266A HIS* 3.6 29.2 + - + +
268A VAL* 4.8 3.9 - - + +
288A HIS* 3.3 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ALA* 3.2 24.4 + - - +
251A SER* 3.3 10.5 + - - +
253A THR* 1.3 78.2 - - - +
255A LEU* 1.3 59.4 + - + +
257A GLN* 3.4 10.3 + - + +
258A ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 3.8 25.8 - - + +
155A HIS* 4.6 7.6 - - + -
156A ARG* 3.8 39.7 - - + +
159A LEU* 3.9 26.6 - - + +
247A HIS* 4.2 18.2 - - + +
251A SER* 3.0 25.2 + - - +
252A PHE* 3.0 17.4 + - + +
254A GLU* 1.3 78.5 - - + +
256A LEU* 1.3 59.0 - - - +
258A ALA* 3.4 8.0 + - + +
259A ALA* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 4.0 25.8 - - + -
172A LEU* 4.2 13.2 - - + -
174A ILE* 3.8 20.2 - - + -
252A PHE* 2.9 37.8 + - + +
253A THR* 3.6 6.5 - - - +
255A LEU* 1.3 73.1 - - - +
257A GLN* 1.3 68.2 + - - +
259A ALA* 3.1 12.7 + - + +
260A PHE* 3.4 17.2 - - + -
266A HIS* 4.3 2.9 - - + +
288A HIS* 3.4 44.0 - - + +
290A LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.0 31.2 + - - +
254A GLU* 3.6 8.7 - - + +
256A LEU* 1.3 73.5 - - + +
258A ALA* 1.3 54.7 + - - +
260A PHE* 2.8 26.2 + - - +
261A GLY 3.2 8.0 + - - -
262A GLY* 3.2 17.0 + - - -
264A CYS* 3.6 29.5 + - - -
266A HIS* 4.0 20.3 + - + +
290A LEU* 4.6 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 5.7 10.1 - - + +
254A GLU 2.9 17.9 + - - +
255A LEU* 3.6 8.5 - - + +
257A GLN* 1.3 76.7 - - - +
259A ALA* 1.3 60.3 + - - +
261A GLY* 3.2 15.2 + - - +
262A GLY 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG 5.3 1.6 - - - +
159A LEU* 3.7 44.0 - - + +
160A LYS* 3.9 14.8 - - - +
163A ALA* 3.5 18.6 - - + +
172A LEU* 6.3 1.1 - - + -
255A LEU 3.1 6.6 + - - +
256A LEU* 3.1 14.3 + - + +
257A GLN 3.1 0.2 + - - -
258A ALA* 1.3 76.7 - - - +
260A PHE* 1.3 60.7 + - + +
292A ARG* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 4.0 21.3 - - + -
166A VAL* 4.4 7.2 - - + -
172A LEU* 4.0 28.9 - - + -
256A LEU* 3.4 20.0 - - - -
257A GLN 2.8 7.4 + - - +
259A ALA* 1.3 81.8 - - + +
261A GLY* 1.3 59.1 + - - +
263A LYS* 3.5 20.0 + - - +
264A CYS* 3.8 24.9 - - + -
290A LEU* 3.7 36.3 - - + -
292A ARG* 3.8 58.7 + - + +
----------------------------------------------------------
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