Contacts of the helix formed by residues 302 - 315 (chain N) in PDB entry 5I2D
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 VAL 302 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146N VAL* 4.1 14.8 - - + -
162N ILE* 4.4 7.6 - - + -
269N LEU* 5.2 7.2 - - + -
277N ALA* 5.9 2.2 - - + -
281N LEU* 4.5 4.7 - - + +
283N ILE* 5.0 3.1 - - - -
285N LEU* 3.7 30.3 - - + -
289N THR 3.9 0.9 - - - +
290N LEU* 3.0 45.4 + - + +
301N GLU* 1.3 78.0 - - - +
303N PHE* 1.3 66.8 + - + +
304N LEU 3.4 1.1 - - - -
305N PRO* 3.1 14.6 - - - +
306N THR* 3.2 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162N ILE* 4.3 10.5 - - + -
172N ILE* 4.2 11.2 - - + -
174N LEU* 4.4 7.0 - - + +
184N MET* 3.5 39.7 - - + -
193N LEU* 4.5 7.6 - - + -
196N LEU* 4.0 22.7 - - + -
197N LEU* 4.6 9.0 - - + -
200N LEU* 4.2 9.2 - - + -
261N ILE* 4.0 20.0 - - + -
290N LEU* 3.8 41.3 - - + -
291N ALA* 4.9 1.6 - - + -
300N ASP* 3.4 19.2 + - - +
302N VAL* 1.3 75.9 - - + +
304N LEU* 1.3 57.9 + - - +
306N THR* 2.5 24.3 + - - -
307N LEU* 2.9 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197N LEU* 5.1 5.8 - - + +
202N TYR* 3.3 30.5 - - + +
206N THR* 5.7 2.5 - - + -
207N LEU* 4.3 19.3 - - + -
210N GLU* 4.3 22.7 - - + -
211N LEU* 4.3 22.4 - - + -
300N ASP* 3.2 17.8 + - - +
303N PHE* 1.3 75.2 - - - +
305N PRO* 1.3 68.8 - - + +
307N LEU* 3.4 13.1 + - + +
308N ARG* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 305 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281N LEU* 4.0 11.6 - - + +
283N ILE* 3.6 40.4 - - + -
300N ASP* 4.6 0.4 - - - +
301N GLU 3.7 11.9 - - - +
302N VAL 3.1 10.5 - - - +
304N LEU* 1.3 94.2 - - + +
306N THR* 1.3 56.1 + - - +
308N ARG* 3.4 31.4 + - + +
309N TYR* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146N VAL* 3.7 29.4 - - + -
148N PHE* 3.4 9.6 - - - -
160N ALA* 5.4 1.3 - - - -
162N ILE* 4.6 7.7 - - + +
174N LEU* 3.5 17.1 - - - +
281N LEU* 3.7 15.9 - - + -
302N VAL* 3.2 31.6 - - + +
303N PHE* 2.5 25.1 + - - -
305N PRO* 1.3 74.1 - - - +
307N LEU* 1.3 59.5 + - - +
309N TYR 3.4 0.7 + - - -
310N LEU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174N LEU* 4.2 8.7 - - + -
182N VAL* 4.0 16.4 - - + -
193N LEU* 3.8 29.2 - - + -
197N LEU* 4.2 13.9 - - + -
211N LEU* 3.7 28.5 - - + -
221N LEU* 3.9 9.6 - - + -
303N PHE 2.9 11.8 + - - +
304N LEU* 3.8 11.9 - - + +
306N THR* 1.3 80.5 + - - +
308N ARG* 1.3 59.1 + - - +
310N LEU* 3.2 13.9 + - + +
311N PHE* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 308 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210N GLU* 4.6 24.1 + - + +
211N LEU* 4.7 14.1 - - + +
214N TYR* 3.5 34.9 - - + +
281N LEU 3.5 22.6 + - - -
282N GLY 4.9 1.6 + - - -
283N ILE* 3.8 16.4 - - - +
