Contacts of the helix formed by residues 149 - 161 (chain F) in PDB entry 5UQ9
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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ILE* 3.6 44.0 - - + +
122F LEU* 3.8 10.7 - - + +
124F VAL* 3.8 11.7 - - + -
146F ASN 3.1 12.4 + - - +
147F LYS 3.0 1.4 - - - -
148F GLU* 1.3 79.1 - - - +
150F TRP* 1.3 63.0 + - - +
151F PRO 3.5 1.1 - - - -
152F HIS* 3.4 3.5 + - - -
153F ILE* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F PRO* 3.5 20.0 - - + -
146F ASN 4.1 1.0 + - - -
147F LYS* 3.0 25.6 + - + +
149F ALA* 1.3 76.1 - - - +
151F PRO* 1.3 67.4 - - + +
153F ILE* 3.9 17.7 - - + -
154F LYS* 2.8 62.3 + - + +
157F PHE* 4.5 3.1 - - + -
158F GLN* 3.9 20.9 - - + -
171F CYS* 3.7 26.5 - - - -
172F ASP* 3.8 19.2 + - - -
173F TRP* 3.5 56.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LYS* 3.4 12.8 - - + +
148F GLU* 3.9 8.5 - - - +
149F ALA 3.7 2.2 - - - -
150F TRP* 1.3 96.9 - - + +
152F HIS* 1.3 67.0 + - + +
154F LYS* 4.0 18.0 - - + +
155F THR* 4.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PRO* 3.3 34.9 - - + +
70F ARG* 2.9 29.4 + - - +
95F GLY 5.7 0.2 + - - -
97F ILE* 3.6 25.8 - - + -
122F LEU* 5.2 3.1 - - + +
148F GLU* 3.5 25.6 + - - +
149F ALA* 3.4 0.9 + - - +
150F TRP 3.1 0.8 - - - -
151F PRO* 1.3 86.8 - - + +
153F ILE* 1.3 60.9 + - - +
154F LYS 3.3 2.1 + - - -
155F THR* 3.8 10.6 + - - -
156F ILE* 3.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 5.3 2.9 - - + -
70F ARG* 3.8 27.4 - - + +
97F ILE* 4.1 4.9 - - + -
99F ILE* 3.7 35.2 - - + -
124F VAL* 4.1 20.2 - - + -
143F PRO* 4.7 0.9 - - + -
149F ALA 3.3 18.3 + - - +
150F TRP* 3.8 22.4 - - + +
152F HIS* 1.3 74.8 - - - +
154F LYS* 1.3 60.3 + - - +
155F THR 3.3 1.8 - - - -
156F ILE* 4.1 6.3 - - - -
157F PHE* 3.0 55.9 + - + +
173F TRP* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F TRP* 2.8 48.3 + - + +
151F PRO* 4.0 13.7 - - + +
152F HIS 3.3 1.4 - - - -
153F ILE* 1.3 78.8 - - - +
155F THR* 1.3 65.5 + - + +
158F GLN* 3.1 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F PHE* 4.0 13.2 - - + -
70F ARG* 5.0 1.0 + - - -
151F PRO 4.6 4.2 + - - -
152F HIS 3.8 12.8 + - - -
154F LYS* 1.3 79.3 - - + +
156F ILE* 1.3 69.4 + - - +
158F GLN* 4.7 0.8 - - - +
159F GLY* 3.2 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ASP* 5.2 7.9 - - + -
6F ILE* 4.7 17.7 - - + -
22F MET* 3.7 35.7 - - + -
27F PHE* 3.8 38.1 - - + -
70F ARG* 3.4 33.2 - - - +
152F HIS 3.8 8.5 - - - +
153F ILE* 3.6 6.2 + - - +
154F LYS 3.4 0.2 - - - -
155F THR* 1.3 81.3 - - - +
157F PHE* 1.3 71.4 + - + +
159F GLY* 3.3 0.9 + - - -
160F ILE* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.9 3.8 - - + -
72F ILE* 4.4 18.4 - - + -
99F ILE* 3.6 32.3 - - + -
126F SER* 3.7 24.9 - - - -
141F LEU* 3.5 36.0 - - + +
143F PRO* 4.2 13.0 - - + -
150F TRP* 4.5 4.0 - + + -
153F ILE* 3.0 49.8 + - + +
154F LYS 4.3 0.4 - - - +
156F ILE* 1.3 84.7 - - + +
158F GLN* 1.3 56.8 + - - +
160F ILE* 3.5 4.2 - - + +
161F ALA* 2.9 30.7 + - - +
171F CYS* 3.6 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F TRP* 3.9 12.8 - - + -
154F LYS* 3.1 47.5 + - - +
155F THR* 4.7 0.8 - - - +
157F PHE* 1.3 78.9 - - - +
159F GLY* 1.3 54.0 + - - +
161F ALA* 3.7 4.4 + - - +
163F LYS* 2.3 34.7 + - - +
169F PRO* 3.9 23.5 - - + +
171F CYS* 2.9 42.5 + - + +
172F ASP* 4.6 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F HIS* 3.1 26.6 + - - -
27F PHE* 5.2 4.5 - - - -
155F THR 3.2 19.5 + - - -
156F ILE* 3.8 1.3 - - - -
157F PHE 3.1 1.4 - - - -
158F GLN* 1.3 80.8 - - - +
160F ILE* 1.3 60.4 + - - +
161F ALA 3.9 1.7 - - - +
163F LYS* 3.8 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LEU* 4.4 21.3 - - + +
21F ASN* 3.3 28.6 + - - +
22F MET* 3.6 49.4 - - + -
25F HIS* 3.8 13.4 + - + -
27F PHE* 4.8 2.7 - - + -
72F ILE* 6.2 1.8 - - + -
137F TYR 4.2 1.7 - - - +
138F GLY* 3.4 7.4 - - - -
139F PRO* 3.2 16.8 - - + +
141F LEU* 4.1 15.0 - - + -
156F ILE* 3.1 18.1 + - + +
157F PHE* 3.5 9.2 - - + +
159F GLY* 1.3 73.8 - - - +
161F ALA* 1.3 69.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F GLY* 4.6 0.2 - - - -
139F PRO* 3.4 16.2 - - - +
141F LEU* 3.9 8.1 - - + -
157F PHE 2.9 18.7 + - - +
158F GLN 4.1 4.7 - - - +
159F GLY 3.4 1.7 - - - +
160F ILE* 1.3 84.1 - - - +
162F ALA* 1.3 69.7 + - - +
163F LYS* 3.5 18.7 - - - +
170F CYS 4.2 4.9 - - - +
171F CYS* 3.7 24.7 - - + -
----------------------------------------------------------
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