Contacts of the strand formed by residues 134 - 139 (chain A) in PDB entry 3RLE
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 ASP 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 3.5 4.2 - - - -
115A VAL* 2.9 37.2 + - + +
129A LEU* 3.4 4.2 - - - +
130A ARG* 2.7 38.3 + - - +
133A SER* 1.3 79.1 - - - +
135A TYR* 1.3 65.0 + - - +
165A VAL* 3.4 17.4 - - + +
166A TYR 3.3 0.9 - - - -
167A ASN* 2.8 30.4 + - - +
174A ARG* 2.8 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 4.4 7.9 - - + -
113A TRP 3.5 4.9 - - - +
114A HIS* 3.2 53.5 + + + -
132A HIS 3.9 5.8 + - - -
133A SER 3.4 16.4 - - - -
134A ASP* 1.3 75.1 - - - +
136A ILE* 1.3 65.4 + - - +
137A ILE* 3.4 4.5 + - + +
165A VAL* 3.4 3.0 - - - -
166A TYR* 2.8 46.8 + + - +
168A THR* 3.8 17.0 - - + +
200A HIS 3.8 8.7 - - - -
201A ARG 3.6 22.7 + - - -
202A ILE* 3.6 33.4 - - + -
203A PRO* 3.6 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 3.4 4.2 - - - -
113A TRP* 2.8 47.7 + - + +
115A VAL* 4.1 23.3 - - + -
129A LEU* 4.4 9.0 - - + -
134A ASP 4.3 0.2 - - - -
135A TYR* 1.3 70.9 - - - +
137A ILE* 1.4 60.1 + - - +
138A GLY 4.0 17.7 - - - +
143A MSE 4.3 10.1 - - + -
149A LEU* 3.8 30.5 - - + -
163A LEU* 4.0 31.2 - - + -
164A TYR 3.6 6.3 - - - +
165A VAL* 4.1 15.9 - - + -
190A LEU* 5.9 1.6 - - + -
194A ILE* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.7 35.0 - - + -
37A PHE* 4.2 10.3 - - + -
111A ASN 3.8 16.9 - - - +
112A VAL* 3.8 12.3 - - + +
113A TRP* 5.5 0.6 - - - -
135A TYR 3.4 14.8 + - - +
136A ILE* 1.4 75.1 - - - +
138A GLY* 1.3 59.1 + - - +
143A MSE 4.8 2.0 - - - -
164A TYR* 2.8 26.4 + - + +
165A VAL 4.4 0.7 - - - +
166A TYR* 4.1 4.0 - - + +
173A CYS* 3.7 23.1 - - - -
202A ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.6 4.5 - - - +
137A ILE* 1.3 82.9 - - - +
139A ALA* 1.4 59.9 + - - +
143A MSE 3.3 17.8 - - - +
163A LEU* 3.6 4.3 - - - +
164A TYR* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY* 1.4 74.5 - - - +
140A ASP* 1.3 61.9 + - - +
141A THR* 3.1 18.7 + - - +
143A MSE 3.6 8.0 - - + +
152A LEU* 3.6 29.8 - - + -
161A LEU* 4.9 1.6 - - + -
162A LYS 3.6 17.0 - - - +
163A LEU* 4.3 1.6 - - + -
164A TYR* 3.6 18.8 - - - -
----------------------------------------------------------
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