Contacts of the helix formed by residues 244 - 256 (chain O) 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 ASN 244 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239O ALA* 3.7 11.8 + - + +
242O SER* 3.2 6.5 + - - +
243O GLY* 1.3 73.4 - - - +
245O VAL* 1.3 68.9 + - - +
246O GLU* 4.2 10.1 - - - -
247O ARG* 3.6 28.0 - - + -
248O PHE* 3.2 22.2 + - - +
272O ILE* 4.6 1.1 - - - +
276O CYS* 4.1 0.9 - - - -
279O GLU* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O ASN* 1.3 74.2 - - - +
246O GLU* 1.3 59.3 + - - +
248O PHE* 3.6 2.4 - - - +
249O GLN* 2.9 28.4 + - + +
272O ILE* 3.9 20.8 - - + +
273O GLN* 5.0 4.3 - - + +
276O CYS* 2.8 34.3 - - + -
299O SER 3.0 11.0 - - - +
300O ALA* 3.2 35.9 - - + +
301O LYS* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O ASN* 4.2 12.8 - - - -
245O VAL* 1.3 80.1 - - - +
247O ARG* 1.3 76.9 + - + +
249O GLN* 2.9 25.1 - - - +
250O THR* 3.1 8.1 + - - -
299O SER 4.7 1.6 + - - +
301O LYS* 4.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239O ALA* 5.7 5.8 - - + -
244O ASN* 3.6 24.1 + - + -
245O VAL 3.4 0.4 - - - -
246O GLU* 1.3 82.9 - - + +
248O PHE* 1.3 63.6 + - - +
250O THR* 3.1 8.0 + - - -
251O LEU* 2.8 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205O LEU* 5.1 10.3 - - + -
236O THR* 4.2 29.8 - - - -
239O ALA* 4.7 15.5 - - + +
240O PHE* 5.3 1.1 - - + -
244O ASN 3.2 17.7 + - - +
245O VAL 3.6 2.2 - - - +
247O ARG* 1.3 77.7 - - - +
249O GLN* 1.3 61.8 + - - +
251O LEU* 2.5 33.9 + - + +
252O LYS* 2.9 33.8 + - + -
268O LEU* 4.4 22.4 - - + -
269O LEU* 5.2 4.9 - - + -
272O ILE* 2.8 52.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 249 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245O VAL* 2.9 17.3 + - + +
246O GLU* 2.9 18.8 + - - +
248O PHE* 1.3 84.8 - - - +
250O THR* 1.3 57.1 + - - +
252O LYS* 3.4 11.0 + - - +
253O THR* 3.7 9.4 + - - -
269O LEU* 6.5 1.1 - - + -
301O LYS* 6.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O GLU 3.1 7.1 + - - -
247O ARG* 3.9 7.0 - - - -
248O PHE 3.1 0.6 - - - -
249O GLN* 1.3 76.4 - - - +
251O LEU* 1.3 63.6 + - - +
252O LYS 3.2 1.7 + - - -
253O THR* 3.6 20.2 + - - -
254O ALA* 4.2 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235O ASP* 5.6 7.6 - - + +
236O THR* 5.7 6.2 + - - +
239O ALA* 5.3 7.0 - - + -
247O ARG* 2.8 16.8 + - + +
248O PHE* 2.5 32.0 + - + +
250O THR* 1.3 73.3 - - - +
252O LYS* 1.3 56.9 + - - -
254O ALA* 4.3 4.0 + - - +
255O TRP* 4.2 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248O PHE* 2.9 31.9 + - + +
249O GLN 3.9 8.1 - - - +
250O THR 3.2 0.2 - - - -
251O LEU* 1.3 75.3 - - - +
253O THR* 1.3 58.9 + - - +
254O ALA 3.1 2.7 - - - -
255O TRP* 5.3 1.3 - - - -
256O GLY* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249O GLN 3.7 6.8 + - - -
250O THR* 3.6 17.6 + - - -
251O LEU 3.5 0.4 - - - -
252O LYS* 1.3 78.9 - - - +
254O ALA* 1.3 62.5 + - - +
256O GLY* 3.9 4.2 + - - -
257O GLN* 4.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250O THR 4.2 5.5 + - - +
251O LEU 4.3 5.6 + - - +
252O LYS 3.1 0.4 + - - -
253O THR* 1.3 77.8 - - - +
255O TRP* 1.3 56.9 + - - +
256O GLY 2.6 14.7 + - - -
257O GLN* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 255 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232O TRP* 3.5 44.6 - - + -
251O LEU 4.2 12.0 + - - +
252O LYS* 3.7 2.3 + - - +
254O ALA* 1.3 76.5 - - - +
256O GLY* 1.3 64.0 + - - +
257O GLN 3.1 1.2 + - - -
258O GLN* 3.1 25.2 - - + +
261O LEU* 3.4 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252O LYS* 2.6 29.9 + - - +
253O THR 4.2 3.4 - - - -
254O ALA 2.6 5.4 + - - -
255O TRP* 1.3 71.6 - - - +
257O GLN* 1.3 53.7 + - - -
258O GLN 3.3 4.0 + - - -
259O PRO 4.3 0.3 - - - +
261O LEU* 3.6 23.2 - - - +
262O ALA* 3.7 15.6 + - - +
----------------------------------------------------------
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