Contacts of the strand formed by residues 138 - 144 (chain A) in PDB entry 4BR6
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 LEU 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.7 3.8 - - + -
99A ALA* 3.7 14.6 - - + +
100A ILE* 3.6 45.5 - - + +
103A ASP* 3.1 16.5 + - - +
104A PHE* 3.9 17.2 - - + -
129A LEU* 4.1 9.4 - - + -
130A ALA 3.2 13.0 - - - +
131A LYS* 3.9 8.5 - - + -
136A GLY 4.0 7.4 - - - +
137A ASN* 1.3 76.2 + - - +
139A ALA* 1.3 60.7 + - - +
156A LEU* 3.7 24.5 - - + -
194A PHE* 4.0 9.0 - - + -
137D ASN* 3.2 24.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
104A PHE* 4.1 7.4 - - - -
128A TRP 3.5 0.5 - - - +
129A LEU* 3.5 4.2 - - - +
130A ALA* 2.8 35.4 + - - +
137A ASN* 3.9 3.1 + - - +
138A LEU* 1.3 75.6 - - - +
140A ILE* 1.3 63.1 + - - +
141A VAL* 4.0 17.6 + - + -
153A LEU* 5.1 11.7 - - + -
137D ASN* 5.4 0.9 - - - +
139D ALA* 5.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 3.8 22.6 - - + -
110A PHE* 3.7 28.3 - - + -
113A GLN* 3.6 19.5 - - + +
114A MET* 3.5 37.9 - - + +
117A ALA* 3.9 26.7 - - + -
127A ALA* 5.1 1.3 - - + -
128A TRP 3.3 8.7 - - - +
129A LEU* 5.0 0.7 - - - -
139A ALA* 1.3 73.8 - - - +
141A VAL* 1.3 71.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA* 3.3 4.2 - - - +
128A TRP* 2.8 54.3 + - + +
130A ALA* 4.7 8.3 - - + -
139A ALA* 4.2 14.8 - - + -
140A ILE* 1.3 81.3 - - - +
142A THR* 1.3 65.6 + - - +
143A ARG* 3.8 26.7 - - - +
149A VAL* 4.5 6.1 - - + -
153A LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA* 4.0 26.9 - - + +
121A ILE* 4.1 23.5 - - + +
126A TRP 3.2 13.5 - - - +
127A ALA* 4.3 2.9 - - + -
128A TRP* 5.5 0.4 - - - -
141A VAL* 1.3 78.8 - - - +
143A ARG* 1.3 79.1 + - - +
901A NA 3.0 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 5.1 1.6 - - - +
125A GLY* 3.2 5.2 - - - -
126A TRP* 3.0 35.7 + - + +
128A TRP* 4.3 9.6 - - + +
141A VAL* 3.8 20.7 - - + +
142A THR* 1.3 90.1 + - - +
144A ALA* 1.3 59.9 + - - +
145A ASN 4.5 0.2 - - - +
147A ASP* 3.0 33.2 - - - +
148A PRO 2.8 23.3 + - - +
149A VAL* 4.1 27.9 - - + +
150A THR 5.0 4.0 + - - +
153A LEU* 4.1 23.0 - - - +
901A NA 3.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 6.1 0.9 - - - -
124A SER 3.8 6.3 - - - +
125A GLY* 4.4 0.2 - - - -
143A ARG* 1.3 72.0 - - - +
145A ASN* 1.3 80.5 + - - +
147A ASP* 3.0 36.1 + - - +
901A NA 3.7 10.0 - - - -
----------------------------------------------------------
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