Contacts of the helix formed by residues 158 - 183 (chain C) in PDB entry 3VJR
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 PRO 158 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 3.5 18.2 - - - +
156C LYS 3.6 3.3 - - - +
157C PRO* 1.3 82.8 - - + +
159C VAL* 1.3 68.7 + - + +
160C SER* 3.2 9.2 - - - +
161C GLU* 2.9 39.2 + - + +
162C GLN 3.0 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PRO 3.7 1.4 + - - -
158C PRO* 1.3 70.1 - - + +
160C SER* 1.3 64.2 + - - +
162C GLN* 3.1 17.1 + - - +
163C LYS* 2.9 53.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PRO* 3.2 7.7 + - - +
159C VAL* 1.3 77.9 - - - +
161C GLU* 1.3 68.6 + - - +
163C LYS* 3.8 9.4 + - - +
164C LEU* 3.4 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 2.9 31.0 + - - -
103C PRO* 3.9 25.5 - - + +
140C ILE 4.4 7.4 - - - +
152C PHE* 4.7 2.4 - - - -
157C PRO* 4.2 6.5 - - + -
158C PRO* 2.9 29.7 + - + +
160C SER* 1.3 79.3 + - - +
162C GLN* 1.3 66.6 + - - +
163C LYS 3.2 0.2 - - - -
164C LEU* 3.1 6.7 + - + +
165C ILE* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TRP* 4.2 15.5 - - + -
157C PRO* 4.0 21.8 - - + +
158C PRO 3.0 10.1 + - - +
159C VAL* 3.5 23.2 - - - +
161C GLU* 1.3 77.3 - - - +
163C LYS* 1.3 74.1 + - - +
165C ILE* 3.2 8.3 + - - +
166C ASP* 2.6 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C VAL* 2.9 40.6 + - + +
160C SER* 4.1 7.4 - - - +
161C GLU 3.2 0.2 - - - -
162C GLN* 1.3 89.0 - - - +
164C LEU* 1.3 58.5 + - + +
166C ASP* 3.3 3.9 + - - +
167C GLU* 3.0 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PRO* 3.7 31.2 - - + +
104C GLY* 3.3 12.1 - - - +
160C SER* 3.4 18.1 + - - +
161C GLU* 3.1 8.8 + - + +
163C LYS* 1.3 79.0 - - + +
165C ILE* 1.3 63.5 + - - +
167C GLU* 3.2 13.4 + - - +
168C ALA 3.0 19.1 + - - -
196C ALA* 3.8 31.6 - - + +
197C GLN* 3.9 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 5.1 4.0 - - + +
26C ALA* 4.6 6.1 - - + -
29C TRP* 3.9 17.3 - - + -
103C PRO* 4.1 8.5 - - + -
104C GLY 4.2 4.5 - - - +
138C ILE* 4.0 12.6 - - + -
139C GLY 3.6 16.8 - - - +
140C ILE* 4.0 23.6 - - + +
157C PRO* 4.4 22.0 - - + -
161C GLU* 2.9 26.1 + - + +
162C GLN* 3.6 7.0 - - - +
164C LEU* 1.3 76.0 - - - +
166C ASP* 1.3 57.1 + - - +
168C ALA* 3.3 4.4 + - - +
169C ILE* 2.9 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TRP* 4.0 21.0 - - - +
33C LEU* 5.4 2.6 - - - +
162C GLN* 2.6 46.3 + - - +
163C LYS* 3.8 4.3 - - - +
165C ILE* 1.3 75.2 - - - +
167C GLU* 1.3 58.8 + - - +
169C ILE* 3.9 11.9 - - - +
170C ASP* 3.0 28.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
163C LYS* 3.0 23.2 + - - +
164C LEU* 3.6 15.3 - - - +
166C ASP* 1.3 73.2 - - + +
168C ALA* 1.3 66.9 + - - +
170C ASP* 3.3 9.9 + - + +
171C GLU* 3.0 23.2 + - - +
194C PHE* 3.7 11.2 - - + -
196C ALA* 3.8 25.0 - - + +
197C GLN 4.8 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLY* 3.6 31.4 - - - +
105C VAL 3.8 16.4 - - - +
106C ALA* 4.3 7.6 - - + +
138C ILE* 5.2 4.5 - - + -
164C LEU 3.0 8.8 + - - +
165C ILE* 3.6 8.1 - - - +
167C GLU* 1.3 75.8 - - - +
169C ILE* 1.3 52.4 + - - +
171C GLU* 3.2 2.9 + - - +
172C ALA* 2.7 37.3 + - - +
191C LEU* 4.7 0.9 - - - +
194C PHE* 3.6 12.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA 3.8 21.8 - - - +
29C TRP* 3.8 18.2 - - + +
30C PHE* 3.8 23.6 - - + +
33C LEU* 3.8 21.1 - - + -
138C ILE* 4.0 26.7 - - + -
165C ILE* 2.9 38.0 + - + +
166C ASP* 3.9 11.9 - - - +
167C GLU 3.3 0.2 - - - -
168C ALA* 1.3 72.7 - - - +
170C ASP* 1.3 58.2 - - - +
172C ALA* 3.6 6.7 - - - +
173C ALA* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.8 17.4 - - + +
37C ARG* 4.5 5.0 + - - -
166C ASP 3.0 19.1 + - - +
167C GLU* 3.4 11.5 - - - +
169C ILE* 1.3 77.3 - - - +
171C GLU* 1.3 61.8 + - - +
173C ALA* 3.5 2.9 + - - +
174C ARG* 3.1 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU 3.0 15.5 + - - +
168C ALA 3.7 3.4 - - - +
