Contacts of the helix formed by residues 213 - 230 (chain B) in PDB entry 1O4X
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 ASN 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PRO 3.5 4.1 + - - +
212B MET* 1.3 73.6 - - - +
214B ALA* 1.3 64.0 + - - +
215B PHE* 2.6 9.2 + - - -
216B MET* 2.4 51.3 + - - +
217B VAL* 2.9 19.4 + - - +
261B ALA* 3.8 4.5 - - - -
265B ARG* 6.0 3.1 - - - +
307C T 3.3 18.2 + - - -
308C G 3.7 34.2 + - - +
309C T 5.3 7.4 - - - +
332D A 3.6 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASN* 1.3 74.7 - - - +
215B PHE* 1.3 57.3 + - - +
217B VAL* 4.0 2.5 - - - +
218B TRP* 3.0 29.9 + - - +
246B TRP* 4.0 11.1 - - + -
257B PHE* 3.6 26.3 - - + +
258B ILE* 3.8 25.8 - - + -
261B ALA* 3.3 14.9 - - + +
308C G 5.4 6.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASN* 2.6 16.0 + - - +
214B ALA* 1.3 72.9 - - - +
216B MET* 1.3 58.8 + - - +
218B TRP* 3.4 31.5 - + - +
219B SER* 2.3 56.7 + - - -
223B ARG* 5.2 1.3 - - - -
239B SER* 6.2 0.7 - - - -
242B LEU* 4.4 13.5 - - + -
243B GLY* 4.4 1.8 - - - -
246B TRP* 3.5 42.5 - + + +
306C T 3.6 36.1 - - + -
307C T 3.4 42.8 - + - +
308C G 4.6 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B MET* 4.0 13.9 - - + +
213B ASN* 2.4 57.1 + - - +
215B PHE* 1.3 77.8 - - - +
217B VAL* 1.3 62.8 + - - +
219B SER* 2.7 19.6 + - - -
220B ARG* 2.9 15.6 + - - +
306C T 4.8 1.3 - - - +
307C T 4.5 0.4 - - - +
332D A 3.4 39.0 - - + +
333D A 3.0 68.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B MET* 3.5 35.4 - - + +
213B ASN 2.9 16.2 + - - +
214B ALA* 4.0 5.4 - - - +
216B MET* 1.3 75.0 - - - +
218B TRP* 1.3 64.2 + - - +
220B ARG* 3.2 22.3 + - + +
221B GLY* 3.6 4.7 + - - -
257B PHE* 5.5 7.6 - - + +
260B GLU* 4.6 19.1 - - + +
261B ALA* 4.7 2.9 - - + -
264B LEU* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA 3.0 19.9 + - - +
215B PHE* 3.4 32.3 - + - +
217B VAL* 1.3 78.0 - - - +
219B SER* 1.3 65.4 + - - +
221B GLY* 3.9 0.7 + - - -
222B GLN* 3.0 65.9 + - + +
242B LEU* 3.7 33.2 - - + -
245B GLU* 4.6 11.7 - - - -
246B TRP* 3.3 41.2 - + + -
249B LEU* 4.1 14.1 - - + +
257B PHE* 3.6 43.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 2.3 49.9 + - - -
216B MET* 2.7 21.7 + - - -
218B TRP* 1.3 82.3 - - - +
220B ARG* 1.3 60.4 + - - +
222B GLN* 4.1 0.7 - - - -
223B ARG* 2.4 58.4 + - - +
242B LEU* 5.0 3.6 - - - -
333D A 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B MET* 4.5 25.7 - - - +
216B MET 2.9 13.3 + - - +
217B VAL* 3.2 14.3 + - - +
219B SER* 1.3 78.1 - - - +
221B GLY* 1.3 60.6 + - - +
223B ARG* 4.1 4.7 - - - +
224B ARG* 3.5 18.0 + - - +
333D A 4.8 4.0 - - - +
334D A 4.2 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL 3.6 7.0 + - - -
218B TRP 4.4 0.2 - - - -
220B ARG* 1.3 78.6 - - - +
222B GLN* 1.3 65.0 + - - +
224B ARG* 3.5 5.3 + - - +
225B LYS* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TRP* 3.0 63.7 + - + +
219B SER* 4.1 2.5 - - - -
221B GLY* 1.3 73.7 - - - +
223B ARG* 1.3 68.5 + - - +
225B LYS* 2.9 37.5 + - - +
226B MET* 2.9 23.2 + - + +
242B LEU* 3.8 16.8 - - + -
245B GLU* 4.5 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 5.2 1.0 - - - -
219B SER* 2.4 54.5 + - - +
220B ARG* 4.1 2.9 - - - +
222B GLN* 1.3 69.9 - - - +
224B ARG* 1.3 62.0 + - - +
226B MET* 3.4 3.1 + - - +
227B ALA* 3.0 23.0 + - + +
235B ASN* 3.8 22.9 - - - +
238B ILE* 4.6 9.5 - - + +
239B SER* 3.9 18.2 + - - +
242B LEU* 4.0 26.5 - - + +
306C T 4.0 9.5 + - - -
333D A 3.7 26.5 + - - -
334D A 3.3 49.5 + - - -
335D G 4.5 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG 3.5 14.7 + - - +
221B GLY* 3.5 6.3 + - - +
222B GLN 3.2 0.4 - - - -
223B ARG* 1.3 80.4 - - - +
225B LYS* 1.3 64.5 + - - +
227B ALA* 3.1 10.9 + - - +
228B GLN* 3.0 57.4 + - - +
334D A 5.1 1.6 - - - -
335D G 3.8 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLY 3.2 13.7 + - - +
222B GLN* 2.9 36.1 + - - +
224B ARG* 1.3 79.2 - - - +
226B MET* 1.3 62.4 + - - +
228B GLN* 3.4 9.7 + - - +
229B GLU* 3.2 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLN* 2.9 15.2 + - + +
223B ARG 3.8 4.0 - - - +
225B LYS* 1.3 78.3 - - - +
227B ALA* 1.3 53.0 + - - +
229B GLU* 4.5 9.9 - - - +
230B ASN* 2.4 70.5 + - - +
238B ILE* 3.8 29.8 - - + -
241B ARG* 4.4 26.5 - - + +
242B LEU* 4.3 20.2 - - + -
245B GLU* 4.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ARG* 3.0 17.7 + - + +
224B ARG* 3.1 17.9 + - - +
226B MET* 1.3 78.4 - - - +
228B GLN* 1.3 57.1 + - + +
230B ASN 3.6 9.4 - - - +
231B PRO* 2.5 38.9 - - + +
238B ILE* 4.6 8.9 - - + +
335D G 5.4 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 3.0 52.9 + - + +
225B LYS* 3.9 9.0 - - - +
226B MET 3.3 0.2 - - - -
227B ALA* 1.3 76.3 - - + +
229B GLU* 1.3 64.5 + - + +
231B PRO* 3.4 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LYS* 3.2 44.6 + - + +
226B MET* 4.0 8.9 - - - +
228B GLN* 1.3 80.4 - - + +
230B ASN* 1.3 73.6 + - - +
231B PRO* 3.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B MET* 2.4 64.3 + - + +
227B ALA* 3.0 9.2 - - - +
229B GLU* 1.3 100.0 - - - +
231B PRO* 1.3 61.0 - - - +
232B LYS 3.2 7.7 + - - +
233B MET* 3.3 28.6 + - + +
238B ILE* 4.0 4.2 - - - +
241B ARG* 4.1 16.0 - - - +
----------------------------------------------------------
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