Contacts of the helix formed by residues 243 - 255 (chain A) in PDB entry 2X86
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 PHE 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 5.1 3.4 - - - -
184A VAL* 3.6 36.7 - - + +
200A LEU* 3.9 19.8 - - + +
204A SER* 4.2 10.3 + - - -
207A PHE* 3.4 33.9 + - + -
209A ARG* 3.7 37.0 - - + -
211A PHE* 3.8 21.3 - + - -
242A SER* 1.3 73.0 - - - +
244A GLN* 1.3 63.7 + - - +
246A VAL* 3.1 7.3 + - + +
247A ALA* 3.0 22.0 + - - +
272A TYR* 3.7 9.6 - - - -
401A ADP 3.6 36.6 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
200A LEU* 4.2 8.0 - - + +
204A SER 4.5 6.5 + - - +
205A GLU* 5.5 6.3 - - - -
242A SER* 3.1 13.1 - - - +
243A PHE* 1.3 79.1 - - - +
245A ALA* 1.3 56.8 + - - +
247A ALA* 3.3 7.5 + - - +
248A ASP* 2.8 66.7 + - - +
259A ILE* 4.2 18.6 - - - +
261A TYR* 3.9 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 4.1 27.1 - - + +
242A SER* 2.9 22.7 + - - +
244A GLN* 1.3 74.2 - - - +
246A VAL* 1.3 64.2 - - - +
248A ASP* 3.2 13.3 + - - +
249A ALA* 3.0 23.2 + - - +
295A VAL* 4.0 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 6.4 0.4 - - + -
184A VAL* 4.9 6.3 - - + -
185A ALA* 4.2 35.9 - - + +
188A LEU* 4.7 5.2 - - + -
211A PHE* 3.7 48.0 - - + -
242A SER 3.5 2.2 + - - +
243A PHE* 3.1 8.7 + - + +
245A ALA* 1.3 76.5 - - - +
247A ALA* 1.3 64.7 + - - +
249A ALA* 3.2 5.0 + - - +
250A THR* 3.0 26.5 + - - +
295A VAL* 3.8 19.5 - - + +
299A VAL* 4.2 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.8 17.9 - - + +
200A LEU* 4.3 6.5 - - + -
243A PHE 3.0 12.0 + - - +
244A GLN* 3.4 12.6 - - - +
246A VAL* 1.3 76.8 - - - +
248A ASP* 1.3 54.2 + - - +
250A THR* 3.2 2.3 + - - -
251A LEU* 2.8 40.2 + - + +
259A ILE* 3.4 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLN* 2.8 52.7 + - - +
245A ALA* 3.3 11.9 - - - +
247A ALA* 1.3 73.9 - - - +
249A ALA* 1.3 62.7 + - - +
251A LEU* 4.0 4.4 - - - +
252A ALA* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ALA 3.0 9.7 + - - +
246A VAL 3.2 7.8 + - - +
248A ASP* 1.3 78.8 - - - +
250A THR* 1.3 61.6 + - - +
252A ALA* 3.5 6.3 - - - +
253A TYR* 3.2 17.3 + - - +
295A VAL* 4.3 9.6 - - + +
296A ALA* 4.3 16.2 - - + +
299A VAL* 3.7 24.6 - - + +
300A THR* 3.8 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ALA* 4.6 1.0 - - - -
188A LEU* 4.1 20.7 - - + +
189A ASN 4.5 1.6 - - - +
192A LEU* 3.9 22.0 - - + -
246A VAL* 3.0 17.2 + - - +
247A ALA* 3.5 10.3 - - - -
249A ALA* 1.3 73.0 - - - +
251A LEU* 1.3 67.6 + - + +
252A ALA 3.1 1.1 - - - -
253A TYR* 3.1 3.8 + - - +
254A HIS* 3.1 24.6 + - + +
299A VAL* 3.4 17.1 - - - +
303A MET* 3.6 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 5.4 1.1 - - + -
192A LEU* 3.8 22.2 - - + -
198A PRO* 3.9 18.8 - - + -
247A ALA* 2.8 29.5 + - + +
248A ASP* 4.2 4.3 - - - +
250A THR* 1.3 76.2 - - + +
252A ALA* 1.3 57.4 + - - +
254A HIS* 3.3 3.0 + - - +
255A LYS* 2.8 26.7 + - - -
256A LYS 3.5 17.9 + - - +
257A GLY 3.0 31.2 - - - +
258A GLN* 4.0 8.1 - - - +
259A ILE* 4.4 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP 3.0 18.8 + - - +
249A ALA* 3.5 8.5 - - - +
251A LEU* 1.3 77.8 - - - +
253A TYR* 1.3 62.5 + - - +
255A LYS* 3.2 26.3 - - - +
300A THR* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 3.2 9.1 + - - +
250A THR 3.1 8.3 + - - +
252A ALA* 1.3 81.0 - - - +
254A HIS* 1.3 74.4 + + - +
255A LYS* 3.2 12.7 + - - +
300A THR* 4.3 18.7 - - + +
303A MET* 3.5 41.6 + - + -
304A ALA* 3.4 32.3 + - + +
307A ASN* 4.0 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASN* 2.8 33.7 + - - -
192A LEU* 3.8 37.2 - - + +
193A ASN* 3.4 24.1 + - - -
250A THR* 3.1 29.9 + - + +
251A LEU 4.0 3.1 - - - +
253A TYR* 1.3 88.4 - + - +
255A LYS* 1.3 68.8 + - - +
256A LYS* 3.0 27.9 + - + +
303A MET* 3.9 5.7 - - - -
307A ASN* 4.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU 2.8 10.2 + - - -
252A ALA* 3.2 24.2 + - - +
253A TYR* 3.2 9.7 - - - +
254A HIS* 1.3 78.1 - - - +
256A LYS* 1.3 58.8 + - - +
----------------------------------------------------------
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