Contacts of the helix formed by residues 280 - 292 (chain B) in PDB entry 1G9Y
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 GLU 280 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 2.8 33.2 - - - +
265B GLY* 4.3 2.8 + - - -
278B LEU* 3.7 5.4 - - + +
279B SER* 1.3 72.4 - - - +
281B ILE* 1.3 67.8 + - - +
282B LYS 3.2 0.7 - - - -
283B PRO* 2.9 20.7 - - + +
284B LEU* 2.9 22.3 + - - +
504D A 3.6 41.2 + - - +
505D A 4.2 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 5.6 2.7 - - + -
279B SER 2.7 9.0 + - - +
280B GLU* 1.3 69.9 - - - +
282B LYS* 1.3 65.0 + - + +
284B LEU* 3.6 6.3 - - - +
285B HIS* 3.0 27.0 + - - +
309B ILE* 3.4 42.7 - - + +
312B LEU* 3.4 34.8 - - + -
503D A 4.3 9.4 - - - +
504D A 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 1.3 84.7 - - + +
283B PRO* 1.3 73.7 - - + +
285B HIS* 3.3 29.0 + - - +
286B ASN* 3.1 21.6 + - - +
309B ILE* 4.7 7.7 - - - +
504D A 4.6 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 5.3 1.3 + - - +
264B VAL* 3.8 36.4 - - + +
278B LEU* 4.3 3.3 - - + +
280B GLU* 2.9 41.1 - - + +
282B LYS* 1.3 85.8 - - + +
284B LEU* 1.3 53.8 + - - +
286B ASN* 3.3 9.7 + - + +
287B PHE* 2.7 36.4 + - - +
504D A 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.0 31.0 - - + +
242B THR 4.6 2.0 - - - +
243B PHE* 3.6 27.6 - - + +
278B LEU* 3.9 30.4 - - + +
279B SER 4.1 9.9 - - - +
280B GLU 2.9 18.5 + - - +
281B ILE* 3.6 5.2 - - - +
283B PRO* 1.3 74.6 - - - +
285B HIS* 1.3 60.8 + - - +
287B PHE* 4.9 0.7 - - + -
288B LEU* 2.8 65.7 + - + +
305B VAL* 4.4 4.9 - - + -
309B ILE* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE 3.0 18.0 + - - +
282B LYS* 3.6 27.0 + - - +
284B LEU* 1.3 77.6 - - - +
286B ASN* 1.3 59.8 + - - +
289B THR* 2.6 49.7 + - + -
306B LEU* 3.6 30.3 - - + +
309B ILE* 3.6 26.9 - - + -
310B GLU* 3.2 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ASN* 3.8 24.8 + - - +
203B THR* 3.0 38.2 + - - +
205B TYR* 3.9 10.3 + - - -
282B LYS* 3.1 14.3 + - - +
283B PRO* 3.6 10.7 + - + +
285B HIS* 1.3 81.2 + - - +
287B PHE* 1.3 64.1 + - - +
289B THR* 3.4 12.0 + - - -
290B GLN* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 4.0 28.9 - + + +
209B PHE* 5.0 2.9 - + - -
210B LEU* 4.7 6.5 - - + -
213B LEU* 3.7 32.5 - - + -
243B PHE* 3.5 42.4 - + - -
262B ILE* 4.0 19.1 - - + -
264B VAL* 6.0 0.2 - - + -
278B LEU* 4.1 20.6 - - + -
283B PRO 2.7 21.6 + - - +
284B LEU 3.7 1.8 - - - +
286B ASN* 1.3 75.0 - - - +
288B LEU* 1.3 68.7 + - + +
290B GLN* 3.2 5.9 + - - +
291B LEU* 3.0 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 4.1 26.7 - - + -
243B PHE* 4.3 10.5 - - + -
284B LEU* 2.8 43.7 + - + +
287B PHE* 1.3 88.5 - - + +
289B THR* 1.3 60.5 + - - +
291B LEU* 4.3 9.6 - - + +
292B GLN* 2.9 35.5 + - - +
302B ALA* 4.4 14.4 - - + +
305B VAL* 3.7 33.7 - - + -
306B LEU* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B HIS* 2.6 44.3 + - + -
286B ASN* 3.5 8.5 - - - -
287B PHE 3.2 0.2 - - - -
288B LEU* 1.3 78.0 - - - +
290B GLN* 1.3 67.2 + - + +
292B GLN* 4.2 4.4 - - - +
293B PRO* 3.4 15.1 - - - +
306B LEU* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B THR 2.9 26.1 + - - -
204B LYS* 3.6 9.4 - - - +
205B TYR* 2.7 42.8 + - + +
210B LEU* 3.4 28.4 - - + +
286B ASN* 3.1 23.9 + - - +
287B PHE 3.2 7.4 + - - +
289B THR* 1.3 83.8 - - + +
291B LEU* 1.3 60.8 + - - +
293B PRO* 3.4 14.7 - - - +
294B PHE* 3.7 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.5 39.4 - - + +
213B LEU* 4.2 9.0 - - + -
214B ALA* 3.5 18.2 - - + +
217B VAL* 4.2 15.0 - - + -
223B ILE* 5.6 0.2 - - + -
243B PHE* 4.3 5.2 - - + -
287B PHE* 3.0 43.3 + - + +
288B LEU* 4.2 8.5 - - + +
290B GLN* 1.3 77.5 - - - +
292B GLN* 1.3 65.9 + - - +
293B PRO 3.2 0.7 - - - -
294B PHE* 2.9 20.3 + - - +
295B LEU* 3.6 31.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 2.9 21.2 + - - +
289B THR* 4.2 5.3 - - - +
291B LEU* 1.3 76.5 - - - +
293B PRO* 1.3 78.3 - - + +
294B PHE 3.1 1.2 + - - -
295B LEU* 3.2 20.2 + - - +
299B GLN* 3.0 45.1 + - + +
302B ALA* 4.2 12.3 - - + -
303B ASN* 2.8 39.5 - - - +
306B LEU* 4.9 4.8 - - + +
----------------------------------------------------------
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