Contacts of the helix formed by residues 250 - 259 (chain E) in PDB entry 1Y8R
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 ASP 250 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E THR* 3.8 18.6 + - - +
248E GLY 3.4 0.2 - - - -
249E TYR* 1.3 74.0 - - - +
251E PRO* 1.3 77.0 - - - +
252E VAL* 3.4 14.6 + - - +
253E LYS* 2.7 49.3 + - + +
254E LEU* 3.0 28.1 + - - +
330E ARG* 4.1 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E TYR 3.4 8.0 - - - +
250E ASP* 1.3 91.1 - - - +
252E VAL* 1.3 55.5 + - + +
254E LEU* 3.4 1.7 - - - +
255E PHE* 2.7 38.4 + - - +
284E TRP* 5.8 3.4 - - + -
322E PHE* 4.5 2.6 - - + -
323E SER* 3.7 35.0 - - - +
326E ILE* 4.2 18.4 - - + -
327E GLU* 3.6 37.7 - - + +
330E ARG* 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E ASP* 3.3 14.5 - - - +
251E PRO* 1.3 79.7 - - + +
253E LYS* 1.3 60.0 + - + +
255E PHE* 3.6 5.1 - - - +
256E THR* 2.7 40.4 + - + +
284E TRP* 4.4 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E TRP* 4.4 11.8 - - + -
247E THR* 3.7 42.0 - - + +
250E ASP* 2.7 36.7 + - + +
252E VAL* 1.3 73.5 - - + +
254E LEU* 1.3 61.9 + - - +
256E THR* 3.4 6.0 + - - -
257E LYS* 3.2 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E LEU* 4.0 25.4 - - + -
240E THR* 6.0 2.9 - - + -
243E TRP* 5.1 8.7 - - + -
244E ALA* 4.1 12.3 - - + -
247E THR* 4.8 5.8 - - - +
249E TYR* 3.8 18.2 - - + -
250E ASP 3.0 38.0 + - - +
251E PRO* 3.4 3.8 - - + +
253E LYS* 1.3 73.6 - - - +
255E PHE* 1.3 70.0 + - - +
257E LYS* 2.9 15.6 + - + +
258E LEU* 2.9 32.1 + - + +
322E PHE* 4.6 3.8 - - + -
326E ILE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E PRO 2.7 21.2 + - - +
252E VAL* 3.6 4.7 - - - +
254E LEU* 1.3 70.2 - - - +
256E THR* 1.3 62.7 + - - +
257E LYS 2.8 3.8 + - - -
258E LEU* 2.8 2.6 + - - -
259E PHE* 2.8 61.0 + + + -
282E LEU* 3.7 30.5 - - + -
283E ASP 3.7 0.9 - - - -
284E TRP* 3.4 51.4 - + + -
287E VAL* 4.1 11.7 - - + -
319E ALA* 4.1 16.6 - - + -
322E PHE* 3.7 26.1 - + + -
361E LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E VAL* 2.7 23.6 + - + +
253E LYS* 3.4 8.0 + - - -
255E PHE* 1.3 81.4 - - + +
257E LYS* 1.3 56.4 + - - +
260E LYS* 3.0 32.1 - - + +
261E ASP* 2.8 34.4 + - - -
283E ASP* 4.4 6.5 - - - +
284E TRP* 4.1 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 257 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E SER* 2.6 30.5 + - - -
240E THR* 5.2 8.8 + - + +
243E TRP* 3.3 45.3 - - + -
253E LYS 3.2 18.9 + - - +
254E LEU* 2.9 7.0 + - + +
255E PHE 2.8 0.2 + - - -
256E THR* 1.3 78.7 - - - +
258E LEU* 1.3 66.7 + - + +
261E ASP* 3.7 16.4 - - + +
262E ASP* 2.7 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E TRP* 4.0 26.1 - - + -
192E LEU* 4.0 41.7 - - + -
196E LEU* 5.2 0.4 - - + -
206E VAL* 4.7 11.2 - - + -
207E SER* 5.5 0.4 - - - +
240E THR* 5.5 4.3 - - + -
254E LEU* 2.9 31.4 + - + +
255E PHE 2.8 3.9 + - - +
257E LYS* 1.3 89.5 - - + +
259E PHE* 1.3 72.7 + - + +
260E LYS 3.5 0.9 - - - -
262E ASP* 3.7 19.5 - - - +
263E ILE* 3.5 18.4 - - - +
322E PHE* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E TRP* 4.3 23.3 - + - -
192E LEU* 5.3 0.4 - - + -
255E PHE* 2.8 51.8 + + + +
258E LEU* 1.3 80.9 - - + +
260E LYS* 1.3 53.0 + - - +
263E ILE* 3.4 14.4 - - - +
281E PRO 3.4 2.1 - - - -
282E LEU* 2.6 35.6 + - + +
322E PHE* 3.5 27.6 - + - -
358E ALA* 4.0 14.4 - - + -
361E LEU* 3.3 42.8 - - + -
362E ARG* 3.9 9.6 - - + -
365E ILE* 3.5 24.4 - - + +
----------------------------------------------------------
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