Contacts of the strand formed by residues 145 - 150 (chain A) in PDB entry 1CT8
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 ASN 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 1.3 76.5 + - - +
146A VAL* 1.3 78.3 + - - +
147A LYS* 4.9 7.8 - - - +
196A ALA* 3.4 4.3 - - - -
197A THR* 2.8 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.5 34.8 - - + -
144A ILE* 5.2 0.2 - - + -
145A ASN* 1.3 90.0 + - - +
147A LYS* 1.3 72.8 + - - +
148A TRP* 4.2 9.2 - - + +
159A VAL* 6.1 1.2 - - + +
161A ASN* 4.9 7.1 + - - +
175A MET* 3.8 23.6 - - + -
177A SER* 4.0 20.6 - - - +
194A CYS* 3.6 30.5 - - - -
195A GLU 3.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN* 4.9 7.4 - - - +
146A VAL* 1.3 83.9 + - - +
148A TRP* 1.3 91.3 + - - +
149A LYS* 5.0 3.4 - - + -
154A GLU* 3.2 36.6 - - + +
155A ARG 2.9 32.9 + - - +
156A GLN* 4.1 16.4 - - + +
159A VAL* 5.1 1.6 - - - +
193A THR 3.5 0.9 - - - +
194A CYS* 3.4 5.5 - - - -
195A GLU* 2.9 51.1 + - + +
197A THR* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.8 15.9 - - + -
132A VAL* 3.5 45.8 - - + -
133A VAL 4.1 0.4 - - - -
134A CYS* 3.5 33.7 - - + -
146A VAL* 4.2 5.6 - - + +
147A LYS* 1.3 86.8 + - - +
149A LYS* 1.3 64.2 + - - +
150A ILE* 6.3 0.2 - - + -
154A GLU* 3.1 25.1 - - - +
155A ARG* 3.1 20.1 + - + +
159A VAL* 3.7 28.0 - - + +
177A SER* 2.9 36.7 + - - -
179A LEU* 4.0 29.3 - - + +
192A TYR* 5.4 2.2 - + + -
193A THR 3.2 22.7 - - - -
194A CYS* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 5.0 2.0 - - + -
148A TRP* 1.3 80.8 - - - +
150A ILE* 1.3 63.3 + - - +
151A ASP 4.0 0.2 - - - -
152A GLY* 3.8 25.5 + - - +
153A SER 3.2 7.6 - - - +
154A GLU* 3.3 39.6 + - + +
191A SER 3.6 3.3 - - - +
192A TYR* 3.7 1.4 - - - -
193A THR* 2.9 44.4 + - + -
195A GLU* 3.4 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP 5.6 0.2 - - - -
149A LYS* 1.3 76.3 - - - +
151A ASP* 1.3 72.0 + - - +
152A GLY 3.0 0.2 - - - -
153A SER* 2.8 25.8 + - - +
155A ARG* 3.8 36.1 - - + -
179A LEU* 4.0 20.0 - - + -
181A LEU* 4.1 11.2 - - + -
189A HIS* 3.4 47.2 - - + +
191A SER 3.4 2.9 - - - -
192A TYR* 3.6 26.7 - - + -
----------------------------------------------------------
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