Contacts of the helix formed by residues 139 - 152 (chain F) in PDB entry 4I02
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 139 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F PHE 4.3 0.8 + - - -
138F LEU* 1.3 75.0 - - - +
140F ALA* 1.3 66.3 + - - +
141F THR* 3.2 12.5 + - - -
142F GLY* 2.9 22.0 + - - -
143F ARG* 2.8 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F ASP* 1.3 74.1 - - - +
141F THR* 1.3 62.7 + - - +
143F ARG* 3.6 24.9 - - - +
144F ILE* 2.9 31.6 + - + +
177F VAL* 6.1 0.4 - - - -
179F CYS* 4.9 6.3 - - + -
183F THR* 4.2 13.5 - - + -
187F ILE* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F ASP* 3.1 13.7 + - - -
140F ALA* 1.3 77.4 - - - +
142F GLY* 1.3 58.4 + - - +
144F ILE* 3.4 1.6 + - - +
145F ALA* 2.9 29.0 + - + +
187F ILE* 3.6 30.7 - - + +
190F MET* 4.1 18.4 - - + +
191F LEU* 4.3 21.7 - - + +
194F GLN* 5.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F LEU* 3.8 21.7 - - - +
139F ASP* 2.9 16.9 + - - -
141F THR* 1.3 77.1 - - - +
143F ARG* 1.3 57.6 + - - +
145F ALA* 3.3 6.2 + - - +
146F GLN* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ASN* 3.4 35.0 + - + +
135F LEU* 3.7 28.0 + - - +
138F LEU* 3.1 27.7 + - + +
139F ASP* 2.8 23.1 + - - +
140F ALA* 3.6 19.0 - - - +
142F GLY* 1.3 77.8 - - - +
144F ILE* 1.3 56.3 + - - +
146F GLN* 3.4 3.6 + - - +
147F THR* 2.9 32.2 + - - -
177F VAL* 2.9 40.2 + - + +
178F GLY 3.7 14.6 + - - -
179F CYS* 4.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F ALA 2.9 21.0 + - - +
141F THR 4.0 2.7 - - - +
143F ARG* 1.3 71.9 - - - +
145F ALA* 1.3 67.7 + - - +
147F THR* 3.2 1.1 + - - -
148F LEU* 2.9 42.8 + - + +
173F ILE* 4.2 11.2 - - + -
177F VAL* 3.9 24.9 - - + -
179F CYS* 4.2 7.4 - - - -
184F VAL* 4.0 27.4 - - + -
187F ILE* 3.8 32.1 - - + -
188F LEU* 4.2 10.8 - - + -
191F LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F THR* 2.9 20.7 + - + +
142F GLY* 3.6 7.9 - - - +
144F ILE* 1.3 79.1 - - - +
146F GLN* 1.3 62.0 + - - +
148F LEU* 3.4 10.3 + - - +
149F LEU* 3.1 27.9 + - + +
191F LEU* 4.6 16.5 - - + +
196F LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F GLU* 4.9 14.3 + - + +
134F ASN* 3.6 33.6 + - - +
138F LEU* 4.7 4.7 - - + +
142F GLY 2.9 17.6 + - - +
143F ARG 3.9 3.4 - - - +
145F ALA* 1.3 76.5 - - - +
147F THR* 1.3 59.2 + - - +
149F LEU* 3.2 23.1 + - - +
150F ASN* 2.9 52.2 + - - +
153F LYS* 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F LYS* 5.1 2.6 + - - -
134F ASN* 5.8 1.7 + - - -
143F ARG 2.9 17.7 + - - -
144F ILE* 3.2 4.9 + - - -
146F GLN* 1.3 76.8 - - - +
148F LEU* 1.3 58.6 + - + +
150F ASN* 3.1 11.5 + - + +
151F LEU* 2.8 48.2 + - + +
173F ILE* 4.7 8.5 - - + -
176F ILE* 3.7 32.8 - - + +
177F VAL* 3.2 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ILE* 2.9 29.9 + - + +
145F ALA* 3.6 6.5 - - - +
147F THR* 1.3 76.3 - - + +
149F LEU* 1.3 62.8 + - + +
151F LEU* 3.4 7.7 + - + +
152F ALA* 3.1 23.2 + - - +
166F ILE* 3.9 23.3 - - + -
173F ILE* 4.5 13.5 - - + -
188F LEU* 4.0 9.2 - - + -
191F LEU* 3.8 27.4 - - + -
197F ILE* 4.1 17.0 - - + -
204F ILE* 4.4 20.6 - - + -
206F VAL* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F ALA* 3.1 17.1 + - + +
146F GLN* 3.4 30.1 - - - +
148F LEU* 1.3 75.6 - - + +
150F ASN* 1.3 64.2 + - - +
152F ALA* 3.3 17.7 + - - +
153F LYS* 3.5 16.9 + - + +
206F VAL* 4.1 18.2 - - + -
207F TYR 5.1 2.9 - - - +
208F GLY 4.9 12.1 - - - +
209F THR 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F VAL* 6.3 0.8 - - - +
130F GLU* 6.1 3.6 - - - +
131F LYS* 5.5 6.5 - - - +
134F ASN* 4.8 5.5 - - - +
146F GLN* 2.9 44.7 + - - +
147F THR* 3.1 12.9 + - + +
149F LEU* 1.3 74.7 - - - +
151F LEU* 1.3 65.8 + - + +
153F LYS* 3.0 44.4 + - - +
154F GLN* 3.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F TYR* 3.7 33.9 - - + -
147F THR* 2.8 42.1 + - + +
148F LEU* 3.4 3.8 + - + +
150F ASN* 1.3 73.9 - - + +
152F ALA* 1.3 61.5 + - - +
153F LYS 3.1 0.2 - - - -
154F GLN* 3.1 26.2 + - + +
156F ASP* 5.1 0.2 - - - +
157F ALA* 3.9 2.9 - - - +
166F ILE* 3.7 37.7 - - + +
168F ILE* 3.6 29.4 - - + -
173F ILE* 4.7 4.3 - - + -
176F ILE* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F LEU 3.1 13.9 + - - +
149F LEU* 3.5 11.0 - - - +
150F ASN 3.2 0.2 - - - -
151F LEU* 1.3 77.0 - - - +
153F LYS* 1.3 58.3 + - + +
154F GLN 3.4 0.4 - - - -
157F ALA* 3.4 15.9 - - - +
164F MET* 3.6 33.0 - - + +
166F ILE* 3.9 11.2 - - - +
206F VAL* 4.2 13.2 - - + -
209F THR 3.9 17.7 - - - +
----------------------------------------------------------
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