Contacts of the helix formed by residues 186 - 203 (chain C) in PDB entry 1YFJ
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 186 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LEU* 3.9 10.5 - - - -
185C TRP* 1.3 80.6 - - - +
187C GLU* 1.3 65.3 + - - +
188C ASP* 3.3 12.8 + - - +
189C GLU* 2.8 35.8 + - - +
190C GLU* 2.9 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LEU* 3.9 18.5 - - + +
186C SER* 1.3 72.3 - - - +
188C ASP* 1.3 60.7 + - - +
190C GLU* 3.3 6.0 + - - +
191C LYS* 3.0 27.9 + - - +
222C LEU* 6.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C SER* 2.9 10.7 + - - +
187C GLU* 1.3 81.4 - - - +
189C GLU* 1.3 68.6 + - - +
191C LYS* 3.5 7.5 + - - +
192C ASP* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C HIS* 2.8 35.1 + - - -
157C PHE* 3.8 4.4 - - + -
158C LYS* 5.4 1.9 + - - -
184C PHE 3.6 22.2 - - - +
185C TRP* 3.8 23.6 - - + -
186C SER* 2.8 25.0 + - - +
188C ASP* 1.3 75.7 - - + +
190C GLU* 1.3 58.6 + - - +
192C ASP* 3.1 19.0 + - - +
193C LEU* 2.9 26.7 + - - +
403C SAH 4.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PRO* 5.7 1.0 - - - +
173C PRO 4.5 3.3 - - - +
175C LEU* 3.4 19.2 + - + +
185C TRP* 2.9 34.2 + - + +
186C SER 2.9 7.7 + - - +
187C GLU* 3.5 12.1 - - - +
189C GLU* 1.3 76.0 - - - +
191C LYS* 1.3 65.1 + - - +
193C LEU* 3.0 5.9 + - + +
194C LEU* 2.9 37.3 + - + +
211C ASN* 4.7 9.0 + - - +
220C ASN* 2.8 30.1 + - - +
223C LEU* 4.1 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLU 3.0 15.6 + - - +
188C ASP* 3.8 8.1 - - - +
189C GLU 3.3 0.2 - - - -
190C GLU* 1.3 75.8 - - - +
192C ASP* 1.3 58.7 + - - +
194C LEU* 3.2 10.2 + - - +
195C ASN* 3.0 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C HIS* 5.8 0.2 - - + -
157C PHE* 4.3 12.9 - - + -
158C LYS* 4.3 22.2 + - + +
188C ASP* 3.1 17.7 + - - +
189C GLU* 3.1 22.8 + - - +
191C LYS* 1.3 78.8 - - - +
193C LEU* 1.3 58.6 + - - +
195C ASN* 3.4 11.0 + - - +
196C LEU* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PHE* 4.2 12.8 - - + -
157C PHE* 3.7 32.9 - - + -
170C VAL* 4.7 8.5 - - + -
172C PRO* 3.6 38.6 - - + -
185C TRP* 4.0 8.7 - - + -
189C GLU 2.9 12.5 + - - +
190C GLU* 3.0 11.4 + - + +
192C ASP* 1.3 75.8 - - - +
194C LEU* 1.3 62.6 + - + +
196C LEU* 3.2 10.9 + - + +
197C LEU* 2.9 40.7 + - + +
209C LEU* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C GLU* 2.9 33.8 + - + +
191C LYS* 3.7 8.3 - - - +
193C LEU* 1.3 81.0 - - + +
195C ASN* 1.3 59.3 + - - +
197C LEU* 3.2 10.2 + - + +
198C ASP* 2.9 31.5 + - - -
209C LEU* 5.0 6.5 - - + -
222C LEU* 5.0 6.1 - - + +
223C LEU* 3.9 24.9 - - + +
226C TRP* 3.7 62.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LYS* 3.0 28.4 + - - +
192C ASP* 3.8 11.4 + - - +
193C LEU 3.2 0.2 - - - -
194C LEU* 1.3 73.9 - - - +
196C LEU* 1.3 67.4 + - - +
198C ASP* 3.1 14.5 + - - +
199C SER* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.1 19.3 - - + -
157C PHE* 4.0 31.6 - - + +
158C LYS* 4.6 10.1 - - + +
162C ILE* 5.3 8.1 - - + -
192C ASP 3.0 14.8 + - - +
193C LEU* 3.4 13.7 - - + +
195C ASN* 1.3 77.1 - - - +
197C LEU* 1.3 58.3 + - + +
199C SER* 2.7 31.8 + - - -
200C LEU* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 4.1 22.2 - - + -
193C LEU* 2.9 24.8 + - + +
194C LEU* 3.5 11.7 - - + +
195C ASN 3.2 0.2 - - - -
196C LEU* 1.3 79.1 - - + +
198C ASP* 1.3 61.5 + - - +
200C LEU* 3.2 17.1 + - + +
201C ASN* 3.1 21.8 + - - +
207C PHE* 3.7 45.2 - - + -
209C LEU* 4.0 24.9 - - + -
226C TRP* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU 2.9 15.0 + - - +
195C ASN* 3.1 15.4 + - - +
197C LEU* 1.3 72.5 - - - +
199C SER* 1.3 57.7 + - - +
201C ASN* 3.4 3.5 + - - +
202C ASP* 3.0 34.3 + - - +
226C TRP* 3.0 24.9 + - - -
229C LYS* 2.9 26.6 + - - -
230C TYR* 2.5 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ASN 2.9 13.2 + - - -
196C LEU* 2.7 18.1 + - - -
198C ASP* 1.3 75.1 - - - +
200C LEU* 1.3 67.4 + - - -
201C ASN 3.1 1.6 - - - -
202C ASP* 3.1 11.3 + - - +
203C ARG* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ILE* 4.3 22.7 - - + -
168C VAL* 3.7 38.8 - - + -
196C LEU* 3.0 37.9 + - + +
197C LEU* 3.2 22.9 + - + +
199C SER* 1.3 77.9 - - - +
201C ASN* 1.3 62.8 + - - +
203C ARG* 3.0 21.8 + - - +
204C GLY 3.0 4.5 + - - -
205C ILE* 2.8 45.4 + - + +
207C PHE* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS* 5.0 9.7 - - - +
197C LEU 3.1 9.3 + - - +
198C ASP 3.5 9.3 + - - +
200C LEU* 1.3 79.8 - - - +
202C ASP* 1.3 67.3 + - - +
204C GLY* 3.0 13.9 + - - -
205C ILE 3.9 0.6 + - - -
207C PHE* 4.3 0.2 - - + -
230C TYR* 3.6 32.7 + - + +
259C ASN* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ASP* 3.0 24.9 + - - +
199C SER* 3.1 11.8 + - - +
201C ASN* 1.3 84.4 + - - +
203C ARG* 1.3 58.7 + - + +
204C GLY* 3.2 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ILE* 2.7 42.0 + - - +
163C LEU* 4.3 0.6 - - - +
164C ASP* 3.8 24.0 + - - +
199C SER* 2.9 25.2 + - - +
200C LEU* 3.0 13.5 + - - +
202C ASP* 1.3 75.3 - - + +
204C GLY* 1.3 60.2 + - - +
205C ILE* 3.4 30.0 + - + +
----------------------------------------------------------
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