Contacts of the helix formed by residues 134 - 157 (chain F) in PDB entry 1IES
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 134 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PRO* 3.7 34.3 - - + -
124E HIS* 4.2 14.4 - - + +
127E ASP* 5.8 1.1 - - + +
107F ASN* 4.5 3.5 + - - +
110F LEU* 3.7 33.7 - - + +
111F LEU* 4.1 19.7 - - + -
114F HIS* 4.0 7.9 - - + -
129F LEU* 3.0 15.9 + - + +
130F GLU* 3.8 30.9 + - + +
133F PHE* 1.3 78.0 - - - +
135F ASP* 1.3 62.0 + - - +
137F GLU* 3.5 5.0 - - - +
138F VAL* 3.2 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLN* 4.6 4.9 + - - -
124E HIS* 3.3 25.8 + - + +
127E ASP* 4.9 7.8 + - - +
130F GLU 4.2 11.2 + - - +
131F SER 5.5 3.6 - - - +
132F HIS 5.4 0.4 - - - -
133F PHE 3.4 0.6 - - - +
134F LEU* 1.3 75.0 - - - +
136F GLU* 1.3 67.5 + - - +
138F VAL* 2.9 13.3 + - - +
139F LYS* 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 5.6 3.6 + - - -
57F GLU* 3.9 29.7 - - - +
58F LYS* 4.6 11.8 + - - -
61F GLY* 6.1 1.6 - - - -
64F ARG* 5.6 4.3 + - - -
132F HIS 3.5 21.6 - - - +
133F PHE* 3.5 13.8 + - - +
135F ASP* 1.3 77.5 - - - +
137F GLU* 1.3 56.3 - - - +
139F LYS* 3.4 11.4 + - - +
140F LEU* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F TYR* 3.8 10.9 + - - -
58F LYS* 3.3 21.5 + - - -
103F GLU* 2.7 40.8 - - - +
106F LEU* 4.7 3.7 - - - +
107F ASN* 3.2 37.9 - - + +
110F LEU* 3.9 9.4 - - + -
133F PHE 3.1 17.7 + - - +
134F LEU 3.5 5.6 - - - +
136F GLU* 1.3 80.3 - - - +
138F VAL* 1.3 55.9 + - - +
140F LEU* 3.4 3.6 + - - +
141F ILE* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLN* 3.9 32.5 - - + +
72E ARG* 4.0 20.9 - - - +
124E HIS* 3.8 39.0 - - + +
107F ASN* 4.9 11.0 - - - +
134F LEU 3.2 12.5 + - - +
135F ASP* 2.9 9.2 + - - +
137F GLU* 1.3 74.5 - - - +
139F LYS* 1.3 64.8 + - - +
141F ILE* 3.6 5.9 + - + +
142F LYS* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLN* 4.0 29.0 + - - +
135F ASP* 2.9 46.8 + - - +
136F GLU* 3.7 10.5 - - - +
138F VAL* 1.3 75.9 - - - +
140F LEU* 1.3 62.6 + - - +
142F LYS* 3.1 5.9 + - - +
143F LYS* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F PHE* 4.9 1.1 - - + -
54F LEU* 3.8 33.4 - - + -
57F GLU* 4.9 7.4 - - - +
58F LYS* 4.0 9.6 - - - +
103F GLU* 3.4 32.8 - - - +
136F GLU* 2.8 25.2 + - + +
137F GLU* 3.9 4.7 - - - +
139F LYS* 1.3 71.9 - - - +
141F ILE* 1.3 63.2 + - + +
143F LYS* 3.1 29.9 + - + +
144F MET* 2.9 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 3.6 36.5 - - + +
6E GLN* 4.1 10.3 - - - +
100F ILE* 4.1 13.5 - - + +
103F GLU* 3.8 29.2 - - + +
104F LYS* 4.2 8.1 - - + +
107F ASN* 4.1 23.8 - - + +
137F GLU* 3.0 30.2 + - - +
