Contacts of the helix formed by residues 164 - 178 (chain C) in PDB entry 2D11
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 THR 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LYS 4.8 4.5 - - - +
163C LEU* 1.3 77.6 - - - +
165C LYS* 1.3 68.1 + - - +
166C GLU* 3.5 10.8 + - - +
167C GLN* 2.9 51.9 + - - +
168C TRP* 3.0 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 6.5 0.7 - - + -
163C LEU 4.0 0.2 + - - -
164C THR* 1.3 80.9 - - - +
166C GLU* 1.3 64.2 + - + +
168C TRP* 3.6 11.2 + - - +
169C GLU* 3.2 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLY* 6.5 1.1 - - - -
164C THR* 3.1 9.8 + - - +
165C LYS* 1.3 83.5 - - + +
167C GLN* 1.3 61.4 + - + +
169C GLU* 4.1 13.9 - - - +
170C GLU* 3.7 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LYS 4.4 1.4 - - - +
163C LEU* 3.3 30.1 - - + +
164C THR* 2.9 43.7 + - - +
166C GLU* 1.3 79.4 - - + +
168C TRP* 1.3 63.3 + - - +
169C GLU 3.4 0.2 - - - -
170C GLU* 3.2 20.1 - - + +
171C ARG* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PRO* 4.7 6.5 - - + -
120C GLU* 5.6 2.0 - - - -
123C VAL* 3.8 26.0 - - + -
153C LEU* 3.7 26.0 - - + -
157C VAL* 3.7 35.2 - - + -
158C LEU* 3.8 27.9 + - + +
161C HIS* 3.9 31.7 + + + +
163C LEU* 3.5 38.6 + - + +
164C THR 3.0 26.0 + - - -
165C LYS* 3.9 9.9 - - - +
166C GLU 3.5 0.2 - - - -
167C GLN* 1.3 73.6 - - - +
169C GLU* 1.3 66.4 + - + +
170C GLU 3.1 1.3 - - - -
171C ARG* 3.0 17.2 + - + +
172C ILE* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLY* 4.2 14.6 - - - +
147C LEU* 3.7 34.7 - - + +
148C ALA* 3.4 36.3 + - - +
152C LEU* 4.5 6.5 - - + -
165C LYS* 3.2 28.1 + - - +
166C GLU* 4.1 14.8 - - - +
167C GLN 3.4 0.2 - - - -
168C TRP* 1.3 79.0 - - + +
170C GLU* 1.3 57.0 + - - +
172C ILE* 3.5 5.1 + - + +
173C GLN* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLU 3.7 13.9 + - - +
167C GLN* 3.2 15.2 + - + +
169C GLU* 1.3 79.1 - - - +
171C ARG* 1.3 66.0 + - + +
173C GLN* 3.4 16.9 + - - +
174C ASN* 3.0 50.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
120C GLU* 2.7 42.8 + - - -
123C VAL* 4.0 20.5 - - + +
163C LEU* 4.0 25.9 - - + +
167C GLN 3.3 15.5 - - - +
168C TRP* 3.0 18.6 + - + +
170C GLU* 1.3 78.0 - - + +
172C ILE* 1.3 62.4 + - - +
174C ASN* 3.4 20.4 + - - +
175C TRP* 3.5 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C VAL* 4.0 20.9 - - + -
126C ALA* 4.0 13.2 - - + -
127C SER* 3.9 14.2 - - - +
130C VAL* 3.9 28.9 - - + -
147C LEU* 3.9 9.9 - - + -
152C LEU* 3.7 28.3 - - + -
153C LEU* 3.9 25.1 - - + -
168C TRP* 3.0 22.9 + - + +
169C GLU* 3.8 4.3 - - + +
171C ARG* 1.3 73.1 - - - +
173C GLN* 1.3 59.6 + - - +
175C TRP* 3.3 6.2 + - - +
176C HIS* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TYR* 3.0 25.3 + - + -
142C HIS 4.6 2.9 - - - +
144C PRO* 4.6 18.2 - - - +
145C GLY 5.3 1.2 - - - +
146C TYR* 3.7 43.8 - - + +
147C LEU* 4.6 0.7 - - - -
169C GLU* 2.9 20.9 + - - +
170C GLU* 3.6 18.8 + - - +
171C ARG 3.3 0.2 - - - -
172C ILE* 1.3 76.0 - - - +
174C ASN* 1.3 67.3 + - - +
176C HIS* 3.2 3.0 + - - +
177C GLU* 3.1 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 3.0 43.3 + - - +
171C ARG* 3.6 15.3 - - - +
172C ILE 3.3 0.4 - - - -
173C GLN* 1.3 81.1 - - - +
175C TRP* 1.3 61.5 + - + +
177C GLU* 3.5 28.8 + - - +
178C GLU* 3.8 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLU* 5.1 6.7 + - - -
123C VAL* 3.6 33.5 - - + +
124C LEU* 3.6 38.7 - - + +
127C SER* 3.2 22.4 - - - -
128C TYR* 5.6 1.3 - - - -
171C ARG* 3.5 11.0 + - - +
172C ILE 3.3 4.4 + - - +
173C GLN 3.3 0.4 - - - -
174C ASN* 1.3 76.7 - - + +
176C HIS* 1.3 59.6 + - - +
178C GLU* 2.9 46.5 + - + +
179C HIS* 3.1 29.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C SER* 4.1 3.3 - - - +
130C VAL* 3.6 32.3 + - + +
131C GLN* 3.4 25.6 + - + +
134C TYR* 4.2 9.6 - - + -
135C GLY 2.9 26.7 + - - -
137C TYR* 3.7 28.5 + + - +
142C HIS* 4.2 5.2 - + - -
146C TYR* 2.8 22.4 + + - +
172C ILE* 3.0 14.4 + - + +
173C GLN* 3.2 12.7 + - - +
175C TRP* 1.3 75.3 - - - +
177C GLU* 1.3 63.7 + - - +
179C HIS* 3.1 22.3 + - - +
180C ARG 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TYR* 3.5 49.3 + - + +
139C LYS* 5.3 7.0 + - - -
173C GLN* 3.1 26.9 + - - +
174C ASN* 3.5 21.0 - - - +
175C TRP 3.2 0.4 - - - -
176C HIS* 1.3 76.0 - - - +
178C GLU* 1.3 63.4 + - + +
179C HIS 3.5 0.9 + - - -
180C ARG* 3.8 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ASN* 3.9 14.8 - - - +
175C TRP* 2.9 39.0 + - + +
177C GLU* 1.3 78.5 - - + +
179C HIS* 1.3 60.5 - - + +
180C ARG* 3.3 5.8 + - - -
----------------------------------------------------------
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