Contacts of the helix formed by residues 250 - 261 (chain A) in PDB entry 1X1O
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 THR 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 3.3 11.7 - - - -
248A ASN 3.8 0.8 + - - +
249A MET* 1.3 79.7 - - - +
251A LEU* 1.3 65.1 + - - +
252A GLU* 3.5 8.2 + - - +
253A ARG* 3.1 48.1 + - - +
254A ALA* 2.9 22.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
120A LEU* 5.2 4.5 - - + -
123A ALA* 3.7 34.1 - - + +
124A TYR* 3.6 45.4 + - + +
127A ALA* 4.1 11.5 - - + +
250A THR* 1.3 74.8 - - - +
252A GLU* 1.3 63.2 + - - +
254A ALA* 3.8 1.6 - - - +
255A LYS* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 3.2 8.0 + - - +
251A LEU* 1.3 79.2 - - - +
253A ARG* 1.3 61.8 + - + +
255A LYS* 3.3 8.0 + - - +
256A ALA* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 5.5 0.9 - - - +
247A GLY 5.1 1.8 - - - -
248A ASN* 2.7 49.9 + - - +
249A MET* 4.0 13.4 - - + +
250A THR* 3.1 32.7 + - - +
252A GLU* 1.3 79.0 - - + +
254A ALA* 1.3 59.6 + - - +
256A ALA* 3.3 6.7 + - - +
257A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 3.7 26.9 - - + -
127A ALA* 5.4 0.4 - - + -
128A LEU* 3.6 13.5 - - + +
249A MET* 3.7 10.9 - - - -
250A THR 2.9 16.6 + - - +
251A LEU 3.8 3.1 - - - +
253A ARG* 1.3 76.2 - - - +
255A LYS* 1.3 58.2 + - - +
257A ALA* 3.5 2.5 + - - +
258A ALA* 3.0 28.4 + - - +
265A VAL* 3.9 22.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
127A ALA* 3.4 33.2 - - + +
128A LEU* 4.2 1.0 - - - +
251A LEU 3.0 18.6 + - - +
252A GLU* 3.6 7.0 - - - +
253A ARG 3.2 0.2 - - - -
254A ALA* 1.3 75.6 - - - +
256A ALA* 1.3 61.2 + - - +
258A ALA* 3.3 4.3 + - - +
259A GLU* 2.8 70.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.0 30.9 - - + +
230A LEU* 6.0 0.4 - - + -
252A GLU* 2.9 19.0 + - + +
253A ARG* 3.6 8.1 - - - +
255A LYS* 1.3 76.5 - - - +
257A ALA* 1.3 56.7 + - - +
259A GLU* 3.2 11.1 + - - +
260A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.6 29.3 - - + +
245A ALA* 4.0 21.3 - - + -
249A MET* 4.8 4.0 - - + -
253A ARG 2.9 16.8 + - - +
254A ALA* 3.8 5.8 - - - +
256A ALA* 1.3 75.9 - - - +
258A ALA* 1.3 63.9 + - - +
260A ALA* 3.0 13.9 + - - +
261A GLY 3.2 8.7 + - - -
262A VAL* 3.4 15.8 + - + +
265A VAL* 4.3 4.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
127A ALA 5.4 0.2 - - - +
128A LEU* 3.6 27.1 - - + -
131A THR* 3.6 22.2 - - + +
132A LYS* 2.8 26.7 + - - +
133A ALA* 3.8 9.0 - - + -
254A ALA 3.0 17.5 + - - +
255A LYS* 3.5 5.6 - - - +
256A ALA 3.2 0.2 - - - -
257A ALA* 1.3 77.2 - - - +
259A GLU* 1.3 57.9 + - - +
261A GLY* 3.0 10.2 + - - -
262A VAL* 4.1 3.3 - - - +
265A VAL* 4.6 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 4.3 16.6 - - + +
255A LYS* 2.8 61.8 + - + +
256A ALA* 3.2 8.9 + - - +
258A ALA* 1.3 76.0 - - - +
260A ALA* 1.3 60.9 + - - +
261A GLY* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.4 7.6 - - + -
230A LEU* 4.5 7.4 - - + -
231A ARG* 4.1 39.7 - - + +
234A VAL* 3.6 20.6 - - + +
256A ALA 2.9 13.8 + - - +
257A ALA* 3.0 16.1 + - - +
259A GLU* 1.3 77.7 - - - +
261A GLY* 1.3 58.2 + - - +
262A VAL* 3.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 3.6 13.8 - - - -
234A VAL* 3.8 20.6 - - - +
243A LEU* 5.6 0.5 - - - +
258A ALA 3.0 11.4 + - - -
259A GLU 3.1 1.5 - - - -
260A ALA* 1.3 81.3 - - - +
262A VAL* 1.3 67.7 + - - +
263A ASP* 3.9 6.1 + - - +
----------------------------------------------------------
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