138F VAL* 4.1 5.2 - - + +
140F LEU* 1.3 74.9 - - - +
142F LYS* 1.4 58.0 + - - +
144F MET* 3.4 8.0 + - - +
145F GLY 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 2.8 38.4 + - - +
40B ASP* 3.8 11.2 - - + +
43B ALA* 5.8 0.2 - - - +
4E ILE* 4.2 13.9 - - + +
70E ASN* 3.4 31.0 - - + +
71E GLN* 3.6 26.5 - - + +
138F VAL 3.1 16.0 + - - +
139F LYS* 3.1 10.0 + - - +
141F ILE* 1.4 75.5 - - - +
143F LYS* 1.3 59.2 + - - +
145F GLY* 2.9 2.1 + - - -
146F ASP* 2.8 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F PHE* 4.0 22.7 - - + -
54F LEU* 5.8 1.2 - - - +
139F LYS 3.0 12.2 + - - +
140F LEU* 3.4 26.1 - - + +
142F LYS* 1.3 76.0 - - - +
144F MET* 1.3 59.6 + - - +
146F ASP* 3.3 10.3 + - + +
147F HIS* 2.9 60.1 + - + +
174F ASP* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.6 17.0 - - - +
50F PHE* 4.2 18.4 - - + -
54F LEU* 3.5 31.0 - - + -
96F MET* 4.5 8.6 - - - +
99F ALA* 3.9 11.2 - - + -
100F ILE* 4.0 31.4 - - + -
103F GLU* 3.8 22.9 - - + -
140F LEU* 2.9 28.1 + - + +
141F ILE* 3.7 4.3 - - - +
143F LYS* 1.3 78.4 - - - +
145F GLY* 1.3 54.9 + - - +
147F HIS* 3.3 7.9 + - - +
148F LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 4.1 3.6 - - - -
3E GLN* 3.0 34.6 + - - -
4E ILE* 3.6 18.2 - - - -
100F ILE* 4.1 4.6 - - - +
141F ILE 2.9 14.3 + - - -
142F LYS 2.9 3.8 + - - -
144F MET* 1.3 71.8 - - - +
146F ASP* 1.3 63.0 + - - +
148F LEU* 3.4 1.1 + - - +
149F THR* 3.2 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 3.3 15.4 - - - -
43B ALA* 3.8 21.4 - - + +
142F LYS* 2.8 46.8 + - - +
143F LYS* 3.4 12.9 - - + +
145F GLY* 1.3 76.0 - - - +
147F HIS* 1.3 65.0 + - + +
149F THR* 3.3 5.2 + - - -
150F ASN* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F PHE* 3.8 28.6 - + - -
96F MET* 4.0 21.3 - - + -
143F LYS* 2.9 48.9 + - + +
144F MET 3.5 4.3 - - - +
146F ASP* 1.3 77.4 - - + +
148F LEU* 1.3 57.4 + - - +
150F ASN* 3.2 3.9 + - - +
151F ILE* 2.8 34.2 + - - +
166F PHE* 3.8 22.4 - + + -
170F THR* 4.0 21.5 - - + +
171F LEU* 4.0 10.5 - - + +
174F ASP* 4.2 10.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
3E GLN* 3.5 22.7 - - + +
93F LEU* 3.5 27.8 - - + -
96F MET* 3.9 16.6 - - + +
97F LYS* 3.5 27.6 - - + +
100F ILE* 3.9 34.5 - - + -
144F MET 2.9 20.2 + - - +
145F GLY 3.6 6.5 - - - +
147F HIS* 1.3 71.0 - - - +
149F THR* 1.3 57.1 + - - +
151F ILE* 3.7 5.2 - - - +
152F GLN* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP 2.9 29.5 + - - +
41B ASP* 3.7 17.7 - - + -
42B VAL 4.0 5.2 + - - -
43B ALA* 3.3 11.4 - - - +
3E GLN* 3.3 22.9 - - - +
145F GLY 3.2 2.7 + - - +
146F ASP 3.3 6.3 + - - -
148F LEU* 1.3 75.8 - - - +
