Contacts of the helix formed by residues 278 - 290 (chain A) in PDB entry 5LXG
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 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 4.2 22.8 - - - -
223A TRP* 4.5 2.8 - - - -
274A LEU 3.7 4.0 + - - -
275A GLY 3.5 8.8 + - - -
276A LEU 3.1 0.8 - - - -
277A SER* 1.3 79.1 - - - +
279A VAL* 1.3 48.9 + - - +
281A PRO* 2.9 19.8 - - - +
282A THR* 2.5 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLY 4.3 9.2 - - - +
276A LEU* 3.2 17.7 + - + +
278A GLY* 1.3 73.6 - - - +
280A VAL* 1.4 66.9 + - + +
282A THR* 3.1 10.0 - - + +
283A MET* 3.1 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.3 22.3 + - + +
241A ILE* 6.5 1.3 - - + -
276A LEU 4.1 7.4 + - - +
277A SER* 3.7 6.4 + - - +
279A VAL* 1.4 74.8 - - + +
281A PRO* 1.4 70.6 - - + +
283A MET* 3.3 12.8 - - - +
284A HIS* 3.0 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 3.7 22.2 - - + -
224A LEU* 3.9 4.9 - - + -
228A PHE* 3.6 6.4 - - + -
238A TYR* 2.6 41.5 - - + -
277A SER* 2.5 30.5 - - - +
278A GLY* 2.9 20.6 - - - +
280A VAL* 1.4 84.4 - - + +
282A THR* 1.3 55.1 + - - +
284A HIS* 3.3 2.4 + - - +
285A PHE* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 3.7 8.0 - - + -
278A GLY 2.5 31.0 - - - +
279A VAL* 3.1 24.2 - - + +
281A PRO* 1.3 75.5 - - - +
283A MET* 1.3 61.0 + - + +
285A PHE* 3.3 7.3 + - - +
286A THR* 3.3 22.1 + - - -
300A MET* 2.8 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.1 40.5 + - + +
280A VAL* 3.3 13.9 - - - +
282A THR* 1.3 73.4 + - - +
284A HIS* 1.3 64.2 + - - +
286A THR* 3.0 10.8 + - - -
287A ILE* 2.9 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.3 26.7 - + - -
234A PRO* 4.2 13.1 - - + +
237A ILE* 6.1 0.4 - - - +
238A TYR* 3.0 27.1 - + - +
280A VAL* 3.0 20.9 + - + +
281A PRO* 3.4 4.7 - - + +
283A MET* 1.3 76.6 - - - +
285A PHE* 1.3 62.0 + - - +
287A ILE* 3.5 8.1 + - - +
288A ALA* 3.2 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 5.5 1.6 - - + -
227A SER* 3.3 49.4 - - - -
228A PHE* 4.1 9.0 - + + -
281A PRO 2.9 14.0 + - - +
282A THR* 3.4 11.7 - - - +
283A MET 3.2 0.2 - - - -
284A HIS* 1.3 79.2 - - - +
286A THR* 1.3 57.2 + - - +
288A ALA* 3.5 2.8 + - + -
289A GLU* 2.9 54.0 + - + +
294A ALA* 3.7 24.5 - - + -
298A GLY* 4.1 22.7 - - - -
300A MET* 4.5 19.5 - - + -
358A LEU* 5.0 7.9 - - + -
361A PHE* 5.0 9.0 - + - -
362A ARG* 3.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR* 3.3 11.3 + - - -
283A MET* 3.0 13.9 + - - -
285A PHE* 1.3 76.1 - - - +
287A ILE* 1.3 57.1 + - + +
290A GLY* 2.7 38.5 + - - +
291A PHE* 3.4 42.7 + - + +
294A ALA* 4.1 17.2 - - + +
295A THR* 6.0 0.4 - - - +
300A MET* 4.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET* 2.9 34.6 + - + +
284A HIS* 4.0 7.0 - - - +
286A THR* 1.3 79.2 - - + +
288A ALA* 1.3 64.0 + - - +
290A GLY* 3.6 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A HIS* 3.2 30.8 + - + +
285A PHE* 3.9 4.0 - - + +
287A ILE* 1.3 79.3 - - - +
289A GLU* 1.3 70.1 + - + +
290A GLY 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A SER 5.1 0.5 - - - +
230A CYS* 5.9 1.4 - - - +
285A PHE* 2.9 48.7 + - + +
288A ALA* 1.3 85.2 - - + +
290A GLY* 1.3 63.8 + - - +
293A LYS* 3.3 54.0 + - + +
294A ALA* 4.7 5.2 - - + +
361A PHE* 3.9 13.1 - - + -
362A ARG* 4.0 17.5 + - - +
365A LEU* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A THR 2.7 19.8 + - - +
287A ILE* 3.6 6.1 + - - -
288A ALA 3.4 2.6 - - - -
289A GLU* 1.3 74.9 - - - +
291A PHE* 1.3 65.2 + - - -
292A VAL* 3.4 4.9 - - - -
293A LYS* 4.1 3.1 - - - -
294A ALA* 3.1 22.7 + - - +
----------------------------------------------------------
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