304N LEU* 2.9 22.0 + - + +
305N PRO* 3.5 19.8 + - - +
307N LEU* 1.3 76.4 - - - +
309N TYR* 1.3 57.3 + - - +
311N PHE* 3.4 2.4 + - - -
312N ALA* 2.9 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 309 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N PHE* 3.4 43.5 - + + -
280N LYS* 3.1 52.3 + - + +
281N LEU* 4.2 10.5 - - + -
305N PRO 2.9 17.8 + - - +
307N LEU 3.3 0.2 - - - -
308N ARG* 1.3 75.4 - - - +
310N LEU* 1.3 60.7 + - - +
312N ALA* 3.4 5.5 + - - +
313N LEU* 2.9 30.2 + - + +
319N GLY 4.2 4.8 + - - -
320N HIS* 3.5 34.6 - + + -
321N GLU* 3.2 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N PHE* 3.7 19.0 - - + -
158N TYR* 3.7 34.3 - - + +
160N ALA* 4.5 3.8 - - + +
174N LEU* 4.1 34.1 - - + +
175N GLU 4.7 0.9 - - - +
176N VAL* 4.2 20.4 - - + -
182N VAL* 5.0 1.1 - - + -
306N THR 2.9 15.6 + - - +
307N LEU* 3.4 21.8 - - + +
309N TYR* 1.3 76.7 - - - +
311N PHE* 1.3 62.4 + - + +
313N LEU* 3.3 4.0 + - + +
314N THR* 2.8 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176N VAL* 4.2 11.4 - - + -
182N VAL* 3.5 32.3 - - + -
211N LEU* 3.5 42.0 - - + -
214N TYR* 3.8 23.4 - + + +
217N LEU* 3.7 48.3 - - + +
218N VAL* 4.3 8.7 - - - -
221N LEU* 4.3 3.6 - - + -
307N LEU* 2.9 27.4 + - + +
308N ARG 3.8 0.7 - - - +
310N LEU* 1.3 80.1 - - + +
312N ALA* 1.3 58.0 + - - +
314N THR* 3.2 5.5 + - - -
315N ALA* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214N TYR* 3.8 25.9 - - + +
308N ARG* 2.9 18.2 + - + +
309N TYR* 3.8 0.4 - - - +
311N PHE* 1.3 76.6 - - - +
313N LEU* 1.3 59.6 + - - +
316N GLY 3.2 2.8 + - - -
317N VAL* 2.9 41.1 + - + +
320N HIS* 3.4 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N PHE* 3.9 30.5 - - + -
158N TYR* 3.7 40.2 + - + +
309N TYR* 2.9 20.7 + - + +
310N LEU 3.6 4.3 - - - +
312N ALA* 1.3 75.6 - - - +
314N THR* 1.3 65.6 + - - +
316N GLY* 3.0 15.0 + - - -
317N VAL 4.9 0.7 - - - +
320N HIS* 3.5 38.1 - - + +
321N GLU* 4.0 11.9 - - - +
322N VAL* 4.1 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 314 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156N GLY 4.0 19.5 - - - +
157N ARG* 4.0 19.2 - - - +
158N TYR* 3.7 22.2 + - - -
176N VAL* 5.1 6.5 - - + +
217N LEU* 4.3 21.3 - - + -
310N LEU* 2.8 31.3 + - - +
311N PHE* 3.6 8.9 - - - -
313N LEU* 1.3 77.6 - - - +
315N ALA* 1.3 61.3 + - - +
316N GLY* 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214N TYR* 4.7 21.8 - - + +
215N GLY* 5.2 2.9 - - - +
217N LEU* 5.3 5.6 - - + +
311N PHE 2.8 17.5 + - - +
312N ALA* 4.0 5.4 - - - +
314N THR* 1.3 76.2 - - - +
316N GLY* 1.3 60.0 + - - +
317N VAL* 3.4 13.0 + - + +
----------------------------------------------------------
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