Contacts of the helix formed by residues 65 - 80 (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 GLY 65 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET* 1.3 74.8 - - - +
66C ILE* 1.3 66.4 - - - -
67C PRO* 3.3 9.0 - - - -
68C SER 3.2 10.8 + - - -
69C CYS* 3.2 15.4 + - - +
156C ALA 5.6 0.4 - - - -
157C ASP* 6.0 0.7 - - - -
180C MET* 3.5 27.3 + - - +
181C GLU* 3.1 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY* 1.3 71.4 - - - -
67C PRO* 1.3 68.9 - - + +
69C CYS* 3.6 7.3 - - - -
70C SER* 2.6 44.3 + - - +
111C THR* 3.8 11.2 - - - +
113C SER* 3.6 28.5 - - - +
115C VAL* 4.1 26.5 - - + -
155C SER* 4.3 10.8 - - - +
157C ASP* 4.4 10.1 + - - +
180C MET 3.2 14.6 + - - +
181C GLU* 3.9 9.4 - - - -
183C ALA* 4.5 1.8 - - + -
184C GLY* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY* 3.5 7.2 - - - -
66C ILE* 1.3 97.6 - - + +
68C SER* 1.3 62.2 + - - +
70C SER* 3.7 5.6 - - - -
71C ILE* 3.5 24.6 + - - +
115C VAL* 5.9 4.3 - - + -
157C ASP* 5.0 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C MET* 5.0 1.4 - - - +
62C HIS 2.9 19.9 + - - -
63C GLY* 3.6 8.6 - - - -
64C MET 3.5 23.5 + - - -
65C GLY 3.2 3.0 + - - -
67C PRO* 1.3 77.6 - - - +
69C CYS* 1.3 67.2 + - - +
71C ILE* 3.0 25.6 + - - +
72C TYR* 3.4 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 3.2 41.3 + - + +
65C GLY 3.2 5.9 + - - +
66C ILE* 3.6 13.7 - - - -
68C SER* 1.3 78.1 - - - +
70C SER* 1.3 55.0 + - - +
72C TYR* 3.9 1.8 - - - -
73C THR* 2.7 40.6 + - + +
181C GLU* 3.2 31.9 - - - -
185C ILE* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 2.6 38.8 + - - +
67C PRO* 3.7 7.2 - - - -
69C CYS* 1.3 77.9 - - - +
71C ILE* 1.3 59.5 + - - +
73C THR* 3.5 6.8 + - - -
74C LYS* 3.0 30.5 + - - +
115C VAL* 5.4 1.4 - - - +
119C ARG* 4.7 6.5 + - - -
184C GLY* 4.2 5.4 + - - -
188C VAL* 3.9 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 3.2 52.9 - - + +
67C PRO 3.5 16.1 + - - +
68C SER* 3.0 12.4 + - - +
70C SER* 1.3 80.4 - - - +
72C TYR* 1.3 65.9 + - + +
74C LYS* 3.6 3.1 - - - +
75C GLU* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 3.8 30.3 + + + +
5C ILE* 4.2 10.3 - - + -
18C MET* 3.9 18.8 - - + -
43C ARG* 4.1 22.3 + - - +
45C MET* 3.6 37.3 - - + +
60C MET* 3.4 28.9 - - + -
61C GLY 4.4 0.7 - - - -
62C HIS* 3.6 16.6 - - + -
68C SER* 3.4 35.3 + - - -
69C CYS 4.0 3.6 - - - +
71C ILE* 1.3 79.9 - - + +
73C THR* 1.3 65.3 + - - +
75C GLU* 3.3 2.3 + - - +
76C LEU* 3.1 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 4.2 14.8 - - - -
62C HIS* 5.5 0.2 - - + -
69C CYS* 2.7 30.6 + - + +
70C SER* 3.5 6.1 + - - -
72C TYR* 1.3 72.6 - - - +
74C LYS* 1.3 63.4 + - - +
76C LEU* 3.6 4.2 - - - +
77C ILE* 3.0 31.7 + - - +
85C ILE* 3.5 29.8 - - + -
185C ILE* 4.1 28.8 - - + -
188C VAL* 3.5 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C SER 3.0 18.7 + - - +
71C ILE* 3.6 3.6 - - - +
72C TYR 3.1 0.6 - - - -
73C THR* 1.3 79.0 + - - +
75C GLU* 1.3 70.6 + - + +
77C ILE* 3.3 3.0 + - - +
78C THR* 2.9 53.8 + - - +
79C ASP* 4.4 5.1 + - - -
188C VAL* 4.0 12.1 - - + -
192C PHE* 3.5 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 2.7 41.3 + - + +
3C PRO* 3.4 14.6 - - + +
4C HIS* 2.8 46.7 + - - +
5C ILE* 3.5 14.2 - - + +
71C ILE* 3.0 19.6 + - + +
72C TYR* 4.9 0.3 - - - -
74C LYS* 1.3 86.5 - - + +
76C LEU* 1.3 55.9 + - - +
78C THR* 3.8 5.4 - - - -
79C ASP* 2.8 29.3 + - - +
80C PHE* 3.3 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.5 25.4 - - + -
12C PHE* 4.1 30.7 - - + -
16C VAL* 4.5 15.3 - - + -
18C MET* 3.7 35.7 - - + -
60C MET* 4.7 3.8 - - - -
72C TYR* 3.1 19.9 + - + +
73C THR* 3.6 6.5 - - - +
75C GLU* 1.3 77.1 - - - +
77C ILE* 1.3 58.5 + - + +
80C PHE* 3.1 25.6 + - + -
82C VAL* 3.3 36.6 + - + +
85C ILE* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 3.0 19.3 + - - +
74C LYS 3.8 3.1 - - - +
76C LEU* 1.3 79.3 - - - +
78C THR* 1.3 61.6 + - + +
81C GLY* 4.3 9.0 + - - -
82C VAL* 4.0 17.8 + - + +
85C ILE* 4.1 21.1 - - + -
188C VAL* 3.9 21.8 - - + -
189C ALA* 4.3 9.0 - - + -
192C PHE* 3.5 35.7 - - + +
193C GLY 4.8 1.6 - - - +
194C ALA* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C MET* 5.2 2.4 - - - +
74C LYS* 2.9 37.5 + - - +
75C GLU* 3.7 1.9 + - - -
77C ILE* 1.3 83.5 - - + +
79C ASP* 1.3 80.9 + - - +
80C PHE 3.8 0.2 - - - -
81C GLY 5.1 0.7 - - - -
192C PHE* 3.5 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA 5.5 1.4 - - - +
2C THR* 3.4 29.2 - - + +
9C MET* 3.2 22.8 + - - +
74C LYS* 4.4 5.4 + - - -
75C GLU* 2.8 19.1 + - - +
78C THR* 1.3 99.1 + - - +
80C PHE* 1.3 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA* 4.5 2.7 - - - -
2C THR* 3.6 33.7 - - + -
5C ILE* 4.1 19.5 - - + -
7C ALA* 3.3 49.1 - - + -
8C GLU 3.6 20.0 - - - -
9C MET* 3.6 16.2 - - - +
10C GLY 5.0 2.1 + - - +
12C PHE* 3.8 34.2 - + + +
13C ALA 4.7 0.7 - - - +
75C GLU 3.3 13.2 - - - -
76C LEU* 3.1 22.8 + - + +
79C ASP* 1.3 81.9 - - + +
81C GLY* 1.3 64.8 + - - +
82C VAL* 3.0 12.3 + - + +
----------------------------------------------------------
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