Contacts of the helix formed by residues 159 - 167 (chain G) in PDB entry 2W8B
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 ASP 159 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PRO* 5.4 3.6 - - - +
210D ASP* 5.8 3.8 - - - +
253D PRO 5.1 1.6 - - - +
254D ASP* 3.5 23.8 - - + +
255D GLY* 4.9 0.9 - - - -
157G GLY* 3.6 0.7 - - - -
158G HIS* 1.3 83.4 + - - +
160G GLU* 1.3 60.8 + - - +
161G ALA* 3.3 18.5 - - - +
162G ALA* 2.8 24.9 + - - +
163G TYR* 2.9 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ASP* 3.4 36.9 + - + +
256D SER* 3.8 13.5 - - - +
257D LYS* 5.0 5.1 + - - +
75G LEU* 5.9 1.0 - - - +
112G ARG* 3.5 26.0 + - - -
159G ASP* 1.3 75.3 - - - +
161G ALA* 1.3 57.4 + - - +
163G TYR* 3.8 6.0 - - - +
164G SER* 2.8 37.9 + - - -
167G ARG* 2.7 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ASP 3.1 9.8 + - - +
255D GLY* 3.5 32.8 - - - +
256D SER* 4.0 1.8 - - - +
155G VAL* 5.1 0.2 - - - -
159G ASP* 3.1 13.6 + - - +
160G GLU* 1.3 76.6 - - - +
162G ALA* 1.3 61.1 + - - +
164G SER* 3.3 14.5 + - - -
165G LYS* 3.4 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G VAL* 3.6 24.7 - - + -
156G LEU 3.8 4.3 - - - +
157G GLY* 3.7 32.1 - - - +
159G ASP* 2.8 15.7 + - - +
161G ALA* 1.3 75.8 - - - +
163G TYR* 1.3 68.0 + - + +
165G LYS* 3.0 5.0 + - - +
166G ASN* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F PHE* 4.5 6.6 - - - -
376F LEU* 4.5 0.9 - - - +
110G ASP* 3.7 17.5 - - + +
111G GLU* 2.7 44.5 + - + +
112G ARG* 3.3 43.3 - - + +
157G GLY 3.7 14.1 - - - -
158G HIS* 3.6 20.9 + - - +
159G ASP* 2.9 21.8 + - - +
160G GLU* 3.8 11.0 - - - +
162G ALA* 1.3 78.9 - - + +
164G SER* 1.3 58.0 + - - +
166G ASN* 3.0 21.0 + - - +
167G ARG* 3.0 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D SER* 4.2 11.4 - - - -
257D LYS* 6.2 0.2 - - - -
274D ASP* 4.7 8.7 + - - -
276D ALA* 3.6 18.9 + - - +
72G TYR* 3.5 19.4 - - - -
73G PHE 4.9 2.0 - - - +
160G GLU* 2.8 23.7 + - - -
161G ALA* 3.3 8.7 + - - -
163G TYR* 1.3 77.6 - - - +
165G LYS* 1.3 62.9 + - - +
166G ASN 3.4 0.3 - - - -
167G ARG* 3.6 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D LYS* 5.6 2.6 - - - +
275D LEU* 5.3 2.6 - - + +
276D ALA* 3.5 28.9 - - + +
72G TYR* 3.7 12.9 + - + +
154G ALA* 4.0 8.6 - - + +
155G VAL* 4.1 36.8 - - + +
161G ALA* 3.4 18.1 + - + +
162G ALA 3.0 7.3 + - - +
164G SER* 1.3 80.9 + - - +
166G ASN* 1.3 60.3 + - - +
167G ARG 3.5 0.2 - - - -
168G ARG* 3.3 19.2 - - - -
1175G SO4 2.8 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 166 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G HIS* 3.4 10.9 - - - +
109G ALA 3.9 14.0 - - - +
110G ASP* 4.6 5.6 - - - +
111G GLU* 5.8 1.0 - - - +
153G PRO* 3.8 11.3 - - + +
154G ALA* 2.7 31.4 + - - +
155G VAL* 2.8 29.5 + - - +
157G GLY 5.4 1.6 + - - -
162G ALA* 2.9 25.2 + - - +
163G TYR* 3.0 12.6 + - - +
165G LYS* 1.3 79.0 - - - +
167G ARG* 1.3 59.8 + - - +
168G ARG* 3.2 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G TYR* 3.5 9.0 - - - -
73G PHE* 2.9 45.7 + - - +
74G ASP* 3.4 12.1 + - - +
75G LEU* 3.8 21.2 - - - +
108G HIS 4.4 0.7 - - - -
110G ASP* 3.0 41.8 + - + +
112G ARG* 3.4 8.5 - - - +
125G ARG* 3.6 31.6 - - - +
160G GLU* 2.7 29.5 + - - -
163G TYR* 3.0 27.6 + - - +
164G SER* 3.6 19.9 + - - -
165G LYS 3.5 1.4 - - - -
166G ASN* 1.3 75.4 - - - +
168G ARG* 1.3 60.0 + - - +
----------------------------------------------------------
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