Contacts of the helix formed by residues 294 - 308 (chain B) in PDB entry 2OG9
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 294 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 3.8 14.8 - - - -
123B ASP* 3.7 4.7 - - - -
124B VAL* 4.2 5.8 - - - -
289B ALA* 2.8 30.0 + - - +
290B PRO* 4.3 2.1 + - - -
292B VAL* 4.0 0.2 - - - +
293B GLY* 1.3 74.5 - - - +
295B ILE* 1.3 67.0 + - - -
296B THR 3.4 1.8 - - - -
297B PRO* 3.3 2.1 - - - +
298B PHE* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 2.9 4.0 + - - -
124B VAL* 4.2 19.7 - - + +
127B TRP* 3.5 55.2 - - + +
138B LEU* 3.7 24.0 - - + -
142B LEU* 5.2 2.9 - - + -
289B ALA* 4.9 0.2 - - - -
294B GLY* 1.3 70.0 - - - -
296B THR* 1.3 60.5 + - - +
298B PHE* 3.4 6.8 - - - +
299B LEU* 2.8 42.5 + - + +
320B LEU* 3.7 23.1 - - + -
324B LEU* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.4 8.7 - - - +
96B ALA* 4.3 25.6 + - + +
99B TRP* 4.2 11.4 - - + -
123B ASP* 2.7 29.7 + - - -
127B TRP* 3.2 16.0 + - - +
295B ILE* 1.3 79.7 - - - +
297B PRO* 1.3 72.0 - - + +
299B LEU* 3.3 13.1 + - - +
300B LYS* 3.4 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 3.6 19.1 - - + +
270B ALA* 4.4 12.7 - - + +
292B VAL* 3.4 20.9 - - + +
293B GLY* 3.3 35.0 - - - +
294B GLY 3.3 8.1 - - - +
296B THR* 1.3 97.4 - - + +
298B PHE* 1.3 60.2 + - - +
300B LYS* 3.2 15.4 + - + +
301B ILE* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PRO* 3.4 46.0 - - + -
288B ASP 4.4 0.2 - - - -
289B ALA* 3.6 24.5 - - + -
292B VAL* 4.1 2.2 - - + +
294B GLY 3.2 19.8 + - - +
295B ILE* 3.2 9.1 + - - +
297B PRO* 1.3 77.3 - - - +
299B LEU* 1.3 60.6 + - + +
301B ILE* 3.2 11.4 + - - +
302B ALA* 2.8 39.4 + - + -
312B LEU* 4.2 8.7 - - + -
314B PRO* 4.0 19.3 - - + -
321B HIS* 3.9 11.7 - + - -
324B LEU* 3.7 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 3.7 34.3 - - + -
142B LEU* 4.2 18.2 - - + -
295B ILE* 2.8 27.4 + - + +
296B THR* 3.7 6.5 - - - +
297B PRO 3.2 0.2 - - - -
298B PHE* 1.3 77.4 - - + +
300B LYS* 1.3 61.3 + - + +
302B ALA* 3.3 7.8 + - + +
303B SER* 2.9 28.9 + - - -
324B LEU* 4.4 20.9 - - + -
327B ALA* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 5.7 5.7 - - - +
99B TRP* 5.8 4.8 - - - -
100B ASP* 5.1 8.9 + - - -
270B ALA* 4.8 13.5 - - + -
296B THR* 3.4 29.6 + - - +
297B PRO* 3.2 14.0 + - + +
299B LEU* 1.3 77.8 - - + +
301B ILE* 1.3 62.3 + - - +
303B SER* 3.3 7.7 + - - -
304B LEU* 3.1 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 3.6 28.7 - - + +
273B HIS* 3.5 37.7 - - + +
277B ILE* 4.4 1.2 - - + +
285B LEU* 3.6 26.5 - - + -
287B PRO* 4.1 15.0 - - + -
292B VAL* 4.0 24.5 - - + -
297B PRO 3.0 15.6 + - - +
298B PHE* 3.4 8.3 - - - +
300B LYS* 1.3 74.7 - - - +
302B ALA* 1.3 60.9 + - - +
304B LEU* 3.1 11.1 + - - +
305B ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 2.8 35.2 + - + +
299B LEU* 3.3 12.1 + - + +
301B ILE* 1.3 75.0 - - - +
303B SER* 1.3 57.2 + - - +
305B ALA* 4.4 5.4 - - - -
306B GLU* 2.9 31.4 + - - +
312B LEU* 5.0 6.5 - - + -
328B TYR* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU 2.9 17.2 + - - -
300B LYS* 3.4 9.0 - - - -
301B ILE 3.1 0.2 - - - -
302B ALA* 1.3 78.1 - - - +
304B LEU* 1.3 63.5 + - - +
306B GLU* 3.4 6.7 + - - +
307B HIS* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 4.7 9.9 - - + +
273B HIS* 6.0 0.2 - - + -
274B GLY* 4.2 25.1 - - - +
277B ILE* 3.6 17.0 - - + +
300B LYS* 3.1 17.8 + - + +
301B ILE* 3.1 13.1 + - - +
303B SER* 1.3 78.2 - - - +
305B ALA* 1.3 61.6 + - - +
307B HIS* 3.4 9.2 + - + +
308B ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.8 7.1 - - + +
285B LEU* 3.9 25.4 - - + -
301B ILE 2.9 15.8 + - - +
302B ALA* 3.8 6.5 - - - +
304B LEU* 1.3 74.1 - - - +
306B GLU* 1.3 63.7 - - - +
308B ALA 3.3 1.2 + - - -
309B GLY 3.1 4.0 + - - -
310B LEU* 2.9 42.5 + - + +
311B MSE 5.3 0.2 - - - +
312B LEU* 4.8 4.0 - - + -
328B TYR* 3.3 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 2.9 18.5 + - - +
303B SER* 3.6 8.2 - - - +
305B ALA* 1.3 76.9 - - - +
307B HIS* 1.3 62.2 + - - +
309B GLY 3.0 14.6 + - - -
328B TYR* 3.2 11.6 + - + -
329B PRO* 3.6 38.9 - - + +
330B ARG* 3.4 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER 3.1 14.5 + - - +
304B LEU* 3.8 10.8 - - + +
306B GLU* 1.3 86.2 + - - +
308B ALA* 1.3 62.7 + - + +
309B GLY* 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.7 25.1 - - + +
304B LEU 3.0 17.7 + - - +
305B ALA 3.8 4.0 - - - +
306B GLU 3.2 0.4 - - - -
307B HIS* 1.3 77.3 - - + +
309B GLY* 1.3 62.0 + - - +
310B LEU* 3.5 18.8 + - + +
----------------------------------------------------------
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