Contacts of the helix formed by residues 44 - 48 (chain N) in PDB entry 1PP9
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 44 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N ALA* 1.3 76.6 - - - +
45N SER* 1.3 58.2 + - - -
46N ARG 3.0 6.3 - - - -
47N TYR* 2.8 31.6 + - - +
48N GLU* 3.8 9.0 + - - +
56N GLY* 6.4 0.4 - - - -
90N SER* 6.1 0.7 - - - -
91N THR 3.4 15.5 - - - -
92N ARG 3.4 9.0 - - - -
95N THR* 4.5 2.7 - - - -
185N TYR* 4.0 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N GLY* 1.3 69.5 - - - -
46N ARG* 1.3 61.1 + - - +
47N TYR 3.0 1.1 - - - -
48N GLU* 3.0 36.1 + - - +
53N ASN* 3.9 2.2 - - - -
91N THR 3.7 3.8 + - - -
92N ARG* 3.4 29.7 + - - +
162N PRO 4.4 1.9 + - - -
165N GLN* 3.1 23.1 + - - -
166N SER 3.4 25.1 + - - -
167N VAL* 3.7 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N SER* 1.3 74.3 + - - +
47N TYR* 1.3 60.9 + - + +
48N GLU 3.3 0.2 - - - -
92N ARG* 2.8 27.2 + - - +
93N GLU* 2.8 39.1 + - + -
162N PRO* 3.1 34.0 - - + +
163N LEU* 3.9 26.5 - - + +
231N LEU* 3.6 36.5 - - + +
232N SER 3.1 25.5 + - - -
233N PRO* 4.2 2.6 - - - +
234N CYS* 3.6 28.0 - - - +
314N TYR* 4.0 7.9 - - - +
315N ALA* 3.6 21.6 - - - +
316N ASP* 4.5 6.7 - - - +
317N THR* 4.9 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N ASP* 3.4 34.4 + - - +
43N ALA* 3.8 0.9 - - - -
44N GLY* 2.8 28.6 + - - +
46N ARG* 1.3 82.2 - - + +
48N GLU* 1.3 61.0 + - + +
52N ASN* 5.6 0.3 + - - -
92N ARG 4.9 0.2 - - - -
93N GLU* 3.7 24.1 + - + +
185N TYR* 5.3 0.4 - - + -
188N ARG* 3.5 23.0 + - - -
189N HIS* 3.4 30.6 + + + +
194N ARG* 3.2 24.5 + - - -
229N PRO* 4.2 12.3 - - + -
230N THR 5.7 0.2 - - - -
231N LEU* 3.6 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N GLY 4.0 1.3 - - - +
45N SER* 3.0 29.3 + - - +
47N TYR* 1.3 81.7 - - - +
49N SER* 1.3 60.0 + - - +
52N ASN* 3.4 18.6 - - - +
53N ASN* 2.8 19.1 + - - -
54N GLY* 2.6 29.6 + - - -
55N ALA 3.6 0.5 + - - -
56N GLY* 3.0 29.8 + - - -
57N TYR 4.5 1.0 + - - -
162N PRO* 4.3 9.9 - - - +
165N GLN* 3.1 19.5 + - - +
167N VAL 4.4 1.4 - - - +
185N TYR* 3.9 21.4 + - + -
189N HIS* 5.6 0.2 - - - -
----------------------------------------------------------
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