Contacts of the helix formed by residues 163 - 174 (chain C) in PDB entry 6WYG
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 163 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 5.1 2.6 - - - +
158C MET 4.1 4.7 + - - -
159C GLY* 2.9 26.9 + - - -
160C ALA* 4.0 1.4 - - - -
161C PRO 3.6 6.1 - - - +
162C GLU* 1.3 73.1 - - - +
164C GLY* 1.3 61.9 + - - +
165C LEU* 3.8 11.8 + - - +
166C ALA* 3.2 32.5 + - - +
167C GLU* 3.5 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PRO 3.9 3.9 + - - -
162C GLU 3.6 6.1 + - - -
163C SER* 1.3 70.1 - - - +
165C LEU* 1.3 59.5 + - - +
167C GLU* 3.3 9.5 + - - +
168C TYR* 3.0 28.8 + - - +
157D CYS* 3.3 27.3 + - - +
206D RFT 4.0 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 4.5 14.6 - - + -
163C SER* 3.2 8.2 + - - +
164C GLY* 1.3 75.5 - - - +
166C ALA* 1.3 56.3 + - - +
168C TYR* 3.6 2.8 - - - +
169C LEU* 2.9 54.3 + - + +
157D CYS 3.5 6.1 + - - -
158D MET* 3.7 54.3 - - + +
165D LEU* 4.8 18.6 - - + -
166D ALA* 4.9 4.3 - - - +
169D LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 4.6 5.8 - - - +
155C LEU* 4.9 0.9 - - - -
158C MET* 3.1 56.1 - - + +
160C ALA* 3.8 11.7 - - + +
163C SER* 3.2 21.5 + - - +
164C GLY 3.2 0.4 - - - -
165C LEU* 1.3 79.2 - - - +
167C GLU* 1.3 57.4 + - - +
170C PHE* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 5.8 1.0 - - - +
48C LEU* 3.7 23.7 - - + +
51C PHE* 3.6 6.7 - - + -
95C SER* 3.6 13.6 + - - -
96C GLY* 2.9 34.3 + - - -
97C LEU* 3.0 17.8 + - - +
155C LEU* 4.4 10.9 - - + +
160C ALA* 4.0 14.0 - - + +
161C PRO* 4.2 6.3 - - + +
163C SER 3.5 12.7 + - - +
164C GLY* 3.3 10.2 + - - +
166C ALA* 1.3 73.1 - - - +
168C TYR* 1.3 61.1 + - - +
170C PHE* 3.4 0.3 + - - +
171C ASP* 2.9 32.2 + - - +
206D RFT 6.0 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 4.0 13.6 - - + +
164C GLY 3.0 17.1 + - - +
165C LEU 3.6 2.7 - - - +
167C GLU* 1.3 78.3 - - - +
169C LEU* 1.3 78.5 + - + +
171C ASP* 3.3 3.4 + - - +
172C LYS* 2.9 49.2 + - + +
154D ASN* 3.5 26.0 - - - +
157D CYS* 6.3 0.4 - - + -
158D MET* 3.4 47.8 - - + -
169D LEU 4.6 1.6 - - - -
170D PHE* 3.5 15.0 - + - -
173D HIS* 3.4 12.0 - + + +
174D THR* 2.8 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 4.5 8.5 - - + -
169A LEU* 4.2 27.4 - - + -
203A FE 4.1 10.1 - - - -
158C MET* 4.2 9.4 - - + -
165C LEU* 2.9 45.6 + - + +
166C ALA 4.1 2.2 - - - +
168C TYR* 1.3 90.4 - - + +
170C PHE* 1.3 57.5 + - - +
172C LYS* 3.1 2.0 + - - -
173C HIS* 2.8 44.8 + - + +
169D LEU* 4.4 15.0 - - + -
173D HIS* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.4 18.2 - + - -
51C PHE* 3.6 18.6 - + - -
100C MET* 4.0 16.6 - - + -
151C HIS* 3.6 36.3 - + + -
154C ASN* 3.8 22.9 - - + -
155C LEU* 3.6 18.2 - - + -
158C MET* 3.6 10.6 - - + +
166C ALA 2.9 18.0 + - - +
167C GLU 3.7 2.9 - - - +
169C LEU* 1.3 75.2 - - - +
171C ASP* 1.3 59.4 + - - +
174C THR* 2.8 53.5 + - + -
175C LEU* 3.2 29.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.4 19.5 - - + +
49C LYS* 4.2 3.8 + - - +
50C ASN* 2.9 42.8 + - - +
51C PHE* 2.9 47.9 + - + -
167C GLU 2.9 18.4 + - - +
168C TYR* 3.3 6.0 - - - +
170C PHE* 1.3 75.4 - - - +
172C LYS* 1.3 73.3 + - - +
175C LEU* 3.5 6.2 - - - -
176C GLY 3.3 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASN* 4.4 9.1 - - - +
168C TYR* 2.9 47.5 + - + +
169C LEU* 3.1 8.5 + - - +
171C ASP* 1.3 88.0 + - - +
173C HIS* 1.3 61.7 + - + +
176C GLY* 3.3 20.4 - - - -
173D HIS* 3.5 39.6 + - + +
174D THR* 3.3 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.1 16.4 - + - +
169A LEU* 4.0 9.7 - - + +
172A LYS* 3.8 34.0 - - + +
173A HIS* 3.5 28.2 + + - -
203A FE 3.1 20.6 - - - -
169C LEU* 2.8 38.7 + - + +
172C LYS* 1.3 74.9 - - + +
174C THR* 1.3 63.5 + - - +
176C GLY* 4.2 3.3 + - - -
173D HIS* 3.3 24.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 2.7 25.6 + - - -
172A LYS* 3.8 9.4 - - - +
151C HIS* 3.6 31.4 - - + +
154C ASN* 5.5 1.6 + - - +
170C PHE* 2.8 39.2 + - + -
173C HIS* 1.3 74.0 - - - +
175C LEU* 1.3 61.1 + - + +
176C GLY 3.2 7.0 + - - -
----------------------------------------------------------
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