170C ASP* 1.3 73.6 - - - +
172C ALA* 1.3 60.4 + - - +
174C ARG* 3.3 9.9 + - - +
175C CYS* 2.9 43.4 + - - -
190C ARG* 2.7 50.4 + - - +
191C LEU* 4.3 8.1 - - + -
194C PHE* 3.5 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.7 3.4 - - + -
106C ALA* 4.4 4.0 - - + -
108C PHE* 4.7 0.7 - - - -
136C LEU* 3.8 37.5 - - + -
138C ILE* 5.7 0.4 - - + -
168C ALA 2.7 21.0 + - - +
169C ILE* 3.7 7.9 - - + +
171C GLU* 1.3 71.1 - - - +
173C ALA* 1.3 55.5 + - - +
175C CYS* 3.2 3.0 + - - +
176C THR* 2.8 38.5 + - - -
191C LEU* 3.8 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.4 18.7 - - + -
33C LEU* 4.1 10.3 - - + -
34C LEU* 4.1 13.5 - - + +
37C ARG* 3.8 23.6 - - - -
169C ILE 2.8 20.3 + - - +
170C ASP 3.6 6.3 - - - +
172C ALA* 1.3 72.0 - - - +
174C ARG* 1.3 61.9 + - - +
176C THR* 3.2 4.2 + - - -
177C GLU* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ARG* 3.4 38.0 - - - +
170C ASP* 3.1 40.1 + - - +
171C GLU* 3.3 15.9 + - - +
173C ALA* 1.3 76.3 - - - +
175C CYS* 1.3 58.7 + - - +
177C GLU* 3.4 10.8 + - - +
178C MET* 3.0 25.9 + - - +
190C ARG* 4.3 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE* 4.3 8.0 - - + -
171C GLU* 2.9 37.2 + - - +
172C ALA* 3.8 4.7 - - - +
174C ARG* 1.3 73.8 - - - +
176C THR* 1.3 60.2 + - - +
178C MET* 3.2 6.8 + - - -
179C TRP* 2.9 24.3 + - - +
187C ALA* 3.2 24.6 - - - +
190C ARG* 3.8 15.0 - - - -
191C LEU* 3.7 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 4.2 24.7 - - + -
30C PHE* 3.4 21.8 - - + -
34C LEU* 4.4 8.3 - - + -
57C LEU* 5.7 1.3 - - + -
93C LEU* 4.3 14.0 - - + +
108C PHE* 3.9 17.6 - - - -
136C LEU* 4.8 0.5 - - - +
172C ALA 2.8 22.5 + - - -
173C ALA 3.5 5.4 - - - -
175C CYS* 1.3 74.5 - - - +
177C GLU* 1.3 64.0 + - + +
179C TRP* 3.2 22.6 - - + +
180C PHE* 3.2 22.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
34C LEU* 4.4 8.2 - - + +
37C ARG* 2.8 48.6 + - - +
38C LEU* 4.0 26.6 - - + +
57C LEU* 4.9 10.7 - - + +
173C ALA 3.1 15.5 + - - +
174C ARG* 3.6 7.9 - - - +
175C CYS 3.3 0.2 - - - -
176C THR* 1.3 74.8 - - + +
178C MET* 1.3 63.4 + - - +
180C PHE* 3.1 20.4 + - - +
181C THR* 3.3 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ARG 3.0 14.1 + - - +
175C CYS* 3.2 10.5 + - - +
177C GLU* 1.3 76.4 - - - +
179C TRP* 1.3 56.0 + - - +
181C THR* 4.0 6.5 - - - -
182C ASP* 2.8 52.2 + - + +
183C GLY 3.4 2.8 + - - +
186C LYS* 3.8 46.4 - - + +
187C ALA* 4.2 8.5 - - + -
190C ARG* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR 4.9 10.8 - - - +
6C ILE* 3.5 30.1 - - + +
93C LEU* 3.9 21.3 - - + -
108C PHE* 3.9 35.9 - + + -
134C HIS* 3.6 39.9 - + + -
175C CYS 2.9 11.2 + - - +
176C THR* 3.2 17.3 - - + +
178C MET* 1.3 76.3 - - - +
180C PHE* 1.3 65.6 + + + +
183C GLY* 3.0 22.7 + - - -
184C LEU* 3.7 45.7 - - + +
187C ALA* 3.6 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 5.7 0.7 - - - -
6C ILE* 3.4 53.4 - - + -
9C ILE* 4.3 4.0 - - + -
57C LEU* 3.6 42.4 - - + -
58C GLY* 3.8 26.0 - - - +
60C GLU* 6.3 0.4 - - + -
62C VAL* 3.7 20.4 - - + -
93C LEU* 6.1 0.2 - - + -
176C THR* 3.2 36.8 - - + -
177C GLU 3.1 8.3 + - - +
179C TRP* 1.3 89.7 - + + +
181C THR* 1.3 61.2 + - + +
183C GLY 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLY* 4.9 11.0 - - - +
177C GLU* 3.3 13.1 + - + +
178C MET* 3.2 7.3 + - - -
180C PHE* 1.3 82.5 - - + +
182C ASP* 1.3 82.6 + - - +
183C GLY 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C MET* 2.8 33.6 + - + +
181C THR* 1.3 98.4 + - - +
183C GLY* 1.3 63.9 + - - +
186C LYS* 4.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C MET 3.4 1.1 + - - +
179C TRP* 3.0 23.1 + - - -
180C PHE 4.6 0.4 - - - -
181C THR 3.9 0.4 - - - -
182C ASP* 1.3 81.2 - - - +
184C LEU* 1.3 64.6 + - - -
185C THR* 3.3 3.5 + - - -
186C LYS* 3.4 1.8 + - - +
187C ALA* 3.1 20.8 + - - +
----------------------------------------------------------
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