Contacts of the strand formed by residues 129 - 134 (chain A) in PDB entry 5JAU
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 THR 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.4 8.8 + - - +
94A ASP* 3.8 30.0 + - + +
95A THR 3.2 18.2 - - - +
96A LEU* 4.4 7.4 - - + -
97A TRP* 4.2 2.9 - - - -
127A SER 3.5 11.0 + - - +
128A MET* 1.3 90.2 - - - +
130A THR* 1.3 62.0 + - - +
131A PRO* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.5 13.0 - - - +
82A ARG* 5.1 3.4 - - - +
84A TYR* 5.2 2.9 - - + -
94A ASP* 3.6 4.8 - - - +
95A THR* 2.8 49.7 + - + +
97A TRP* 4.5 11.9 - - + -
129A THR* 1.3 75.1 - - - +
131A PRO* 1.4 71.2 - - - +
132A ALA* 2.8 12.2 + - + +
158A THR 5.6 0.2 - - - +
161A SER* 2.6 37.3 + - - +
165A ILE* 3.3 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.3 31.6 - - + +
57A PRO 3.7 11.9 - - - +
58A ARG* 3.6 48.9 + - + +
65A VAL* 4.7 2.9 - - - +
94A ASP* 3.7 13.2 - - - +
129A THR 4.8 0.7 - - - +
130A THR* 1.4 85.0 - - - +
132A ALA* 1.3 58.7 + - - +
133A ASN* 5.8 0.2 + - - -
165A ILE* 3.6 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.6 23.8 - - + -
66A GLY 4.3 0.2 - - - -
67A CYS* 3.7 26.0 - - + -
84A TYR* 4.7 2.7 - - + -
94A ASP* 3.5 7.7 + - - -
95A THR* 2.8 34.1 + - - +
130A THR* 2.8 7.5 + - + +
131A PRO* 1.3 73.3 - - - +
133A ASN* 1.3 60.8 + - - +
134A TRP 3.2 0.3 + - - -
165A ILE* 4.1 13.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
65A VAL 2.8 30.3 + - - +
66A GLY* 3.2 3.8 - - - -
67A CYS 3.0 18.9 + - - -
87A SER* 4.1 0.8 + - - -
89A ASP 3.7 10.3 + - - -
90A ASN* 2.9 39.2 + - - +
92A ARG* 3.0 34.2 + - + +
93A LEU 3.8 5.8 - - - -
94A ASP* 5.1 2.4 - - - +
131A PRO 5.8 0.6 + - - -
132A ALA* 1.3 68.6 - - - +
134A TRP* 1.4 66.1 + - - +
135A ASN 3.3 0.9 + - - -
136A SER* 3.3 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A CYS* 3.3 24.0 - - - -
68A THR* 3.6 14.1 - - - -
69A ASP* 3.4 33.9 - - - -
82A ARG* 3.7 18.2 - - - -
92A ARG* 3.8 13.7 + - - +
93A LEU* 2.9 26.1 + - + +
94A ASP 4.3 7.9 - - - +
95A THR* 3.5 31.0 - - + +
96A LEU 5.7 0.7 - - - -
132A ALA 3.2 2.2 + - - -
133A ASN* 1.4 69.3 - - - +
135A ASN* 1.3 92.2 + - - +
136A SER 3.2 1.2 + - - -
251A LEU* 3.9 28.2 - - + +
----------------------------------------------------------
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