Contacts of the strand formed by residues 181 - 191 (chain C) in PDB entry 2PWP
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 LEU 181 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 3.6 6.9 - - - +
151C TYR 3.4 15.7 - - - +
152C ASP 4.0 1.6 - - - +
154C ILE* 3.7 26.0 - - + +
177C ILE* 3.1 22.7 + - + +
178C TYR 3.6 1.6 - - - +
179C ASN 3.2 8.2 - - - +
180C ALA* 1.3 81.8 - - - +
182C LYS* 1.3 61.2 + - - +
185C GLY* 4.0 6.7 - - - -
186C TYR 3.4 39.5 - - - +
212C PHE* 3.7 33.7 - - + -
237C LYS* 3.2 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 6.1 0.7 - - - -
149C ASN* 3.1 37.2 + - - +
150C THR* 3.7 17.7 - - - +
151C TYR 2.8 19.5 + - - +
152C ASP* 3.5 26.2 - - - +
181C LEU* 1.3 77.9 - - - +
183C PRO* 1.3 75.5 - - + +
184C ASN 3.1 4.7 - - - +
185C GLY* 3.0 13.1 + - - +
237C LYS* 3.0 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 3.2 20.6 - - - +
182C LYS* 1.3 90.2 - - + +
184C ASN* 1.3 68.5 + - - +
185C GLY 3.5 0.2 - - - -
237C LYS* 3.4 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER* 5.6 0.5 + - - -
182C LYS* 3.1 3.1 - - - +
183C PRO* 1.3 90.5 - - - +
185C GLY* 1.3 63.1 + - - +
186C TYR* 3.4 22.5 - - + +
237C LYS* 4.7 3.8 - - - -
238C THR* 3.5 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TYR 4.4 2.5 - - - -
152C ASP* 3.2 17.7 - - - -
181C LEU* 4.0 16.2 - - - +
182C LYS* 3.0 17.5 + - - +
183C PRO 3.5 0.8 + - - -
184C ASN* 1.3 82.4 - - - +
186C TYR* 1.3 62.3 + - - -
235C CYS 4.4 0.3 - - - +
237C LYS* 3.7 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO* 4.7 11.2 - - + -
74C VAL* 3.6 23.6 + - + +
75C SER* 3.8 38.4 - - - -
152C ASP 3.0 9.1 + - - +
153C VAL* 3.3 6.5 - - + +
154C ILE 2.9 23.9 + - - +
181C LEU* 3.4 7.0 - - - +
184C ASN* 3.4 21.1 + - + +
185C GLY* 1.3 72.3 - - - -
187C CYS* 1.3 60.1 + - - +
235C CYS 3.5 3.4 - - - +
236C SER* 3.3 38.4 - - - -
237C LYS 5.1 0.4 - - - -
238C THR* 3.7 17.8 + - - +
240C THR* 4.8 3.5 + - - -
241C GLY 4.0 6.0 + - - -
242C LEU* 3.6 22.4 - - + -
246C ASN* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 3.2 13.0 - - + +
156C VAL* 3.9 16.8 - - - -
174C TYR* 4.5 17.3 - - - -
177C ILE* 3.7 33.0 - - + -
181C LEU* 4.1 5.1 - - + +
186C TYR* 1.3 76.3 - - - +
188C VAL* 1.3 74.2 + - - +
189C ALA* 4.7 1.3 - - - -
212C PHE* 4.3 0.2 - - + -
233C LEU 3.8 0.9 - - - +
235C CYS* 2.7 50.3 + - + +
242C LEU* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C MET* 3.3 28.9 - - - +
70C VAL* 4.7 0.7 - - + -
71C PRO* 3.7 32.7 - - + +
154C ILE 3.0 4.0 + - - +
155C ILE* 3.4 17.5 - - + +
156C VAL* 2.8 25.3 + - - +
186C TYR 4.3 0.4 - - - -
187C CYS* 1.3 79.5 - - - +
189C ALA* 1.3 62.7 + - - +
232C ILE* 3.6 14.1 - - + -
233C LEU 3.1 2.7 - - - -
234C CYS* 3.9 24.0 - - - -
242C LEU* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C MET* 4.1 5.4 - - - -
156C VAL* 3.6 22.9 - - + -
174C TYR* 3.2 28.3 - - + +
187C CYS* 4.7 2.9 - - - -
188C VAL* 1.3 77.2 - - - +
190C GLN* 1.3 68.5 + - - +
191C CYS 3.2 0.2 + - - -
204C MET* 5.5 0.4 - - + -
232C ILE* 3.6 2.8 - - - -
233C LEU* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C TYR* 3.4 32.8 - - + +
67C MET* 3.6 7.1 - - + +
156C VAL* 3.0 16.1 + - - +
158C SER* 3.0 29.9 + - - +
159C SER 3.7 13.2 - - - +
169C PHE* 3.8 17.6 - - - -
189C ALA* 1.3 76.6 - - - +
191C CYS* 1.3 85.5 + - - +
192C GLU* 3.0 28.0 + - - +
204C MET* 5.5 2.1 - - - +
230C ILE* 3.5 23.6 - - + +
231C GLY 3.8 4.3 - - - +
401C SPD 3.8 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PHE* 5.2 2.0 - - - -
189C ALA 3.9 0.7 - - - +
190C GLN* 1.3 87.3 + - - +
192C GLU* 1.3 74.8 + - - +
200C THR* 5.3 1.3 - - - -
201C ILE* 4.3 13.5 - - - -
204C MET* 3.9 35.0 - - - -
217C TYR* 3.9 21.5 - - + -
230C ILE* 3.1 2.9 - - - +
231C GLY 2.8 23.1 + - - +
233C LEU* 3.7 27.8 - - + +
----------------------------------------------------------
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