Contacts of the helix formed by residues 153 - 170 (chain C) in PDB entry 1C72
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 153 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MET* 3.0 26.9 - - - +
86C CYS* 3.6 22.2 - - - +
87C GLY* 4.6 0.9 - - - +
96C VAL* 4.3 4.8 - - + +
148C VAL* 3.3 32.4 - - + +
151C LYS* 3.6 9.2 + - + +
152C LEU* 1.3 79.0 - - - +
154C PHE* 1.3 64.2 + - - +
155C VAL* 3.0 14.9 + - - +
156C ASP* 2.8 37.2 + - - +
157C PHE* 3.6 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.5 5.8 - - + -
73C ASN* 5.0 1.8 - - - -
76C LEU* 4.0 34.7 - - + +
77C ARG* 3.8 31.0 - - + -
80C ALA* 3.7 20.9 - - + -
85C MET* 3.2 18.8 + - + +
86C CYS* 4.2 16.4 - - - -
96C VAL* 3.4 38.1 - - + -
100C GLU* 4.1 10.3 - - + -
153C THR* 1.3 75.1 - - - +
155C VAL* 1.3 64.4 + - + +
156C ASP 3.1 0.4 - - - -
157C PHE* 3.0 32.9 + - - +
158C LEU* 3.3 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG 5.5 0.4 - - - +
96C VAL* 3.8 22.0 - - + +
99C LEU* 3.4 43.1 - - + -
100C GLU* 3.8 19.3 - - + +
103C LEU* 3.9 4.0 - - + +
147C PHE* 3.9 13.9 - - + -
148C VAL* 4.9 7.0 - - + -
153C THR* 3.0 14.9 + - - +
154C PHE* 1.3 85.5 - - + +
156C ASP* 1.3 61.1 + - - +
158C LEU* 3.3 7.2 + - + +
159C ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TRP* 3.4 17.2 - - + +
147C PHE* 2.9 33.6 + - - +
148C VAL* 4.6 0.7 - - - +
151C LYS 4.1 1.2 - - - +
152C LEU* 3.3 25.4 - - + +
153C THR* 2.8 42.8 + - - +
155C VAL* 1.3 81.7 - - - +
157C PHE* 1.3 55.6 + - - +
159C ALA* 4.5 2.0 - - - -
160C TYR* 3.1 28.1 + - - +
183C PHE* 3.5 19.5 - - + -
187C PHE* 4.2 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 3.8 21.5 - - + +
18C LEU* 3.5 28.6 - - + +
19C LEU* 3.6 29.4 - - + -
22C TYR* 4.0 25.1 - + + -
76C LEU* 5.0 2.9 - - + -
85C MET* 3.8 20.6 - - + -
152C LEU* 3.9 18.6 - - + -
153C THR 3.6 10.5 - - - -
154C PHE* 3.0 13.9 + - - +
156C ASP* 1.3 76.8 - - - +
158C LEU* 1.3 62.8 + - - +
160C TYR* 3.9 4.1 - - - +
161C ASP* 3.2 23.0 + - - +
187C PHE* 3.6 31.9 - + - -
193C ILE* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU 6.1 0.2 - - - +
15C ALA* 3.8 11.9 - - + -
72C SER* 6.0 1.1 - - - +
73C ASN* 4.2 18.8 - - - +
76C LEU* 3.6 26.2 - - + -
100C GLU* 4.6 21.8 - - + +
103C LEU* 3.6 18.8 - - + -
107C ARG* 4.2 20.0 - - - +
154C PHE* 3.3 31.1 + - + +
155C VAL* 3.3 7.1 + - - +
157C PHE* 1.3 76.2 - - - +
159C ALA* 1.3 63.8 + - - +
161C ASP* 3.4 4.2 + - - +
162C VAL* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.8 1.1 - - + -
103C LEU* 3.4 23.0 - - + +
137C LEU* 5.8 0.7 - - + -
147C PHE* 3.7 36.8 - - + -
155C VAL 2.9 17.2 + - - +
156C ASP 4.0 3.4 - - - +
157C PHE 3.4 0.2 - - - -
158C LEU* 1.3 76.5 - - - +
160C TYR* 1.3 57.0 + - - +
162C VAL* 3.3 1.0 + - - +
163C LEU* 2.8 39.5 + - + +
183C PHE* 4.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C HIS* 4.4 11.0 - - - -
18C LEU* 3.9 21.8 - - + -
156C ASP 3.1 19.7 + - - +
157C PHE 3.9 4.0 - - - +
159C ALA* 1.3 75.8 - - - +
161C ASP* 1.3 55.9 + - - +
163C LEU* 3.7 0.7 - - - +
164C ASP* 2.8 47.0 + - + +
167C ARG* 4.2 4.9 + - - -
183C PHE* 3.9 11.6 - + + -
184C LEU* 3.5 28.5 - - + -
187C PHE* 3.5 40.6 - + + -
188C GLU* 2.9 45.0 + - + +
197C MET* 3.4 16.2 - - + +
202C PHE* 5.9 0.2 - + - -
204C LYS* 4.0 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 3.1 23.9 + - - +
11C GLY 4.0 3.3 - - - +
12C LEU 4.9 0.9 - - - +
14C HIS* 3.4 30.9 - - + +
15C ALA* 3.5 12.7 + - + +
107C ARG* 2.9 25.3 + - - +
