Contacts of the helix formed by residues 240 - 251 (chain A) in PDB entry 2XIK
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
----------------------------------------------------------
114A GLU* 2.6 35.5 + - - -
239A HIS* 1.3 74.7 - - - +
241A LYS* 1.4 59.9 + - - +
242A PRO* 3.4 17.6 - - - +
243A PHE* 3.1 11.3 + - - +
244A LYS* 3.0 25.2 + - - +
269A PHE* 4.5 2.1 - - - -
272A ARG* 5.2 5.6 + - - -
273A TYR* 4.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A HIS 3.8 1.0 + - - -
240A SER* 1.4 69.8 - - - +
242A PRO* 1.4 64.6 - - + +
244A LYS* 3.2 12.5 + - + +
245A GLU* 2.9 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A SER* 3.4 16.6 - - - +
241A LYS* 1.4 91.5 - - + +
243A PHE* 1.4 54.3 + - - +
245A GLU* 3.5 15.2 + - - +
246A PHE* 3.1 21.0 + - - +
267A HIS* 3.5 4.7 - - + -
268A LYS* 4.6 7.4 - - + -
269A PHE* 3.3 36.1 - - + +
272A ARG* 3.9 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.7 24.0 - - + +
117A ILE* 3.7 28.7 - - + -
121A LEU* 4.4 0.9 - - + -
205A ALA* 3.5 31.0 - - + -
209A ALA* 3.6 23.1 - - + -
235A LEU* 3.5 13.2 - - + -
239A HIS* 4.1 6.5 - - + -
240A SER* 3.1 23.0 + - - +
242A PRO* 1.4 74.4 - - - +
244A LYS* 1.3 66.0 + - - +
246A PHE* 3.3 2.6 + - + +
247A VAL* 3.2 37.1 + - + +
269A PHE* 3.6 34.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 3.5 45.6 + - + +
236A GLU* 5.1 0.4 - - - +
237A GLY 2.9 33.3 + - - +
239A HIS* 3.4 25.7 + - - +
240A SER 3.0 12.6 + - - +
241A LYS* 3.6 12.1 - - + +
243A PHE* 1.3 77.2 - - - +
245A GLU* 1.4 55.7 + - + +
247A VAL* 3.6 3.3 + - - +
248A GLU* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LYS* 2.9 39.5 + - + +
242A PRO* 3.6 16.7 - - - +
243A PHE 3.2 0.2 - - - -
244A LYS* 1.4 74.6 - - + +
246A PHE* 1.3 58.3 + - - +
248A GLU* 3.4 16.7 + - - +
249A ALA* 3.0 28.6 + - - +
267A HIS* 3.9 13.5 + - + +
268A LYS* 5.6 3.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
121A LEU* 3.7 27.1 - - + -
125A LEU* 4.1 12.6 - - + -
201A LEU* 4.0 24.2 - - + -
205A ALA* 4.3 11.7 - - + -
242A PRO 3.1 14.1 + - - +
243A PHE* 3.5 9.0 - + - +
245A GLU* 1.3 74.6 - - - +
247A VAL* 1.3 68.0 + - + +
249A ALA* 3.3 5.4 + - - +
250A CYS* 3.2 37.5 + - - -
264A LEU* 3.8 19.2 - - + +
267A HIS* 3.6 32.0 - + + -
269A PHE* 4.0 14.6 - + + -
270A ILE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLY* 4.3 2.9 - - - +
205A ALA* 3.8 27.4 - - + -
206A ILE* 3.8 32.5 - - + +
233A PRO 4.9 0.2 - - - +
234A THR* 4.6 2.5 - - - -
235A LEU* 4.0 24.7 - - + +
243A PHE* 3.2 28.1 + - + +
244A LYS 3.8 4.5 - - - +
246A PHE* 1.3 78.1 - - + +
248A GLU* 1.3 57.8 + - - +
250A CYS* 3.1 7.0 + - - +
251A LEU* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PRO 5.9 1.6 - - - -
234A THR* 6.1 4.6 - - + +
244A LYS 3.1 18.4 + - - +
245A GLU* 3.6 15.3 - - - +
246A PHE 3.4 0.2 - - - -
247A VAL* 1.3 78.0 - - - +
249A ALA* 1.3 64.2 + - - +
251A LEU* 3.5 19.8 + - - +
252A ASN* 4.0 5.4 + - - +
----------------------------------------------------------
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 GLU 3.0 14.3 + - - +
246A PHE* 3.4 12.8 - - - +
247A VAL 3.3 0.2 - - - -
248A GLU* 1.3 76.7 - - - +
250A CYS* 1.3 62.3 + - - +
252A ASN* 4.1 7.3 + - - +
257A PHE 4.4 2.4 - - - +
258A ARG* 3.9 6.8 - - - -
259A PRO* 3.4 33.7 - - + +
264A LEU* 4.5 6.7 - - + -
267A HIS* 4.7 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.5 27.1 - - - +
199A TRP* 3.7 8.5 + - - -
201A LEU* 4.1 5.6 - - - -
202A GLY* 3.5 19.7 - - - -
246A PHE* 3.2 32.1 + - - -
247A VAL 3.1 4.8 + - - +
249A ALA* 1.3 79.6 - - - +
251A LEU* 1.3 58.0 + - - +
252A ASN 3.3 5.3 + - - -
258A ARG* 3.3 22.7 - - - -
264A LEU* 3.7 30.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
199A TRP* 3.2 55.2 - - + +
202A GLY* 3.9 10.1 - - - +
203A ILE* 3.9 15.9 - - + -
206A ILE* 3.7 25.8 - - + -
232A PRO* 3.1 27.7 - - + +
233A PRO* 3.5 29.8 - - + +
247A VAL* 2.9 22.5 + - + +
248A GLU* 3.7 10.3 - - - +
249A ALA 3.5 0.6 - - - -
250A CYS* 1.3 74.1 - - - +
252A ASN* 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