Contacts of the helix formed by residues 181 - 192 (chain C) in PDB entry 1PR1
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 GLU 181 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 3.2 26.9 - - + -
63C GLY 3.6 6.8 - - - +
65C GLY 3.1 23.4 + - - +
66C ILE* 3.9 6.1 - - - -
69C CYS* 3.2 23.7 - - - -
87C ARG* 2.9 26.6 + - - +
155C SER* 3.9 0.7 - - - -
179C GLU* 2.9 2.4 + - - -
180C MET* 1.3 78.2 - - - +
182C ALA* 1.3 68.9 + - - +
183C ALA 3.3 2.7 - - - -
184C GLY* 2.9 14.0 + - - -
185C ILE* 3.0 13.4 + - - +
247C FMB 2.4 44.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 4.3 0.4 - - - +
109C ALA* 3.9 14.8 - - + -
153C LEU* 4.2 6.3 - - + -
155C SER* 3.5 1.6 - - - +
179C GLU* 2.8 31.1 + - - +
181C GLU* 1.3 70.4 - - - +
183C ALA* 1.3 62.9 + - - +
185C ILE* 3.1 7.4 + - - +
186C TYR* 3.0 30.0 + - + -
198C THR* 3.5 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 4.5 2.0 - - + -
109C ALA* 3.7 23.5 - - + +
111C THR* 3.5 33.9 - - + +
115C VAL* 6.1 0.2 - - - -
116C ASN* 3.4 16.3 + - - +
127C ALA* 4.1 10.7 - - + +
155C SER* 2.8 21.0 + - - +
182C ALA* 1.3 73.2 - - - +
184C GLY* 1.3 59.7 + - - +
186C TYR 4.1 0.4 - - - -
187C GLY* 3.3 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 3.8 31.5 - - - +
69C CYS* 4.9 1.3 - - - -
70C SER* 4.2 4.5 + - - -
115C VAL* 5.0 1.8 - - - -
119C ARG* 4.4 7.5 + - - -
181C GLU 2.9 8.5 + - - -
183C ALA* 1.3 79.2 - - - +
185C ILE* 1.3 59.9 + - - +
187C GLY* 3.3 1.9 + - - -
188C VAL* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 4.5 6.1 - - + -
69C CYS* 3.6 24.9 - - + -
73C THR* 4.1 25.8 - - + -
85C ILE* 4.3 11.4 - - + +
87C ARG* 3.5 40.8 - - + -
181C GLU* 3.0 12.8 + - + +
182C ALA* 3.7 7.6 - - - +
184C GLY* 1.3 75.2 - - - +
186C TYR* 1.3 62.2 + - + +
188C VAL* 3.3 6.5 + - - +
189C ALA* 2.8 28.5 + - + +
196C ALA* 3.8 22.9 - - + -
197C LEU 6.0 0.9 - - - +
198C THR* 4.8 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
106C GLY* 2.7 27.8 + - - -
108C GLY 4.4 2.9 - - - -
109C ALA* 4.0 18.6 - - + -
125C PHE* 4.7 3.0 - - - -
127C ALA* 3.4 37.2 - - + -
128C ILE 3.6 19.8 - - - +
129C ALA* 3.5 14.1 - - + +
182C ALA* 3.0 18.2 + - + +
183C ALA 4.1 0.2 - - - +
185C ILE* 1.3 79.9 - - + +
187C GLY* 1.3 61.8 + - - +
189C ALA* 3.7 6.0 - - + +
190C ALA* 3.0 24.6 + - - +
196C ALA* 3.8 32.1 - - + -
197C LEU* 3.9 0.7 - - - -
198C THR* 2.9 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ASN* 3.9 11.2 - - - -
119C ARG* 3.8 24.3 + - - -
125C PHE* 4.4 12.5 - - - -
183C ALA 3.3 6.0 + - - -
184C GLY 3.3 6.6 + - - -
185C ILE 3.2 0.4 - - - -
186C TYR* 1.3 77.3 - - - +
188C VAL* 1.3 58.3 + - - +
190C ALA* 3.5 1.7 + - - +
191C GLU* 2.9 30.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
70C SER* 3.9 22.2 - - - +
73C THR* 3.5 27.4 - - - +
74C LYS* 4.0 9.4 - - + +
77C ILE* 3.9 16.4 - - + -
119C ARG* 3.6 18.2 - - - +
184C GLY 3.0 19.5 + - - +
185C ILE 3.7 4.0 - - - +
186C TYR 3.3 0.2 - - - -
187C GLY* 1.3 74.1 - - - +
189C ALA* 1.3 59.7 + - - +
191C GLU* 3.1 0.4 + - - -
192C PHE* 2.8 57.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
77C ILE* 4.3 14.1 - - + -
85C ILE* 6.5 0.2 - - + -
185C ILE* 2.8 18.3 + - + +
186C TYR* 3.7 7.2 - - - +
188C VAL* 1.3 75.8 - - - +
190C ALA* 1.3 57.4 + - - +
193C GLY* 3.0 10.0 + - - -
194C ALA* 2.8 45.0 + - + +
195C LYS 4.3 0.4 - - - +
196C ALA* 4.0 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 4.0 23.8 - - + -
186C TYR 3.0 17.7 + - - +
187C GLY 3.8 3.4 - - - +
189C ALA* 1.3 76.2 - - - +
191C GLU* 1.3 64.7 + - - +
192C PHE 3.4 0.3 + - - -
193C GLY* 3.6 7.0 + - - -
194C ALA 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ARG* 2.8 40.3 + - + +
187C GLY 2.9 17.8 + - - +
188C VAL 3.8 2.2 - - - +
190C ALA* 1.3 77.5 - - - +
192C PHE* 1.3 89.2 + - + +
193C GLY 3.6 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LYS* 3.5 39.3 - - + -
77C ILE* 3.5 29.1 - - + +
78C THR* 3.5 20.8 - - + +
119C ARG* 5.3 0.7 - - - -
188C VAL* 2.8 41.1 + - + +
189C ALA 3.8 0.2 - - - -
191C GLU* 1.3 111.7 - - + +
193C GLY* 1.3 62.8 + - - +
194C ALA 3.7 1.1 - - - -
----------------------------------------------------------
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