Contacts of the helix formed by residues 221 - 230 (chain H) in PDB entry 5GJQ
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 221 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H VAL* 5.5 0.5 - - - +
219H GLY 3.6 0.2 - - - -
220H THR* 1.3 81.7 - - - +
222H LYS* 1.3 66.7 + - - +
223H THR 3.3 2.2 - - - -
224H LEU* 3.5 20.6 - - - +
225H CYS* 3.3 26.9 + - - -
343H PHE* 3.6 4.0 - - - -
501H ADP 3.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H LEU* 4.0 19.7 - - + +
215H PHE* 3.9 12.8 - - - +
216H GLY 3.1 14.5 + - - +
217H PRO 3.3 20.8 + - - -
220H THR* 4.0 3.8 - - - -
221H GLY* 1.3 78.6 - - - +
223H THR* 1.3 61.8 + - - +
225H CYS* 3.3 4.7 + - - +
226H ALA* 3.2 19.1 + - - +
273H PHE* 5.0 3.1 - - - -
320H ALA* 4.9 7.4 - - + -
321H THR 2.7 32.9 + - - +
322H ASN* 3.0 23.4 - - - +
343H PHE* 3.4 31.2 - - + -
501H ADP 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H LYS* 1.3 77.3 - - - +
224H LEU* 1.3 52.5 + - - +
226H ALA* 3.4 6.8 + - - +
227H ARG* 2.5 43.5 + - - +
273H PHE* 5.4 0.9 - - - -
275H ASP* 2.8 26.3 + - - +
320H ALA* 5.3 0.3 - - - +
501H ADP 2.8 29.6 + - - +
314I ASN* 5.4 0.3 + - - -
317I ASP* 5.1 3.5 + - - -
318I GLY* 3.8 10.5 - - - -
319I PHE* 3.2 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H VAL* 2.8 33.3 - - + +
176H ASP* 4.0 7.9 - - + +
177H VAL* 4.9 7.9 - - + -
221H GLY* 3.5 12.9 + - - +
223H THR* 1.3 75.3 - - - +
225H CYS* 1.3 55.6 + - - +
227H ARG* 2.9 31.8 - - - +
228H ALA* 2.1 42.7 + - - +
501H ADP 2.8 69.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 225 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H TYR* 6.3 0.2 - - - -
177H VAL* 4.2 24.2 - - - -
180H CYS* 5.7 0.9 - - - -
183H GLN* 5.7 0.7 - - - -
184H ILE* 4.5 7.9 - - - -
187H LEU* 3.7 24.2 - - + -
214H LEU* 3.9 8.5 - - + -
221H GLY 3.3 14.9 + - - +
222H LYS 3.3 9.1 + - - +
224H LEU* 1.3 80.7 - - - +
226H ALA* 1.3 50.4 + - - +
228H ALA* 3.6 7.2 - - - -
229H VAL* 2.3 45.4 + - - +
318H LEU* 5.6 0.9 - - - -
343H PHE* 3.7 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H LEU* 5.4 0.6 - - - +
222H LYS 3.2 9.3 + - - +
223H THR* 3.5 5.6 - - - +
225H CYS* 1.3 76.0 - - - +
227H ARG* 1.3 54.4 + - - +
229H VAL* 3.1 1.9 + - - -
230H ALA* 2.8 28.1 + - - +
237H PHE* 3.3 19.6 - - + -
273H PHE* 3.6 35.8 - - + -
318H LEU* 5.0 2.8 - - - +
319I PHE* 3.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H PRO* 3.3 28.0 - - + +
171H ASP 5.2 1.0 + - - +
172H VAL* 3.2 30.0 - - + +
223H THR* 2.5 53.1 + - - +
224H LEU* 2.9 32.4 - - - +
226H ALA* 1.3 69.6 - - - +
228H ALA* 1.3 64.3 + - - +
231H ASN* 3.2 23.6 + - - +
501H ADP 4.9 9.7 + - - -
318I GLY* 5.7 0.9 - - - -
319I PHE* 3.6 34.0 + - + +
320I ASP 4.1 15.2 + - - -
321I SER* 4.8 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H VAL* 2.9 24.6 - - + +
173H THR* 4.8 0.6 - - - +
174H TYR* 4.7 18.5 - - + -
177H VAL* 4.5 13.9 - - + -
224H LEU 2.1 31.1 + - - +
225H CYS* 3.5 11.7 - - - +
227H ARG* 1.3 71.3 - - - +
229H VAL* 1.3 67.3 + - + +
231H ASN* 3.0 12.5 + - - +
232H ARG* 3.1 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H TYR* 4.3 17.3 - - + +
187H LEU* 4.2 21.1 - - + -
191H VAL* 3.1 37.9 - - + -
192H GLU* 5.2 4.3 - - - +
225H CYS* 2.3 38.0 + - - +
226H ALA* 3.8 3.6 - - - +
228H ALA* 1.3 78.4 - - + +
230H ALA* 1.3 54.4 + - - +
231H ASN 2.6 11.8 + - - -
232H ARG 3.4 0.8 - - - -
233H THR* 2.8 29.7 + - - +
237H PHE* 4.2 5.8 - - + -
271H LEU* 3.7 8.7 - - + -
318H LEU* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H VAL* 5.4 5.7 - - + +
169H LYS* 3.9 18.2 - - - +
170H PRO* 4.2 16.6 - - + -
226H ALA 2.8 16.1 + - - +
229H VAL* 1.3 71.9 - - - +
231H ASN* 1.3 60.9 + - - +
233H THR* 3.6 19.1 - - - +
237H PHE* 3.2 43.4 - - + +
319I PHE* 4.4 3.4 - - + -
----------------------------------------------------------
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