150F ASN* 1.3 65.2 + - - +
152F GLN* 3.3 14.4 + - - +
153F ARG* 3.0 29.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
43B ALA* 3.0 23.3 + - - +
44B LEU* 3.9 4.4 - - - +
164B TYR* 3.8 26.2 - - + -
167B GLU* 5.6 0.6 + - - -
146F ASP* 3.0 23.6 + - - +
147F HIS* 3.6 3.9 + - - +
149F THR* 1.3 76.6 + - - +
151F ILE* 1.3 65.2 + - - +
153F ARG* 2.7 38.7 - - - +
154F LEU* 3.3 25.9 + - - +
166F PHE* 4.0 16.2 - - + -
170F THR* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F THR* 3.6 27.4 - - + +
93F LEU* 4.1 23.8 - - + +
96F MET* 3.5 33.7 - - + -
147F HIS 2.8 25.1 + - - +
148F LEU* 3.8 4.3 - - - +
150F ASN* 1.3 70.4 - - - +
152F GLN* 1.3 65.5 + - - +
154F LEU* 3.1 4.3 + - + -
155F VAL* 2.8 45.8 + - + +
162F GLY 6.0 0.2 - - - +
163F GLU* 5.4 2.7 - - + -
166F PHE* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E GLN* 4.9 3.8 + - - +
93F LEU* 3.8 18.8 - - + +
97F LYS* 3.8 28.5 - - - +
148F LEU* 2.8 34.0 + - - +
149F THR* 3.6 13.3 - - - +
151F ILE* 1.3 72.8 - - - +
153F ARG* 1.3 59.9 + - - +
155F VAL* 4.8 3.5 - - - +
156F GLY* 3.1 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP 4.8 2.8 + - - -
42B VAL* 2.9 36.7 + - - +
44B LEU* 3.2 23.2 - - - +
160B GLY* 3.5 34.2 - - - +
163B GLU* 4.0 15.2 + - - -
164B TYR* 4.2 11.7 - - - +
149F THR* 3.0 17.6 + - - +
150F ASN* 2.7 57.6 - - - +
152F GLN* 1.3 76.1 - - - +
154F LEU* 1.3 62.6 - - + +
156F GLY* 4.0 0.9 - - - -
157F SER* 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 3.7 28.6 - - + +
164B TYR* 3.5 53.6 - - + -
150F ASN 3.3 16.3 + - - +
151F ILE* 3.1 6.6 + - - +
153F ARG* 1.3 75.4 - - - +
155F VAL* 1.3 60.2 + - + +
157F SER* 3.1 7.3 + - - -
158F GLN* 2.9 28.4 + - - +
162F GLY* 3.7 19.4 - - - +
165F LEU* 4.8 3.1 - - + -
166F PHE* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F LEU* 4.4 23.6 - - + -
151F ILE* 2.8 36.4 + - + +
152F GLN* 5.0 1.3 - - - +
154F LEU* 1.3 71.2 - - - +
156F GLY* 1.3 66.0 + - - +
157F SER 4.0 0.3 - - - +
158F GLN 4.1 0.2 - - - -
159F ALA* 3.4 46.1 + - + +
162F GLY 4.5 0.7 - - - -
163F GLU* 4.1 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F GLN 3.1 20.7 + - - -
153F ARG 4.0 1.1 - - - -
154F LEU 3.2 0.2 - - - -
155F VAL* 1.3 80.7 - - - +
157F SER* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 3.7 33.4 + - - +
160B GLY* 3.7 8.3 + - - -
161B LEU* 3.3 29.4 + - - -
153F ARG 3.0 14.7 + - - -
154F LEU 3.1 7.5 + - - -
155F VAL 4.0 0.4 - - - +
156F GLY* 1.3 81.4 - - - +
158F GLN* 1.3 68.4 + - - +
159F ALA 4.1 0.7 + - - -
----------------------------------------------------------
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