Contacts of the strand formed by residues 160 - 176 (chain C) in PDB entry 5J0Z
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 TRP 160 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.7 37.1 + - + +
32C ASP* 4.0 1.8 + - - -
114C LEU* 5.4 0.9 - - + -
122C ASP* 3.7 11.2 - - - -
124C GLN* 3.8 25.8 - - + -
157C LEU* 2.8 47.4 + - + +
158C THR 3.5 12.6 + - - -
159C GLY* 1.3 85.3 + - - +
161C ASP* 1.3 64.4 + - - +
162C ILE* 4.5 5.4 - - - +
190C ILE* 3.6 18.4 - - + -
191C SER 3.4 9.9 - - - -
192C ARG* 3.2 77.4 - - + +
193C GLN* 3.4 16.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
160C TRP* 1.3 75.4 - - - +
162C ILE* 1.3 61.5 + - - +
163C GLU* 3.8 7.1 - - - +
190C ILE* 3.2 8.1 - - - +
191C SER* 2.7 50.4 + - - +
192C ARG 4.8 1.2 - - - +
193C GLN* 3.5 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C CYS* 5.2 1.6 - - - -
151C LYS* 4.1 24.0 - - + -
155C VAL* 3.5 43.5 - - + +
156C PHE* 4.3 0.7 - - - -
157C LEU* 3.9 26.0 - - + +
160C TRP 4.5 1.3 - - - +
161C ASP* 1.3 78.4 - - - +
163C GLU* 1.3 67.1 + - - +
188C LEU* 3.5 32.3 - - + -
189C ARG 3.8 3.8 - - - +
190C ILE* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C SER* 5.1 0.2 + - - -
151C LYS* 3.6 12.6 + - - -
161C ASP* 3.8 6.5 - - - +
162C ILE* 1.3 78.4 - - - +
164C SER* 1.3 63.1 + - - +
189C ARG* 2.9 26.6 + - + +
190C ILE 3.8 3.5 + - - -
191C SER* 3.4 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LYS* 4.0 7.0 - - - +
163C GLU* 1.3 83.7 - - - +
165C PHE* 1.3 61.3 + - - +
166C THR* 4.0 14.9 + - - -
188C LEU* 3.5 8.8 - - - +
189C ARG* 3.0 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.3 30.5 - - + -
24C LEU* 3.6 31.9 - - + -
128C ILE* 4.4 10.5 - - + -
149C VAL* 4.1 13.3 - - + +
150C GLY* 3.3 23.7 - - - +
151C LYS* 3.8 25.8 + - + +
164C SER* 1.3 73.4 - - - +
166C THR* 1.3 64.1 + - - +
186C TYR* 3.7 42.4 - + + -
187C GLN 3.5 19.5 - - - -
188C LEU* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C VAL* 4.7 6.3 - - - -
164C SER* 4.1 14.9 + - - -
165C PHE* 1.3 81.2 - - - +
167C ALA* 1.3 66.2 + - - +
186C TYR* 3.7 4.5 - - - +
187C GLN* 2.9 26.7 + - - +
189C ARG* 3.0 29.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
144C VAL* 4.0 24.2 - - + -
146C LEU* 5.1 5.9 - - + +
149C VAL* 4.9 3.3 - - + +
166C THR* 1.3 79.7 - - - +
168C VAL* 1.3 60.2 + - - +
169C VAL* 2.9 19.2 + - - +
184C LEU* 5.6 0.2 - - + -
185C ASP 3.5 9.4 - - - +
186C TYR* 3.8 31.0 - - + -
187C GLN* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ALA* 1.3 65.4 - - - +
169C VAL* 1.3 65.6 - - + +
170C LYS* 3.2 23.1 + - + +
184C LEU* 3.2 21.3 - - - +
185C ASP* 3.0 27.3 + - + +
187C GLN* 3.3 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ALA* 4.7 3.5 - - - +
144C VAL* 3.8 24.0 + - + +
146C LEU* 4.0 32.5 - - + -
167C ALA 2.9 15.8 + - - +
168C VAL* 1.3 72.2 - - + +
170C LYS* 1.3 62.9 + - + +
171C PRO* 3.3 12.1 - - - +
184C LEU* 4.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C VAL* 3.2 21.3 - - + +
169C VAL* 1.3 83.3 - - + +
171C PRO* 1.3 78.7 - - + +
172C ALA* 3.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 4.4 8.1 - - + -
142C LEU 3.1 26.7 - - - +
143C ALA* 5.2 2.0 - - + -
169C VAL 3.3 11.1 - - - +
170C LYS* 1.3 95.2 - - + +
172C ALA* 1.3 59.0 + - - +
173C ASN* 3.0 26.0 + - - +
182C SER* 3.7 9.6 - - - +
183C LYS 3.4 21.5 - - - +
184C LEU* 4.1 13.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
170C LYS* 3.3 8.8 + - + +
171C PRO* 1.3 70.6 - - - +
173C ASN* 1.3 63.7 + - - +
174C PHE* 4.0 6.1 - - + -
183C LYS* 3.4 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 3.3 30.3 - - - +
171C PRO* 3.0 19.0 + - - +
172C ALA* 1.3 76.5 - - - +
174C PHE* 1.3 65.8 + - - +
180C LEU* 4.2 16.7 - - + +
181C GLU 3.4 11.4 - - - +
182C SER* 2.9 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 5.4 4.5 - - - -
152B ASN* 5.8 6.5 - - - -
131C ILE* 4.4 12.3 - - + -
172C ALA 4.0 4.7 - - - -
173C ASN* 1.3 86.1 - - - +
175C ALA* 1.3 71.9 + - - +
176C LEU* 3.8 25.0 + - + -
180C LEU* 3.4 10.2 - - - +
181C GLU* 2.8 52.2 + - + +
183C LYS* 4.1 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PHE* 1.3 83.0 - - - +
176C LEU* 1.3 60.4 + - - +
177C GLU 4.2 0.4 - - - -
178C ASP* 5.4 7.4 - - - +
179C ARG 3.5 12.1 - - - +
180C LEU* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.4 55.0 - - + +
25B ILE* 6.1 0.4 - - + -
42B PHE* 3.9 17.3 - - + -
152B ASN* 5.1 1.8 - - - +
131C ILE* 5.6 1.6 - - + -
133C ARG* 2.7 30.6 + - - +
174C PHE* 3.8 22.8 + - + -
175C ALA* 1.3 74.7 - - - +
177C GLU* 1.3 71.4 + - + +
178C ASP 3.5 0.4 - - - -
179C ARG 2.9 12.7 + - - +
181C GLU* 3.6 33.4 - - + +
----------------------------------------------------------
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