Contacts of the helix formed by residues 244 - 248 (chain B) in PDB entry 1U2X
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 GLY 244 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN* 3.4 26.5 + - - +
220B ILE* 3.9 20.0 - - - +
243B SER* 1.3 78.3 - - - +
245B TYR* 1.3 65.8 + - - +
246B GLN* 3.2 19.9 + - - -
247B GLY* 3.0 15.9 + - - -
1001B SO4 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.8 20.3 + + - -
220B ILE* 5.4 4.9 - - + -
242B PHE* 3.4 36.2 - - + +
243B SER* 3.4 10.3 - - - -
244B GLY* 1.3 78.6 - - - +
246B GLN* 1.3 58.1 + - - +
247B GLY 3.0 0.2 - - - -
248B LEU* 3.0 36.5 + - + +
262B LEU* 4.4 10.1 - - + -
265B ALA* 3.8 25.2 + - + +
269B ILE* 4.6 2.8 - - - +
281B VAL* 4.1 17.7 - - + -
282B GLU 5.7 0.7 - - - -
283B PHE* 6.3 0.4 - + - -
291B LEU* 4.5 0.3 - - - +
295B ILE* 3.5 34.7 - - + +
299B ILE* 3.8 42.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN* 3.5 5.7 - - - +
119B GLN* 2.8 24.8 + - - +
213B ARG* 3.7 11.3 + - - -
244B GLY* 3.2 21.3 + - - -
245B TYR* 1.3 74.4 + - - +
247B GLY* 1.3 62.3 + - - +
248B LEU 3.2 5.1 + - - +
282B GLU 5.2 1.7 - - - +
284B ALA* 3.6 23.3 + - + +
285B SER 4.0 18.4 - - - +
286B VAL* 4.0 16.8 - - + +
291B LEU* 4.4 5.0 - - - +
295B ILE* 4.0 10.4 - - - +
1001B SO4 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LYS* 5.5 8.7 - - - -
213B ARG* 3.7 13.5 + - - -
217B ILE 5.9 0.4 - - - -
218B SER* 3.3 24.1 - - - -
220B ILE* 4.1 11.7 - - - -
244B GLY 3.0 13.6 + - - -
246B GLN* 1.3 78.9 - - - +
248B LEU* 1.3 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ARG* 4.1 7.3 + - - -
218B SER 3.7 7.9 - - - +
220B ILE* 3.8 22.9 - - + +
245B TYR* 3.0 29.9 + - + +
246B GLN 3.2 3.2 - - - +
247B GLY* 1.3 83.8 - - - +
249B ARG* 1.3 62.7 + - - +
252B TYR* 3.5 16.6 - - - +
258B ALA* 4.5 5.2 - - + +
261B TYR* 3.6 28.5 - - + -
262B LEU* 3.9 34.1 - - + -
291B LEU* 3.4 32.6 - - + +
295B ILE* 5.1 0.7 - - + -
----------------------------------------------------------
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