Contacts of the helix formed by residues 249 - 259 (chain B) in PDB entry 6HYI
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 ASN 249 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE 3.7 2.8 + - - +
248B LEU* 1.3 75.8 - - - +
250B THR* 1.3 65.6 + - - +
251B LYS* 3.3 9.1 + - - +
252B ASP* 2.8 38.1 + - - +
253B ILE* 2.9 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 6.6 0.2 - - + -
249B ASN* 1.3 76.2 - - - +
251B LYS* 1.3 65.4 + - - +
253B ILE* 3.3 8.9 + - + +
254B LYS* 3.2 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.3 9.2 + - - +
250B THR* 1.3 79.3 - - - +
252B ASP* 1.3 70.3 + - - +
254B LYS* 3.3 7.9 + - - +
255B VAL* 3.2 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.3 24.9 - - + +
249B ASN* 2.8 33.0 + - - +
251B LYS* 1.3 81.8 - - - +
253B ILE* 1.3 65.2 + - - +
255B VAL* 3.2 10.3 + - - +
256B VAL* 2.9 30.0 + - + +
343B LEU* 5.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 3.8 30.3 - - + +
239B LEU* 3.8 25.7 - - + +
240B THR* 4.3 15.0 - - + -
245B PHE* 3.7 33.4 - - + +
248B LEU* 3.9 21.8 - - + +
249B ASN 2.9 21.8 + - - +
250B THR* 3.3 8.5 + - - +
252B ASP* 1.3 74.7 - - - +
254B LYS* 1.3 58.8 + - - +
256B VAL* 3.3 5.7 + - - +
257B ALA* 2.8 27.0 + - - +
461B ARG* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TYR* 5.9 6.7 - - - -
232B MET* 3.7 31.5 - - + +
236B THR* 5.1 1.6 - - - +
250B THR* 3.2 13.5 + - + +
251B LYS* 3.6 10.3 - - - +
252B ASP 3.2 0.6 - - - -
253B ILE* 1.3 75.8 - - - +
255B VAL* 1.3 63.7 + - + +
257B ALA* 3.7 1.2 - - - +
258B GLY* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN* 5.3 4.5 - - - +
222B ALA* 3.6 28.8 - - + +
223B PRO 4.6 1.3 - - - +
224B TYR* 6.5 0.2 - - - -
251B LYS* 3.2 29.3 + - + +
252B ASP* 3.7 11.2 - - - +
254B LYS* 1.3 78.6 - - + +
256B VAL* 1.3 64.9 + - - +
258B GLY* 3.2 3.2 + - - -
259B ALA* 3.1 20.4 + - - +
343B LEU* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 4.0 15.9 - - + -
245B PHE* 4.0 14.1 - - + -
248B LEU* 4.1 11.0 - - + -
252B ASP 2.9 20.1 + - - +
253B ILE* 3.7 5.4 - - - +
255B VAL* 1.3 77.0 - - - +
257B ALA* 1.3 63.9 + - - +
259B ALA* 3.0 16.9 + - - +
260B MET* 3.4 16.2 + - - +
335B LEU* 4.0 24.5 - - + -
339B THR* 4.5 3.6 - - + -
343B LEU* 4.2 19.1 - - + -
344B VAL* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LYS* 3.4 15.4 - - - -
232B MET* 3.4 30.1 - - + -
235B ILE* 3.6 31.1 - - + +
236B THR* 4.2 5.6 - - - +
239B LEU* 3.9 6.9 - - + +
253B ILE 2.8 16.2 + - - +
254B LYS 3.7 0.2 - - - +
256B VAL* 1.3 76.2 - - - +
258B GLY* 1.3 62.0 + - - +
260B MET* 3.1 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PRO 4.0 4.3 - - - -
224B TYR* 3.7 26.0 - - - -
225B PHE 2.9 26.5 + - - +
227B LYS* 3.1 16.8 + - - -
232B MET* 4.2 2.2 - - - -
254B LYS 2.9 15.7 + - - -
255B VAL* 3.2 4.4 + - - -
257B ALA* 1.3 76.9 - - - +
259B ALA* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ALA* 4.3 1.3 - - + -
223B PRO* 3.2 35.5 + - + +
225B PHE* 3.5 16.6 - - - -
255B VAL 3.1 9.5 + - - +
256B VAL 3.0 12.1 + - - +
258B GLY* 1.3 76.8 - - - +
260B MET* 1.3 62.6 + - - +
261B GLN* 3.9 1.2 + - - +
334B VAL 4.0 3.8 - - - +
335B LEU* 3.7 18.6 - - + +
336B ASP* 4.6 3.2 + - - +
339B THR* 4.2 11.2 - - + -
----------------------------------------------------------
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