Contacts of the helix formed by residues 303 - 308 (chain E) in PDB entry 1E81
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 303 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ASP 3.2 10.3 - - - -
218E THR* 3.2 17.5 - - - -
220E LEU 3.2 14.8 + - - -
221E LEU* 4.4 1.4 - - - +
301E ILE 3.2 8.7 + - - -
302E PHE* 1.3 76.4 - - - +
304E ASP* 1.3 67.2 + - - -
305E VAL 3.1 3.6 - - - -
306E ALA* 2.9 13.6 + - - +
307E LEU* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 304 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP 4.4 4.4 - - - +
12E ASP 4.1 8.8 - - - +
13E ALA* 4.3 2.6 - - - -
14E TYR* 3.7 33.1 - - + -
155E LEU* 3.4 14.2 - - + +
216E THR* 2.6 35.3 - - - +
217E GLY 5.0 0.5 - - - -
218E THR 2.7 19.4 + - - +
219E THR* 3.4 16.7 + - - +
275E PHE* 6.3 0.2 - - + -
303E GLY* 1.3 69.9 - - - -
305E VAL* 1.3 63.3 + - - +
307E LEU* 4.4 1.6 - - - -
308E LYS* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E THR 3.0 23.1 + - - +
220E LEU* 3.5 10.8 - - - -
221E LEU* 4.0 23.1 - - + +
268E ILE* 3.6 29.5 - - + +
272E TYR* 4.1 15.8 - - - +
273E ILE* 4.5 9.4 - - + -
275E PHE* 3.4 32.3 - - + -
286E GLY* 3.8 9.2 - - - +
287E ILE* 5.1 0.2 - - + -
303E GLY 3.0 0.6 + - - -
304E ASP* 1.3 78.1 - - - +
306E ALA* 1.3 59.0 + - - +
308E LYS* 4.1 16.7 - - - +
309E ALA 4.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E LEU* 4.0 16.6 - - + -
259E PHE* 3.9 23.5 - - + -
268E ILE* 3.6 21.8 - - + -
302E PHE* 4.0 19.1 - - + -
303E GLY 2.9 8.0 + - - +
305E VAL* 1.3 77.7 - - - +
307E LEU* 1.3 66.9 + - + +
308E LYS 3.4 0.7 - - - -
309E ALA* 3.2 18.7 + - - +
310E ALA* 4.0 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E ALA* 5.1 3.6 - - + +
155E LEU* 4.5 9.9 - - + +
214E ALA* 4.4 16.2 - - + -
215E ASP 3.9 6.3 - - - +
216E THR* 3.5 42.6 - - + +
302E PHE* 3.5 24.2 - - + +
303E GLY 3.1 16.1 + - - +
304E ASP* 4.1 5.2 - - - +
306E ALA* 1.3 73.8 - - + +
308E LYS* 1.3 57.5 + - - +
309E ALA 3.0 5.4 - - - -
310E ALA* 2.8 30.8 + - - +
312E VAL* 3.9 25.2 - - + +
314E PHE* 4.8 3.8 - - + -
323E PHE* 4.1 16.4 - - + -
326E LYS* 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU 4.5 2.8 + - - -
11E ASP* 3.0 43.0 + - - +
14E TYR* 3.6 9.6 - - - +
155E LEU* 3.4 37.5 - - + +
156E GLY 4.4 3.1 - - - +
157E TYR* 3.7 27.2 + - - +
158E HIS* 5.5 0.4 - - - -
272E TYR* 3.7 32.4 + - + -
275E PHE* 4.5 12.3 - - - -
304E ASP* 2.9 28.5 + - + +
305E VAL* 4.1 5.8 - - - +
307E LEU* 1.3 75.4 - - - +
309E ALA* 1.3 57.1 + - - +
310E ALA 3.2 1.8 - - - -
326E LYS* 3.0 20.9 + - - +
----------------------------------------------------------
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