Contacts of the helix formed by residues 256 - 264 (chain B) in PDB entry 3UAJ
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 GLN 256 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY* 3.0 30.6 + - - +
262A SER* 3.2 21.6 + - - -
61B ILE* 2.9 40.8 + - + +
218B LEU* 3.7 24.8 - - + +
237B MET* 4.7 3.6 - - + -
253B LEU* 3.4 27.8 - - + +
255B SER* 1.3 69.8 + - - +
257B GLU* 1.4 62.3 + - - +
258B GLY 3.4 2.5 - - - -
259B ALA* 3.3 18.8 + - + +
260B MET* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLY* 5.7 3.0 - - - -
255A SER* 5.8 2.9 - - - +
61B ILE* 4.1 9.9 - - + +
62B GLU* 5.6 1.2 - - - +
201B MET* 3.7 24.7 - - + +
202B LYS* 5.4 11.1 - - - +
255B SER* 3.2 18.9 + - - +
256B GLN* 1.4 77.3 - - - +
258B GLY* 1.3 57.3 + - - +
260B MET* 3.5 4.7 + - - +
261B HIS* 2.8 50.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU 3.5 14.4 - - - -
254A GLY* 5.4 0.2 - - - -
255A SER 3.3 22.3 + - - +
256A GLN* 2.9 29.2 - - - +
259A ALA* 4.7 0.2 - - - -
256B GLN 3.4 0.2 - - - -
257B GLU* 1.3 76.8 - - - +
259B ALA* 1.4 63.3 + - - +
260B MET 3.3 0.2 - - - -
261B HIS* 3.5 3.2 + - - +
262B SER* 3.4 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER 4.6 0.8 + - - -
259A ALA* 3.8 33.9 - - + +
262A SER* 5.5 0.2 - - - +
256B GLN* 3.3 33.7 + - + +
257B GLU 3.3 0.4 - - - -
258B GLY* 1.4 77.0 - - - +
260B MET* 1.3 62.6 + - + +
262B SER* 3.8 6.8 + - - -
263B ALA* 3.6 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 4.5 7.0 - - + -
125B ILE* 3.9 11.4 - - + -
199B MET* 3.7 30.7 - - + -
201B MET* 3.9 20.2 - - + -
212B TRP* 3.7 21.8 - - + -
216B LEU* 4.1 26.9 - - + -
218B LEU* 4.8 11.2 - - + -
256B GLN* 3.2 17.0 + - - +
257B GLU 3.8 6.7 - - - +
258B GLY 3.3 0.4 - - - -
259B ALA* 1.3 76.7 - - - +
261B HIS* 1.4 52.9 + - - +
263B ALA* 3.0 8.1 + - - +
264B LEU* 2.8 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A VAL 4.9 6.0 + - - -
253A LEU* 2.8 48.6 + - + +
254A GLY* 5.0 2.9 - - - -
201B MET* 4.5 11.2 - - - -
206B TRP* 4.5 23.8 - + - -
257B GLU* 2.8 46.8 + - + -
258B GLY 3.5 6.5 + - - +
260B MET* 1.4 75.3 - - - +
262B SER* 1.3 59.9 + - - +
264B LEU* 3.5 14.0 + - + +
265B ALA* 3.5 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.6 13.4 - - - +
256A GLN* 3.1 28.1 + - - -
259A ALA* 6.1 0.7 - - - -
258B GLY 3.4 3.7 + - - -
259B ALA* 3.8 10.3 - - - -
260B MET 3.2 0.6 - - - -
261B HIS* 1.3 76.4 - - - +
263B ALA* 1.4 58.8 + - - +
265B ALA* 3.5 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TRP* 3.8 31.9 - - + +
259B ALA 3.6 10.3 + - - +
260B MET* 3.0 11.5 + - - +
262B SER* 1.4 75.9 - - - +
264B LEU* 1.4 58.6 + - - +
265B ALA 3.3 5.9 + - - -
266B GLY* 4.5 3.8 + - - -
267B ALA* 4.9 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B MET* 3.7 25.4 - - + -
201B MET* 4.8 3.8 - - - -
206B TRP* 3.6 60.0 + - + +
208B VAL* 3.7 22.0 - - + -
212B TRP* 4.7 8.3 - - + -
260B MET* 2.8 33.8 + - + +
261B HIS* 3.5 12.1 + - + +
262B SER 3.4 0.4 - - - -
263B ALA* 1.4 76.1 - - - +
265B ALA* 1.4 60.0 + - - +
266B GLY 3.3 2.9 - - - -
267B ALA* 3.3 22.9 - - + +
----------------------------------------------------------
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