Contacts of the helix formed by residues 183 - 194 (chain N) in PDB entry 2X86
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 SER 183 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170N VAL 4.1 6.3 + - - -
171N TYR* 3.5 23.5 - - - +
175N GLU* 2.7 35.9 + - - -
181N MET 3.9 0.4 + - - -
182N ALA* 1.3 77.4 - - - +
184N VAL* 1.3 64.1 + - - +
185N ALA* 3.5 9.3 - - - +
186N PHE* 3.0 16.3 + - - +
187N HIS* 3.1 18.2 + - - -
211N PHE* 6.5 0.7 - - - -
401N ADP 5.3 1.1 - - - -
402N BMA 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182N ALA 3.7 0.2 + - - -
183N SER* 1.3 70.9 - - - +
185N ALA* 1.3 66.9 + - - +
187N HIS* 3.1 9.6 + - + +
188N LEU* 2.9 43.8 + - + +
199N LYS 4.8 1.1 - - - +
200N LEU* 3.9 22.9 - - + -
211N PHE* 5.6 6.2 - - + -
243N PHE* 3.6 32.5 - - + +
246N VAL* 4.9 8.1 - - + -
401N ADP 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N TYR* 4.6 10.1 - - + -
183N SER* 3.5 11.6 - - - +
184N VAL* 1.3 78.5 - - - +
186N PHE* 1.3 64.0 + - - +
188N LEU* 3.3 3.1 + - - +
189N ASN* 3.0 23.7 + - - +
246N VAL* 4.2 22.2 - - + +
250N THR* 4.6 2.7 - - - -
299N VAL* 4.7 5.4 - - + -
302N TYR* 4.0 19.3 - - + -
303N MET* 3.6 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175N GLU* 3.6 7.6 - - + +
176N GLY* 3.5 38.8 - - - -
179N GLY* 5.5 2.0 - - - -
182N ALA* 3.8 20.0 - - + -
183N SER* 3.0 16.0 + - - +
185N ALA* 1.3 80.7 - - - +
187N HIS* 1.3 70.9 + + - +
189N ASN* 3.2 5.5 + - - +
190N THR* 3.1 55.9 + - + +
302N TYR* 3.3 28.9 - - - +
306N LEU* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 187 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179N GLY 2.9 27.2 + - - -
180N SER* 3.8 11.0 - - - -
182N ALA* 3.1 15.0 - - - +
183N SER 3.1 13.3 + - - -
184N VAL* 3.1 12.2 + - + +
186N PHE* 1.3 88.4 - + - +
188N LEU* 1.3 58.6 + - + +
190N THR* 3.3 9.1 + - - -
191N GLN* 2.9 48.4 + - - +
199N LYS 6.1 0.4 - - - +
401N ADP 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N VAL* 2.9 35.9 + - + +
185N ALA 3.7 3.4 - - - +
187N HIS* 1.3 77.1 - - + +
189N ASN* 1.3 64.5 + - - +
191N GLN* 3.4 20.1 + - - +
192N LEU* 2.9 30.9 + - - +
198N PRO* 3.8 14.1 - - + -
199N LYS 3.5 29.2 - - - +
200N LEU* 5.0 2.2 - - + -
246N VAL* 4.6 2.0 - - + -
247N ALA* 3.8 35.7 - - + +
250N THR* 4.1 20.4 - - + +
251N LEU* 5.5 1.1 - - + -
259N ILE* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185N ALA 3.0 17.4 + - - +
186N PHE 3.6 4.3 - - - +
188N LEU* 1.3 77.6 - - - +
190N THR* 1.3 67.5 + - - +
192N LEU* 3.3 2.6 + - - +
193N ASN* 3.0 42.3 + - - +
250N THR* 4.5 1.7 - - - +
254N HIS* 2.8 34.8 + - - -
303N MET* 3.6 9.3 - - - +
306N LEU* 3.6 40.3 + - + +
307N ASN* 3.4 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186N PHE* 3.1 49.2 + - + +
187N HIS* 3.4 12.6 + - - -
189N ASN* 1.3 82.6 - - - +
191N GLN* 1.3 67.1 + - - +
193N ASN* 3.4 7.4 + - - +
194N ASN* 3.1 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N HIS* 2.9 31.0 + - - +
188N LEU* 3.4 15.7 - - - +
190N THR* 1.3 79.7 + - - +
192N LEU* 1.3 58.8 + - - +
194N ASN* 3.3 6.1 + - - +
196N GLU* 2.9 53.6 + - - +
197N SER 3.9 14.1 - - - +
198N PRO* 3.3 7.1 - - + +
199N LYS* 3.0 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188N LEU* 2.9 21.5 + - + +
189N ASN 3.7 3.8 - - - +
190N THR 3.2 0.2 - - - -
191N GLN* 1.3 75.0 - - - +
193N ASN* 1.3 60.6 + - - +
194N ASN 3.1 4.7 - - - -
195N GLY* 3.2 6.2 + - - -
196N GLU 4.2 6.1 - - - +
198N PRO* 3.9 31.0 - - + -
250N THR* 3.9 8.5 - - + -
251N LEU* 3.8 21.5 - - + -
254N HIS* 3.8 38.6 - - + +
256N LYS* 2.8 41.2 + - + +
257N GLY* 4.1 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189N ASN* 3.0 40.4 + - - +
190N THR* 3.9 7.0 - - - +
192N LEU* 1.3 75.6 - - - +
194N ASN* 1.3 61.1 + - - +
195N GLY 3.3 2.1 + - - -
254N HIS* 3.4 18.1 + - - -
256N LYS* 5.1 0.4 - - - +
306N LEU 5.2 1.2 + - - -
307N ASN* 3.4 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N THR* 3.1 27.8 + - - +
191N GLN* 3.6 6.2 - - - +
192N LEU 3.1 1.0 - - - -
193N ASN* 1.3 81.2 - - - +
195N GLY* 1.3 55.4 + - - +
196N GLU* 3.0 30.8 + - - +
108R GLU* 5.3 1.4 - - - +
----------------------------------------------------------
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