Contacts of the helix formed by residues 283 - 293 (chain A) in PDB entry 6XWQ
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 THR 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET* 5.2 0.7 - - - -
270A ALA* 4.6 2.8 + - - +
273A THR* 4.0 20.0 - - - +
274A ALA* 4.3 7.3 + - + -
277A THR* 4.8 4.7 - - - -
279A SER 3.6 12.6 - - - +
280A SER 3.1 14.1 + - - +
282A GLY* 1.3 78.7 - - - +
284A LEU* 1.3 64.4 + - - +
285A PRO* 3.4 5.4 - - - -
286A VAL* 3.3 22.1 + - - +
287A THR* 3.0 21.2 + - + +
406A VAL* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.7 29.4 - - + -
64A VAL* 6.2 0.9 - - - -
197A TYR* 4.5 12.1 - - + +
280A SER 4.6 3.4 - - - +
281A SER* 4.7 13.5 - - - +
282A GLY 3.6 0.8 - - - -
283A THR* 1.3 77.2 - - - +
285A PRO* 1.3 71.4 - - + +
287A THR* 3.2 16.5 - - + +
288A MET* 2.9 39.7 + - - +
306A LEU 3.4 28.9 - - - +
307A PRO* 4.2 17.5 - - + +
310A ALA* 3.6 21.3 - - + -
311A THR* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 4.5 31.4 - - + +
200A VAL* 3.5 37.9 - - + -
201A GLY* 4.8 5.8 - - - +
204A MET* 6.3 0.7 - - + -
281A SER 5.9 0.2 - - - +
283A THR* 3.6 2.7 - - - -
284A LEU* 1.3 92.5 - - + +
286A VAL* 1.3 63.7 + - + +
288A MET* 3.4 5.2 + - + +
289A ARG* 2.9 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 5.7 8.7 - - + -
204A MET* 5.1 10.5 - - + -
269A ASP 3.7 15.7 - - - +
270A ALA* 3.7 22.4 - - + -
273A THR* 4.3 17.3 - - + +
283A THR* 3.3 18.9 + - - +
284A LEU 3.3 0.6 - - - -
285A PRO* 1.3 84.1 - - + +
287A THR* 1.3 58.5 + - - +
289A ARG* 3.4 17.4 + - + +
290A VAL* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA* 4.1 4.0 - - - -
283A THR* 3.0 17.4 + - + +
284A LEU* 3.2 30.3 - - + +
286A VAL* 1.3 77.3 - - - +
288A MET* 1.3 64.8 + - + +
290A VAL* 3.2 9.6 - - - +
291A ALA* 2.9 27.7 + - - +
306A LEU* 4.0 10.8 - - + +
310A ALA* 5.9 0.9 - - + -
406A VAL* 4.2 18.8 + - + +
409A ASP* 5.5 1.7 - - + +
410A LEU* 3.2 28.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 3.3 45.1 - - + +
284A LEU* 2.9 35.6 + - - +
285A PRO* 4.0 3.6 - - + +
287A THR* 1.3 80.9 - - + +
289A ARG* 1.3 56.9 + - - +
291A ALA* 3.2 1.2 + - - -
292A GLU* 2.9 25.8 + - - +
302A PHE* 3.2 51.3 - - + +
303A SER* 4.9 8.7 - - - +
306A LEU* 4.3 11.0 - - + -
307A PRO* 4.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PRO* 2.9 22.7 + - - +
286A VAL* 3.4 24.2 - - + +
288A MET* 1.3 75.9 - - - +
290A VAL* 1.3 59.7 + - + +
292A GLU* 4.8 1.8 - - - -
293A GLU* 3.1 39.7 - - + +
294A GLU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LYS 3.3 26.7 - - - +
267A ALA* 4.6 2.2 - - - -
269A ASP* 4.6 17.3 - - + +
270A ALA* 3.8 15.3 - - + +
286A VAL* 2.9 17.3 + - + +
287A THR* 3.2 23.3 - - - +
289A ARG* 1.3 77.9 - - + +
291A ALA* 1.3 59.3 + - - +
292A GLU 3.5 0.4 - - - -
294A GLU* 3.3 14.4 - - + +
295A MET* 2.9 27.2 + - + +
410A LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR 2.9 18.1 + - - +
288A MET 3.2 3.6 + - - +
290A VAL* 1.3 78.6 - - - +
292A GLU* 1.3 53.6 + - - +
295A MET* 3.2 13.3 - - + +
296A GLY 2.6 28.3 + - - -
297A VAL* 3.2 24.7 + - + +
302A PHE* 4.1 2.9 - - + -
306A LEU* 3.6 22.9 - - + -
410A LEU* 4.1 7.2 - - + -
413A THR* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET 2.9 17.5 + - - +
289A ARG* 4.8 0.9 - - - -
291A ALA* 1.3 76.8 - - - +
293A GLU* 1.3 81.6 + - + +
296A GLY* 3.4 16.8 - - - -
297A VAL 2.9 30.1 + - - +
298A ASP* 4.5 4.2 - - - +
299A LYS* 4.4 15.9 + - - +
302A PHE* 3.6 24.4 - - + -
427A LYS* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 3.1 31.2 + - + +
292A GLU* 1.3 87.1 - - + +
294A GLU* 1.3 60.0 + - + +
427A LYS* 2.8 22.4 + - - -
----------------------------------------------------------
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