Contacts of the helix formed by residues 149 - 162 (chain A) in PDB entry 5FDK
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 ALA 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 5.1 9.4 - - + -
128A LYS* 4.2 15.0 - - + +
134A CYS* 3.1 38.6 + - - +
135A PHE* 4.0 3.8 - - - +
147A LEU 3.8 0.4 + - - -
148A GLU* 1.3 75.8 - - - +
150A ASP* 1.3 69.6 + - - +
152A LEU* 3.2 11.8 + - + +
153A PHE* 2.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 4.4 12.5 - - - +
148A GLU* 3.7 17.4 - - + +
149A ALA* 1.3 74.2 - - - +
151A LYS* 1.3 66.1 + - + +
153A PHE* 2.6 31.1 + - - +
154A TYR* 3.1 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.7 18.4 - - + -
148A GLU* 4.1 21.1 - - + +
150A ASP* 1.3 81.3 - - + +
152A LEU* 1.3 65.3 + - - +
154A TYR* 2.8 25.1 + - - +
155A PHE* 3.0 25.3 + - + -
175A THR* 3.7 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 6.2 0.9 - - + -
113A LEU* 6.5 1.8 - - + -
116A PHE* 4.3 22.0 - - + -
121A ILE* 3.3 33.0 - - + -
124A MET* 4.0 14.6 - - + -
136A VAL* 3.6 22.9 - - + -
147A LEU* 3.8 22.6 - - + +
148A GLU 3.4 12.2 + - - +
149A ALA* 3.2 13.2 + - + +
150A ASP 3.2 0.6 - - - -
151A LYS* 1.3 79.1 - - - +
153A PHE* 1.3 57.8 + - - +
155A PHE* 3.3 4.4 + - + -
156A TRP* 2.9 30.6 + - + +
167A ILE* 5.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 5.9 6.3 - - + -
149A ALA 2.9 11.2 + - - +
150A ASP* 2.6 22.2 + - - +
152A LEU* 1.3 69.8 - - - +
154A TYR* 1.3 65.5 + - - +
156A TRP* 3.1 8.9 + - - +
157A ASP* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP 3.1 6.1 + - - +
151A LYS* 2.8 20.4 + - - +
153A PHE* 1.3 74.5 - - - +
155A PHE* 1.3 77.6 + + - +
157A ASP* 2.7 29.4 - - - +
158A ARG* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 5.5 6.5 - - + +
147A LEU* 4.2 4.3 - - + -
151A LYS* 3.0 37.1 + - + -
152A LEU* 3.9 8.5 - - + +
154A TYR* 1.3 90.1 - + - +
156A TRP* 1.3 62.9 + - - +
158A ARG* 3.5 27.8 + - - +
159A LYS* 3.0 22.0 + - - +
164A ARG 4.8 2.3 - - - +
167A ILE* 3.4 48.7 - - + -
171A GLU* 3.8 28.5 - - + -
175A THR* 3.3 34.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.4 34.1 - - + -
114A GLN* 5.6 0.2 - - - -
116A PHE* 3.6 31.9 - + + -
117A HIS* 4.2 16.2 - - - -
118A ASP* 5.0 3.8 + - - -
121A ILE* 4.1 37.7 - - + +
152A LEU* 2.9 23.6 + - + +
153A PHE* 3.5 10.1 - - - +
154A TYR 3.1 0.6 - - - -
155A PHE* 1.3 77.6 - - - +
157A ASP* 1.3 59.0 + - + +
158A ARG 3.2 0.2 - - - -
159A LYS* 3.1 42.9 - - + +
160A GLU* 2.8 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE 3.1 11.5 + - - +
154A TYR* 2.7 36.1 - - - +
156A TRP* 1.3 74.2 - - + +
158A ARG* 1.3 55.5 + - - +
159A LYS 3.2 0.4 - - - -
160A GLU* 3.3 15.7 - - + -
161A LYS* 2.4 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.0 40.0 + - + +
155A PHE* 3.5 31.0 + - - +
157A ASP* 1.3 83.2 + - - +
159A LYS* 1.3 62.1 + - - +
161A LYS* 4.2 3.4 - - - +
162A ASN 2.9 30.5 + - - +
163A GLY* 4.0 2.0 + - - +
164A ARG* 3.1 30.2 + - - +
166A SER 3.1 23.2 + - - -
171A GLU* 2.8 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 4.9 9.2 - - + +
114A GLN* 5.2 7.4 - - + +
155A PHE 3.0 13.6 + - - +
156A TRP* 3.1 52.3 - - + +
158A ARG* 1.3 78.9 - - - +
160A GLU* 1.3 64.7 + - - +
161A LYS 3.5 0.3 + - - -
162A ASN* 3.7 13.0 - - - -
163A GLY 3.8 13.0 - - - +
164A ARG 3.9 11.1 + - - +
165A LYS* 4.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 2.8 18.8 + - + +
157A ASP* 3.3 22.9 - - + -
158A ARG 3.2 0.6 - - - -
159A LYS* 1.3 82.7 - - + +
161A LYS* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 2.4 38.6 + - + +
158A ARG* 4.2 4.9 - - - +
160A GLU* 1.3 78.6 - - - +
162A ASN* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 2.9 17.2 - - - +
159A LYS 3.7 8.1 - - - -
161A LYS* 1.3 84.3 - - - +
163A GLY* 1.3 60.6 + - - +
----------------------------------------------------------
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