Contacts of the helix formed by residues 152 - 170 (chain C) in PDB entry 4U1D
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 152 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE* 1.3 77.4 - - - +
153C SER* 1.3 57.3 + - - +
154C TRP 3.0 0.9 - - - -
155C LEU* 3.1 10.4 + - - +
156C ARG* 2.9 28.1 + - + +
195C ARG* 4.8 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LYS* 2.6 32.5 + - - -
151C ILE 4.4 3.0 + - - +
152C THR* 1.3 80.5 - - - +
154C TRP* 1.3 64.0 + - - +
156C ARG* 4.0 7.6 - - - +
157C PHE* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL 3.8 14.1 - - - -
61C GLU 4.3 8.5 - - - -
63C LYS* 3.5 38.6 - - + +
100C VAL* 6.0 0.4 - - + -
103C LYS* 3.4 50.3 - - + -
104C ILE* 4.7 6.0 - - + +
107C GLU* 3.9 33.8 + - + -
151C ILE* 3.2 35.1 + - + +
152C THR 3.0 0.4 - - - -
153C SER* 1.3 82.8 + - - +
155C LEU* 1.3 62.0 + - + +
157C PHE* 3.5 18.1 - + - +
158C THR* 2.8 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 4.4 14.1 - - + -
151C ILE* 2.9 23.3 + - + +
152C THR* 3.1 9.8 + - - +
154C TRP* 1.3 72.7 - - - +
156C ARG* 1.3 60.7 + - - +
158C THR* 3.1 4.8 + - - -
159C TRP* 2.9 28.2 + - - +
189C PHE* 3.9 20.4 - - + -
193C TYR* 3.8 39.0 - - + +
195C ARG* 3.7 39.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 2.9 16.9 + - + +
153C SER* 4.0 8.3 - - - +
155C LEU* 1.3 76.5 - - - +
157C PHE* 1.3 56.3 + - - +
159C TRP* 3.4 13.7 + - - +
160C GLU* 2.9 48.3 + - + +
163C ARG* 5.5 0.2 - - - +
195C ARG* 3.9 12.2 - - - +
198C GLU* 3.4 21.6 + - - +
201C ARG* 3.6 29.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
60C VAL* 4.3 25.8 - - + -
63C LYS* 3.7 51.4 - - + -
65C GLY* 3.8 17.3 - - - -
68C LEU* 4.0 23.3 - - + -
100C VAL* 4.1 15.7 - - + -
153C SER 2.9 20.7 + - - +
154C TRP* 3.5 21.1 - + - +
155C LEU 3.2 0.2 - - - -
156C ARG* 1.3 75.2 - - - +
158C THR* 1.3 59.3 + - - +
160C GLU* 3.3 8.6 + - + +
161C SER* 2.8 46.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 3.2 29.1 - - + +
101C GLU* 5.6 1.8 - - + +
103C LYS* 6.0 0.2 - - - +
104C ILE* 3.1 27.5 - - + +
154C TRP* 2.8 19.1 + - - -
155C LEU 3.1 9.2 + - - -
157C PHE* 1.3 73.6 - - - +
159C TRP* 1.3 59.9 + - - +
161C SER* 3.1 2.3 + - - -
162C TYR* 2.9 55.4 + - + +
189C PHE* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LEU 2.9 11.7 + - - +
156C ARG* 3.6 17.3 - - - +
158C THR* 1.3 76.0 - - - +
160C GLU* 1.3 77.6 + - + +
161C SER 3.2 0.2 + - - -
162C TYR* 3.3 2.9 + - + +
163C ARG* 2.9 52.9 + - + +
186C THR* 3.8 29.2 - - + -
189C PHE* 4.3 10.9 - + + -
190C CYS* 4.1 9.4 - - - -
198C GLU* 3.1 71.5 - - + +
201C ARG* 3.6 26.2 - - + +
202C LEU* 3.5 25.8 - - + -
205C MET* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY* 6.5 1.6 - - - -
69C LYS* 3.5 23.9 + - - +
156C ARG* 2.9 47.8 + - + +
157C PHE* 3.7 8.5 - - + +
159C TRP* 1.3 86.9 + - + +
161C SER* 1.3 57.0 + - - +
163C ARG* 3.2 35.2 + - - +
164C ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 3.4 31.2 - - - -
97C ILE* 4.3 2.9 - - - -
100C VAL* 4.0 19.2 - - - +
157C PHE* 2.8 36.1 + - - -
158C THR* 3.4 9.2 - - - -
159C TRP 3.1 0.2 - - - -
160C GLU* 1.3 75.3 - - - +
162C TYR* 1.3 66.3 + - - +
164C ALA* 3.3 2.9 + - - +
165C VAL* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 3.6 36.1 - - + -
100C VAL* 6.0 1.1 - - + -
101C GLU* 2.4 38.7 + - + +
158C THR* 2.9 39.0 + - + -
159C TRP* 3.6 7.2 - - + +