157C PHE 3.2 16.1 + - - +
158C LEU* 3.4 7.2 + - - +
160C TYR* 1.3 83.7 - - + +
162C VAL* 1.3 62.5 + - - +
164C ASP 3.3 0.2 + - - -
165C GLN* 3.1 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 3.8 36.8 - - + +
106C LEU* 4.3 26.2 - - + -
107C ARG* 4.3 26.2 - - + +
158C LEU 3.0 23.5 + - - +
159C ALA 3.7 2.7 - - - +
161C ASP* 1.3 76.0 - - - +
163C LEU* 1.3 69.4 + - + +
165C GLN* 3.2 13.1 + - - +
166C GLN* 3.2 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 6.4 0.7 - - + -
134C LEU* 4.4 18.8 - - + -
137C LEU* 4.3 24.0 - - + -
147C PHE* 5.1 4.9 - - + -
159C ALA* 2.8 22.7 + - + +
162C VAL* 1.3 78.6 - - + +
164C ASP* 1.3 61.3 + - - +
166C GLN* 3.1 9.8 + - + +
167C ARG* 2.9 30.9 + - - +
176C LEU* 4.7 6.0 - - + +
180C LEU* 4.0 31.0 - - + +
183C PHE* 4.0 13.7 - - + -
184C LEU* 3.7 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 2.9 21.3 + - - +
14C HIS* 4.3 2.3 + - - -
160C TYR* 2.8 34.2 + - + +
161C ASP* 3.5 6.3 - - - +
163C LEU* 1.3 72.0 - - - +
165C GLN* 1.3 57.4 + - - +
167C ARG* 3.1 28.4 + - - +
168C MET* 2.9 47.3 + - - +
184C LEU* 4.8 1.5 - - - +
204C LYS* 2.8 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 3.5 14.1 - - - +
11C GLY 4.4 8.3 + - - -
107C ARG* 3.9 29.2 + - - +
110C PHE* 3.8 26.8 - - + -
161C ASP* 3.1 30.3 + - - +
162C VAL* 3.4 11.3 - - - +
163C LEU 3.2 0.2 - - - -
164C ASP* 1.3 77.1 - - - +
166C GLN* 1.3 68.7 + - - +
168C MET* 3.6 2.4 + - - +
169C PHE* 3.3 21.8 + - - +
207C ILE* 3.4 41.6 - - + +
208C PHE* 4.6 3.9 - - - -
214C TRP* 5.2 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
----------------------------------------------------------
106C LEU* 5.2 2.6 + - - +
107C ARG* 6.0 1.0 - - - +
110C PHE* 3.8 34.0 - - - +
126C TYR* 3.1 30.5 + - - -
130C LEU* 4.1 20.2 - - + +
134C LEU* 5.2 8.5 - - + -
162C VAL* 3.2 28.7 + - + +
163C LEU* 3.1 14.5 + - + +
165C GLN* 1.3 80.1 + - - +
167C ARG* 1.3 58.6 + - - +
169C PHE* 3.1 7.4 + - - +
170C VAL* 2.9 34.1 + - + +
176C LEU* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TYR* 4.2 6.3 + - - -
163C LEU 2.9 14.0 + - - +
164C ASP* 3.1 26.6 + - - +
166C GLN* 1.3 77.9 - - - +
168C MET* 1.3 64.2 + - + +
170C VAL 4.6 0.2 - - - -
171C PRO* 3.2 34.9 - - + +
176C LEU* 3.9 25.4 - - + -
184C LEU* 3.7 27.6 - - - +
188C GLU* 3.0 38.3 + - - -
204C LYS* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG* 4.7 3.6 - - - -
164C ASP* 2.9 37.8 + - - +
165C GLN 4.0 4.9 - - - +
166C GLN 3.2 0.2 - - - -
167C ARG* 1.3 86.3 - - + +
169C PHE* 1.3 64.2 + - - +
171C PRO* 4.0 9.3 - - - +
204C LYS* 3.8 31.4 - - + -
207C ILE* 4.7 7.0 - - + -
214C TRP* 3.6 17.6 - - + -
216C ASN* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PHE* 3.5 35.4 - + + -
113C LEU* 4.2 10.1 - - + -
114C CYS* 4.6 0.9 - - - -
119C PHE* 4.3 15.5 - + - -
123C LYS* 4.2 24.0 - - + -
126C TYR* 4.5 10.3 - + - -
127C LEU* 3.6 27.4 - - + -
130C LEU* 6.2 0.2 - - + -
165C GLN 3.3 14.0 + - - +
166C GLN* 3.1 12.3 + - - +
168C MET* 1.3 82.1 - - - +
170C VAL* 1.3 72.0 + - + +
171C PRO* 3.7 4.8 - - - +
214C TRP* 3.7 38.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 4.4 13.5 - - + -
130C LEU* 4.3 18.2 - - + -
166C GLN* 2.9 12.0 + - + +
167C ARG 3.9 1.8 - - - -
169C PHE* 1.3 93.0 - - + +
171C PRO* 1.3 63.2 - - - +
172C ASP* 3.1 25.2 + - - +
173C CYS* 3.3 31.0 + - + +
176C LEU* 3.9 7.6 - - + +
----------------------------------------------------------
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