Contacts of the helix formed by residues 162 - 173 (chain C) in PDB entry 2WWR
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 GLY 162 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C GLY 2.8 13.9 + - - -
161C LEU* 1.3 72.4 - - - +
163C ARG* 1.3 63.8 + - - -
164C ILE 3.5 1.6 - - - -
165C GLY 4.0 3.3 - - - +
166C GLN* 2.8 32.7 + - - +
188C ARG* 4.1 20.1 - - - +
216C CYS 5.3 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 4.4 17.3 + - - +
108C THR* 3.4 29.3 - - + +
162C GLY* 1.3 71.2 - - - -
164C ILE* 1.3 64.8 + - + +
166C GLN* 3.4 22.0 + - - +
167C ALA* 3.3 15.6 + - - +
170C ARG* 5.5 0.5 + - - -
191C GLU* 2.5 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 5.5 9.2 - - + -
107C LEU* 4.7 13.9 - - + -
108C THR* 4.3 23.3 - - + +
111C THR* 4.4 14.8 - - + -
112C ALA 4.3 16.4 - - - +
162C GLY* 4.5 0.2 - - - -
163C ARG* 1.3 75.9 - - + +
165C GLY* 1.3 65.3 + - - +
167C ALA* 3.0 4.9 + - - +
168C ILE* 2.9 39.3 + - + +
215C ALA* 4.3 16.6 - - + +
216C CYS 5.8 5.4 - - - -
243C ILE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ILE* 4.0 24.3 - - - +
160C GLY 4.3 3.1 + - - -
161C LEU* 4.1 17.9 - - - -
162C GLY* 3.9 6.2 + - - +
163C ARG 3.4 0.2 - - - -
164C ILE* 1.3 80.4 - - - +
166C GLN* 1.3 61.3 + - - +
168C ILE* 3.3 11.2 + - - +
169C ALA* 3.1 21.0 + - - +
215C ALA* 4.3 4.6 - - - +
216C CYS 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LEU* 3.8 22.6 + - + +
162C GLY* 2.8 27.5 + - - +
163C ARG* 3.4 23.4 + - - +
164C ILE 3.3 0.2 - - - -
165C GLY* 1.3 74.0 - - - +
167C ALA* 1.3 53.7 + - - +
169C ALA* 3.1 3.6 + - - +
170C ARG* 2.7 54.0 + - - +
188C ARG* 4.9 4.6 - - - +
191C GLU* 3.3 49.9 + - - +
195C PHE* 3.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR* 4.0 14.8 - - + +
109C ASP* 4.6 2.9 - - - +
112C ALA* 3.3 22.4 - - + -
163C ARG 3.3 11.0 + - - +
164C ILE 3.0 6.8 + - - +
166C GLN* 1.3 79.0 - - - +
168C ILE* 1.3 62.3 + - - +
170C ARG* 3.5 15.7 + - - +
171C ARG* 3.0 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ALA* 3.9 11.9 - - - +
115C ALA* 3.9 28.5 - - + -
116C VAL* 4.2 14.4 - - + +
119C LEU* 5.9 0.4 - - + -
158C ILE* 5.3 6.7 - - + -
164C ILE* 2.9 36.1 + - + +
165C GLY* 3.5 7.4 - - - +
167C ALA* 1.3 74.8 - - - +
169C ALA* 1.3 61.8 + - - +
171C ARG* 3.2 5.4 + - - +
172C LEU* 3.0 43.6 + - + +
213C VAL* 3.9 30.7 - - + -
215C ALA* 4.0 12.3 - - + -
243C ILE* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ILE* 4.0 19.9 - - + +
161C LEU* 5.1 0.9 - - + -
165C GLY 3.1 11.7 + - - +
166C GLN 3.1 8.2 + - - +
168C ILE* 1.3 77.9 - - - +
170C ARG* 1.3 62.2 + - - +
172C LEU* 3.2 2.7 + - - +
173C LYS* 3.1 26.0 + - - +
180C PHE* 4.0 17.3 - - + -
195C PHE* 3.6 33.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASP* 5.5 3.2 + - - -
163C ARG 5.5 0.2 + - - -
166C GLN* 2.7 45.0 + - - +
167C ALA* 3.5 25.1 - - - +
168C ILE 3.3 0.2 - - - -
169C ALA* 1.3 74.2 - - - +
171C ARG* 1.3 66.2 + - - +
173C LYS* 3.7 8.7 + - - +
174C PRO* 3.5 15.1 - - - +
194C GLU* 2.7 41.1 + - - +
195C PHE* 3.6 9.4 - - + -
174D PRO* 3.6 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASP* 3.3 43.6 + - - +
112C ALA* 3.9 26.8 - - - +
113C GLU* 4.2 4.6 + - - +
116C VAL* 4.0 7.2 - - + -
167C ALA* 3.0 36.8 + - - +
168C ILE 3.2 6.8 + - - +
170C ARG* 1.3 86.1 - - - +
172C LEU* 1.3 58.2 + - - +
173C LYS 3.4 0.4 - - - -
174C PRO* 3.4 9.4 - - - +
175C PHE* 3.2 24.4 - - - -
152D THR* 5.0 1.0 + - - -
174D PRO* 3.7 29.9 + - - +
175D PHE* 3.9 55.1 + - + -
176D GLY* 5.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C VAL* 3.8 26.5 - - + -
119C LEU* 4.0 22.9 - - + -
151C LEU* 3.8 28.3 - - + -
156C VAL* 4.0 26.0 - - + -
158C ILE* 5.9 0.4 - - + -
168C ILE* 3.0 37.8 + - + +
169C ALA* 3.2 4.7 + - - +
171C ARG* 1.3 75.7 - - - +
173C LYS* 1.3 67.0 + - - +
174C PRO 3.4 0.4 - - - -
175C PHE* 3.2 22.5 + - + +
177C VAL* 3.6 13.0 - - + +
180C PHE* 4.4 11.2 - - + -
213C VAL* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ALA 3.1 15.1 + - - +
170C ARG* 3.8 8.1 - - - +
172C LEU* 1.3 76.9 - - - +
174C PRO* 1.4 64.4 - - + +
176C GLY* 3.0 20.1 + - - -
177C VAL* 3.7 9.8 + - - +
180C PHE* 4.0 19.7 - - + -
194C GLU* 4.1 24.7 - - - +
195C PHE* 4.6 18.4 - - + -
----------------------------------------------------------
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