161C SER* 1.3 75.3 - - - +
163C ARG* 1.3 62.6 + - - +
165C VAL* 3.4 2.1 + - - +
166C LEU* 3.0 30.4 + - - +
182C VAL* 3.9 5.5 - - + +
185C LYS* 3.9 24.4 + - + -
186C THR* 3.2 31.6 - - + +
189C PHE* 3.7 33.9 - + + +
----------------------------------------------------------
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
----------------------------------------------------------
464B ASP* 6.0 0.4 + - - -
467B LYS* 5.7 5.5 - - - +
69C LYS* 6.0 0.4 - - - +
156C ARG* 5.5 0.2 - - - +
159C TRP* 2.9 44.6 + - + +
160C GLU* 3.2 36.0 + - - +
162C TYR* 1.3 75.2 - - - +
164C ALA* 1.3 57.7 + - - +
166C LEU* 3.3 4.4 + - - +
167C ASP* 2.9 34.1 + - + +
186C THR* 6.1 0.4 - - - -
201C ARG* 4.1 15.1 - - - +
205C MET* 4.2 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS* 3.7 39.3 - - + +
72C LEU* 6.3 2.7 - - + -
73C HIS* 4.5 4.5 - - - -
96C PHE* 4.9 7.9 - - + -
160C GLU 2.9 20.1 + - - +
161C SER* 3.7 6.3 - - - +
163C ARG* 1.3 77.4 - - - +
165C VAL* 1.3 56.7 + - - +
167C ASP* 3.2 7.4 + - - +
168C LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 5.1 4.5 - - + -
93C ALA* 4.0 19.5 - - + +
96C PHE* 3.4 28.7 - - + -
97C ILE* 3.7 17.7 - - + -
161C SER 2.9 20.9 + - - +
162C TYR 3.8 3.4 - - - +
164C ALA* 1.3 74.6 - - - +
166C LEU* 1.3 58.7 + - - +
168C LEU* 3.1 9.1 + - + +
169C LEU* 2.9 40.2 + - + +
182C VAL* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C TYR 3.0 19.3 + - - +
163C ARG 3.6 4.3 - - - +
165C VAL* 1.3 75.4 - - - +
167C ASP* 1.3 60.8 - - - +
168C LEU 3.1 0.4 - - - -
169C LEU* 3.5 0.6 + - - -
170C ARG* 3.2 22.0 + - - +
179C TYR* 3.6 27.8 - - + +
182C VAL* 3.6 27.1 - - + -
183C VAL* 3.5 35.0 - - + +
186C THR* 4.0 13.9 - - + +
202C LEU* 3.7 30.5 - - + -
205C MET* 3.8 13.9 - - + -
206C LEU* 4.3 3.6 - - + -
209C HIS* 3.6 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B TRP* 4.2 15.2 - - + +
464B ASP* 4.2 15.1 - - - +
467B LYS* 4.1 15.0 + - - -
73C HIS* 4.1 8.7 + - + -
163C ARG* 2.9 20.6 + - + +
164C ALA* 3.2 7.2 + - - +
166C LEU* 1.3 75.6 - - - +
168C LEU* 1.3 58.4 + - - +
170C ARG* 3.2 45.1 + - - +
205C MET* 4.1 9.0 - - - +
209C HIS* 3.1 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 3.7 36.1 - - + +
73C HIS* 3.4 46.2 - - + +
76C LYS* 3.7 37.8 + - + +
89C VAL* 4.9 9.4 - - + +
93C ALA* 5.1 7.0 - - + -
164C ALA 2.9 15.8 + - - +
165C VAL* 3.1 8.7 + - - +
167C ASP* 1.3 81.8 - - - +
169C LEU* 1.3 73.8 + - + +
170C ARG* 3.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 4.6 12.6 - - + -
90C GLY* 5.2 1.1 - - - -
93C ALA* 3.7 20.2 - - + -
165C VAL* 2.9 31.9 + - + +
166C LEU* 3.9 0.7 - - - -
168C LEU* 1.3 90.9 - - + +
170C ARG* 1.3 64.8 + - - +
171C ASN 3.5 1.7 + - - -
172C ASN* 3.8 14.8 + - - +
175C LEU* 4.1 24.4 - - + +
176C GLU* 5.8 0.2 - - - -
178C THR* 3.6 33.4 - - + +
179C TYR* 3.6 38.1 - - + +
182C VAL* 4.4 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
463B TRP* 2.9 41.0 + - - +
466B GLU* 4.2 19.7 + - - +
467B LYS* 3.5 37.7 - - - +
470B LEU* 6.0 3.2 - - - +
166C LEU 3.2 14.6 + - - +
167C ASP* 3.2 35.7 + - - +
168C LEU 3.3 3.9 - - - +
169C LEU* 1.3 79.2 - - - +
171C ASN* 1.3 75.6 + - + +
172C ASN* 3.4 3.3 + - - +
179C TYR* 4.1 8.1 - - - -
209C HIS* 3.7 34.0 + - + +
----------------------------------------------------------
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