Contacts of the strand formed by residues 129 - 134 (chain A) in PDB entry 1PR9
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 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.1 3.6 - - - -
78A ASP 3.5 14.1 - - - -
79A LEU* 4.6 3.6 - - - -
122A LEU* 4.0 9.9 - - - -
127A VAL 3.9 0.4 + - - -
128A PRO* 1.3 76.2 - - - +
130A ALA* 1.3 64.2 + - - +
171A LYS 3.1 8.0 + - - +
172A ILE* 3.3 11.6 - - - +
173A ARG* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP 3.7 5.7 + - - -
79A LEU* 3.5 11.6 - - + +
80A LEU 3.1 21.8 + - - -
118A VAL* 6.1 0.2 - - - +
122A LEU* 4.8 1.6 - - - +
129A GLY* 1.3 76.1 - - - +
131A ILE* 1.3 65.9 + - - +
172A ILE* 4.4 1.4 - - - +
173A ARG* 3.3 28.3 - - + +
222A LEU 4.3 7.4 - - - +
223A LEU* 3.8 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.5 22.2 - - + +
82A ASN* 3.6 27.6 - - - +
115A SER* 4.2 18.8 - - - +
118A VAL* 5.2 8.1 - - + -
119A ALA* 5.1 3.8 - - + -
122A LEU* 5.9 1.3 - - + -
130A ALA* 1.3 82.1 - - - +
132A VAL* 1.3 66.8 + - - +
133A ASN* 3.7 8.1 - - - +
163A MET* 4.1 19.1 - - + -
167A LEU* 4.5 5.6 - - + -
172A ILE* 4.0 20.2 - - + -
173A ARG 2.8 11.4 + - - +
174A VAL* 3.3 15.5 - - + -
175A ASN* 2.9 26.2 + - - -
222A LEU 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU 2.9 9.0 + - - +
81A VAL* 3.4 5.8 - - + +
82A ASN 2.9 26.3 + - - +
131A ILE* 1.3 77.5 - - - +
133A ASN* 1.3 73.6 + - - +
134A VAL* 4.9 1.8 - - + +
175A ASN* 3.4 8.3 - - + +
177A VAL* 4.2 15.7 - - + +
219A ILE* 3.9 31.4 - - + +
222A LEU* 3.9 27.4 - - + +
223A LEU* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN* 2.8 34.1 + - + +
111A VAL* 3.7 3.9 - - - +
131A ILE* 3.7 4.3 - - - +
132A VAL* 1.3 72.1 - - - +
134A VAL* 1.3 61.3 + - - +
135A SER 3.3 2.8 + - - -
156A LEU* 4.0 27.7 - - + +
160A THR* 3.0 29.9 + - - +
163A MET* 4.2 10.1 - - - -
174A VAL* 3.8 19.6 - - - +
175A ASN 2.8 12.1 + - - +
176A ALA* 3.1 5.0 - - + +
177A VAL 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.1 0.4 - - + -
81A VAL* 4.2 7.6 - - + -
82A ASN 2.9 21.6 + - - +
83A ASN* 3.7 26.7 - - + +
132A VAL* 4.9 0.4 - - + +
133A ASN* 1.3 70.9 - - - +
135A SER* 1.3 59.4 + - - +
153A LYS* 2.8 27.4 + - - -
156A LEU* 3.5 6.5 - - - +
177A VAL* 3.9 22.7 - - + +
179A PRO* 4.6 8.3 - - + -
215A VAL* 5.1 4.7 - - + -
219A ILE* 4.1 17.0 - - + -
245A NAP 3.4 32.9 + - - +
----------------------------------------------------------
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