Contacts of the helix formed by residues 255 - 266 (chain A) in PDB entry 1EUB
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 PRO 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLY 3.1 13.7 - - - +
238A ALA* 3.1 4.7 - - - -
239A LEU* 2.9 35.0 - - + +
241A PHE* 4.5 6.3 - - + -
246A TYR* 3.2 34.3 - - + +
253A MET* 3.1 5.8 - - - -
254A LEU* 1.3 95.2 - - + +
256A ASP* 1.3 65.6 + - - +
257A ASP 2.9 4.5 + - - -
258A ASP* 2.3 34.4 + - - +
259A VAL* 3.1 3.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLY 3.6 0.4 + - - +
253A MET* 2.3 56.0 + - - +
254A LEU* 2.6 24.9 + - - +
255A PRO* 1.3 71.6 - - - +
257A ASP* 1.3 65.8 + - - +
259A VAL* 2.8 10.2 + - + -
260A GLN* 2.7 33.4 + - + +
261A GLY 3.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 3.5 13.2 + - - +
234A LYS* 3.7 3.6 + - - -
236A PRO* 2.7 45.6 - - - +
237A GLY 3.1 8.2 + - - +
238A ALA* 2.8 25.6 - - + -
255A PRO 2.9 0.2 + - - -
256A ASP* 1.3 81.0 - - - +
258A ASP* 1.3 54.8 + - - +
260A GLN* 5.2 3.6 - - - -
261A GLY* 2.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TRP* 4.7 9.6 - - + -
148A VAL* 4.7 5.5 - - - +
233A SER* 4.4 4.0 - - - -
238A ALA* 3.2 4.9 - - + +
239A LEU* 3.4 40.3 - - + +
240A MET* 4.0 13.9 - - + -
255A PRO* 2.3 39.1 + - - +
257A ASP* 1.3 78.1 - - - +
259A VAL* 1.3 62.9 + - - +
262A ILE* 2.6 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 3.8 36.9 - - + +
246A TYR* 5.9 0.4 - - - +
253A MET* 3.6 43.3 - - + -
255A PRO* 3.3 15.3 - - + +
256A ASP* 2.8 11.1 + - + +
258A ASP* 1.3 82.1 - - - +
260A GLN* 1.3 62.3 + - + +
262A ILE* 2.6 26.3 - - - +
263A GLN* 2.8 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASP* 2.7 19.4 + - + +
257A ASP* 5.0 3.5 - - - +
259A VAL* 1.3 77.0 - - + +
261A GLY* 1.3 74.6 + - - +
263A GLN* 3.5 20.2 - - - +
264A SER* 2.8 34.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
112A LYS* 4.2 5.4 - - - -
233A SER* 5.6 2.0 - - - -
257A ASP 2.8 25.4 + - - -
260A GLN* 1.3 90.6 + - - +
262A ILE* 1.3 59.1 + - - +
264A SER* 3.8 2.5 - - - -
265A LEU* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 3.3 29.4 - - - +
145A TRP* 3.2 38.4 - - + -
148A VAL* 3.6 19.5 - - + -
149A THR* 3.0 25.5 + - + -
225A GLY 5.6 0.4 - - - +
233A SER* 5.1 2.0 - - - +
240A MET* 5.4 5.2 - - + -
257A ASP 5.1 0.2 - - - +
258A ASP* 2.6 45.3 - - + +
259A VAL 2.6 21.8 - - - +
261A GLY* 1.3 70.1 - - - +
263A GLN* 1.3 68.2 + - - +
264A SER 3.0 5.4 - - - -
266A TYR* 2.9 28.1 + - + +
267A GLY 3.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL 2.8 28.3 - - - +
149A THR* 3.4 9.1 + - - -
150A PRO* 5.1 5.9 - - + +
259A VAL* 2.8 14.8 - - + +
260A GLN* 2.9 21.4 + - - +
262A ILE* 1.3 83.1 - - - +
264A SER* 1.3 69.7 + - - +
267A GLY* 3.8 12.8 - - - -
268A PRO* 4.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN* 2.8 27.5 + - - -
261A GLY* 3.8 2.0 - - - -
263A GLN* 1.3 88.7 - - - +
265A LEU* 1.3 74.0 + - - +
267A GLY 4.0 1.1 - - - -
268A PRO* 3.8 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 5.2 12.6 - - + -
112A LYS* 2.9 74.9 - - + +
113A TRP* 4.6 1.6 + - - -
261A GLY 3.0 10.7 + - - +
264A SER* 1.3 93.5 - - - +
266A TYR* 1.3 62.0 + - - +
267A GLY 3.4 0.3 + - - -
268A PRO 3.9 10.9 - - - +
269A GLY* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU 4.4 5.5 + - - -
112A LYS* 3.5 26.2 - - + -
113A TRP 5.4 0.2 - - - -
115A LYS* 2.8 52.4 - - + +
116A MET* 4.3 3.6 - - - -
145A TRP* 3.9 18.4 - + - -
149A THR* 4.2 0.4 - - - +
151A LEU* 3.1 29.7 - - + +
191A PRO* 4.8 2.9 - - - +
228A LEU* 2.3 66.8 + - + +
229A GLY* 3.4 7.4 - - - -
262A ILE* 2.9 22.7 + - + +
265A LEU* 1.3 75.1 - - - +
267A GLY* 1.3 71.2 + - - +
268A PRO 4.5 1.5 - - - -
269A GLY* 5.4 0.4 - - - -
----------------------------------------------------------
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