Contacts of the helix formed by residues 249 - 256 (chain Z) in PDB entry 5V09
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 249 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247Z ASN* 3.1 13.5 + - - +
248Z PRO* 1.3 75.0 - - - +
250Z ILE* 1.3 68.9 + - - +
251Z VAL* 3.3 20.7 + - - +
252Z LYS* 3.3 44.7 + - + +
253Z VAL* 3.4 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217Z TYR* 3.9 39.7 - - + +
221Z LEU* 5.0 3.6 - - + -
242Z LEU* 3.9 28.9 - - + -
248Z PRO 3.3 5.3 + - - +
249Z ASP* 1.3 76.5 + - - +
251Z VAL* 1.3 69.2 + - + +
253Z VAL* 3.3 12.9 + - + -
254Z ILE* 2.9 48.0 + - + +
275Z PHE* 3.8 26.7 - - + -
279Z ASN* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249Z ASP* 3.2 16.3 - - - +
250Z ILE* 1.3 87.0 - - + +
252Z LYS* 1.3 60.3 + - + +
254Z ILE* 3.3 9.5 + - + +
255Z LYS* 2.9 54.6 + - - +
272Z ILE* 3.8 24.4 - - + +
275Z PHE* 6.1 1.3 - - + -
276Z ILE* 5.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247Z ASN* 4.5 16.8 + - - +
249Z ASP* 3.3 37.6 + - + +
250Z ILE 3.3 0.4 - - - -
251Z VAL* 1.3 78.1 - - + +
253Z VAL* 1.3 57.6 + - - +
255Z LYS* 3.2 13.5 + - + +
256Z LYS* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241Z VAL* 3.6 28.3 - - + +
242Z LEU* 4.9 4.0 - - + -
245Z ALA* 3.8 14.4 - - + +
247Z ASN* 3.2 37.5 - - + +
248Z PRO* 5.2 0.9 - - + -
249Z ASP 3.4 9.4 - - - +
250Z ILE* 3.5 21.5 - - + +
251Z VAL 3.2 0.4 - - - -
252Z LYS* 1.3 76.3 - - - +
254Z ILE* 1.3 57.9 + - + +
256Z LYS 2.8 18.7 + - - -
257Z ILE* 2.9 13.7 + - - +
260Z TYR* 3.8 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221Z LEU* 4.1 16.4 - - + -
230Z LEU* 5.5 1.6 - - + -
241Z VAL* 6.0 0.4 - - - -
250Z ILE* 2.9 31.7 + - + +
251Z VAL* 3.6 7.6 - - - +
253Z VAL* 1.3 76.8 - - + +
255Z LYS* 1.3 61.1 + - - +
257Z ILE* 3.2 28.9 - - + +
267Z VAL* 3.9 7.9 - - + +
271Z TYR* 4.1 20.2 - - + -
272Z ILE* 3.7 24.5 - - + -
275Z PHE* 3.6 54.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251Z VAL* 2.9 37.7 + - + +
252Z LYS* 3.4 13.9 - - + +
254Z ILE* 1.3 77.7 - - - +
256Z LYS* 1.3 61.7 + - + +
257Z ILE* 3.4 1.5 + - - -
258Z GLY 5.0 1.4 + - - -
267Z VAL* 5.0 12.0 - - + +
269Z GLU* 4.8 11.0 + - - -
272Z ILE* 4.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247Z ASN* 6.2 1.1 - - - +
252Z LYS* 2.9 16.6 + - + +
253Z VAL 2.8 5.3 + - - -
255Z LYS* 1.3 80.3 - - + +
257Z ILE* 1.3 59.3 + - - +
258Z GLY 3.1 2.9 - - - -
259Z HIS* 2.8 49.7 + - + +
260Z TYR* 2.9 34.9 + - + +
----------------------------------------------------------
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