Contacts of the helix formed by residues 106 - 111 (chain A) in PDB entry 2YPR
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 ARG 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER 3.5 7.8 + - - +
103A ARG* 3.3 23.7 + - + +
104A ALA 3.3 0.6 - - - -
105A LEU* 1.4 73.4 - - - +
107A TYR* 1.4 63.2 - - + +
108A TYR 3.4 0.3 + - - -
109A TYR* 3.5 32.4 + - + +
110A ASP* 3.1 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 5.2 8.8 + - - -
43A GLY 5.3 3.1 + - - -
48A GLN* 5.4 9.5 + - - -
103A ARG 5.1 1.1 - - - +
104A ALA* 3.5 15.3 + - - +
105A LEU 3.2 0.6 - - - -
106A ARG* 1.4 82.9 - - + +
108A TYR* 1.3 93.7 + + - +
109A TYR 3.4 0.2 - - - -
110A ASP* 3.9 7.5 + - - +
111A LYS* 3.5 28.8 + - + +
113A ILE* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 4.8 1.1 - - - -
48A GLN* 3.8 9.6 + - - +
49A LEU* 3.4 32.3 + - + +
50A TRP* 3.2 47.7 + + + -
104A ALA 3.6 21.5 - - - -
105A LEU* 3.0 17.2 + - + +
107A TYR* 1.3 103.2 - + - +
109A TYR* 1.3 57.0 + - - +
110A ASP 3.5 0.2 - - - -
111A LYS* 3.9 3.1 - - - -
112A ASN 3.1 5.4 + - - -
113A ILE* 2.9 53.5 + - + -
114A MET* 3.2 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER 5.1 1.8 + - - -
105A LEU* 3.6 19.0 - - + +
106A ARG* 3.7 30.5 + - + +
107A TYR 3.4 0.6 - - - -
108A TYR* 1.3 77.4 - - - +
110A ASP* 1.3 64.5 + - - +
112A ASN* 3.3 21.3 + - - -
114A MET* 3.4 12.8 - - + +
115A SER* 3.6 36.8 - - - -
116A LYS* 3.3 18.9 - - + +
124A TYR* 3.1 32.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 3.1 22.8 - - - +
107A TYR* 3.9 7.7 + - - +
109A TYR* 1.3 73.6 - - - +
111A LYS* 1.4 59.5 + - - +
112A ASN* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.5 31.3 + - + +
108A TYR* 4.1 3.6 - - - +
109A TYR 3.4 0.6 - - - -
110A ASP* 1.4 75.7 - - - +
112A ASN* 1.4 67.5 + - - +
113A ILE* 3.3 29.1 + - + +
130A GLY 4.3 6.1 - - - +
134A ALA* 4.9 4.4 - - + +
----------------------------------------------------------
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