Contacts of the helix formed by residues 138 - 154 (chain E) in PDB entry 5X6E
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 GLY 138 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E PHE 3.9 7.4 + - - +
135E SER 4.2 2.0 + - - -
136E ILE 2.8 9.1 + - - -
137E ASN* 1.3 101.1 + - - +
139E LYS* 1.3 63.3 + - - -
140E LEU 3.2 2.9 - - - -
142E SER* 2.8 14.7 + - - -
139F LYS* 5.2 7.0 - - - -
17G T 3.7 6.5 - - - -
18H G 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E GLY* 1.3 69.3 - - - -
140E LEU* 1.3 64.0 + - - +
142E SER* 3.2 14.5 - - - +
143E ILE* 3.0 28.1 + - - +
179E GLY* 3.4 39.5 + - - +
180E ILE* 4.2 24.0 - - + -
189E ILE* 4.9 3.4 - - + -
135F SER* 3.7 15.1 + - - +
138F GLY* 4.5 14.6 - - - +
17G T 2.9 26.3 + - - +
18G G 2.7 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ASN* 3.7 9.9 - - - +
138E GLY 3.2 1.0 - - - -
139E LYS* 1.3 76.2 - - - +
141E GLY* 1.3 61.2 + - - +
143E ILE* 3.0 14.5 + - - +
144E CYS* 3.0 40.6 + - - -
189E ILE* 4.6 16.1 - - + +
192E LYS* 5.1 15.9 - - + -
193E LEU* 5.4 6.2 - - + +
213E TYR* 5.0 5.6 - - - +
217E TYR* 3.7 30.7 - - + +
16G A 5.6 9.0 - - - +
17G T 3.7 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP 4.2 8.0 - - - +
134E PHE* 4.5 1.0 - - - -
137E ASN* 2.8 28.4 + - - +
140E LEU* 1.3 77.0 - - - +
142E SER* 1.3 55.9 + - - +
144E CYS* 3.7 13.0 - - - +
145E GLY* 2.5 31.9 + - - -
217E TYR* 4.2 13.5 - - - +
218E ALA* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP 4.5 0.2 + - - -
134E PHE* 3.4 49.1 + - - -
137E ASN* 3.5 0.6 - - - +
138E GLY 2.8 22.0 + - - -
139E LYS* 3.2 22.7 - - - +
140E LEU 3.1 0.6 - - - -
141E GLY* 1.3 76.5 - - - +
143E ILE* 1.3 55.6 + - - +
145E GLY 3.3 0.5 + - - -
146E GLN* 2.9 27.0 + - - +
178E SER* 4.0 15.7 - - - -
179E GLY 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LYS 3.0 13.6 + - - +
140E LEU 3.1 7.9 - - - +
142E SER* 1.3 75.0 - - - +
144E CYS* 1.3 54.0 + - - +
146E GLN* 3.1 6.2 + - - +
147E LEU* 2.6 61.3 + - + +
174E LEU* 4.6 13.2 - - + +
178E SER* 3.7 15.5 - - - +
180E ILE* 3.6 26.9 - - + -
186E VAL* 4.0 14.8 - - + -
189E ILE* 4.0 23.8 - - + -
190E ILE* 4.9 11.7 - - + -
193E LEU* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E LEU* 3.0 36.3 + - - -
141E GLY* 3.4 10.5 + - - -
143E ILE* 1.3 76.2 - - - +
145E GLY* 1.3 56.1 + - - +
147E LEU* 3.8 2.8 - - - +
148E LEU* 3.0 30.0 + - - +
193E LEU* 4.2 19.3 - - - -
213E TYR* 4.5 0.7 - - - -
214E LEU* 3.7 32.5 - - + +
217E TYR* 3.7 25.6 - - + -
218E ALA* 4.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP* 5.5 0.2 - - - -
134E PHE* 4.0 5.4 - - - -
141E GLY 2.5 23.4 + - - -
142E SER 3.6 1.6 - - - -
143E ILE 3.1 0.2 - - - -
144E CYS* 1.3 72.4 - - - +
146E GLN* 1.3 62.4 + - - +
148E LEU* 3.2 5.9 + - - +
149E ILE* 3.0 28.3 + - - +
218E ALA* 3.9 18.3 - - - +
221E LEU* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLN* 6.2 0.2 - - - +
62E TYR* 4.9 7.3 - - - +
130E LYS* 3.6 20.3 + - - +
134E PHE* 4.1 4.3 - - + -
142E SER 2.9 16.3 + - - +
143E ILE* 3.7 4.7 - - - +
145E GLY* 1.3 74.4 - - - +
147E LEU* 1.3 63.0 + - - +
149E ILE* 3.2 14.1 + - - +
150E LEU* 3.0 55.1 + - + +
174E LEU* 5.1 7.2 - - + +
177E SER* 3.5 46.1 + - - +
178E SER* 5.3 1.6 - - - +
301E GSH 3.5 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ILE* 2.6 49.5 + - + +
144E CYS* 3.8 5.4 - - - +
146E GLN* 1.3 73.7 - - + +
148E LEU* 1.3 50.3 + - - +
150E LEU* 3.3 13.8 + - + +
151E THR* 2.4 44.5 + - - +
164E ILE* 5.4 2.6 - - + +
169E LEU* 6.2 1.3 - - + -
174E LEU* 4.9 16.4 - - + -
190E ILE* 5.5 5.2 - - + -
193E LEU* 4.8 13.5 - - + -
199E ILE* 4.6 21.5 - - + -
206E PHE* 5.1 14.4 - - + -
208E VAL* 6.1 1.1 - - + -
214E LEU* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E CYS 3.0 18.5 + - - +
145E GLY* 3.4 4.0 - - - +
147E LEU* 1.3 75.6 - - - +
149E ILE* 1.3 58.6 + - - +
151E THR* 3.3 7.0 + - - -
152E TYR* 2.9 62.6 + - + -
211E LEU* 5.0 3.1 - - + -
214E LEU* 3.8 17.2 - - + +
215E LYS* 3.7 44.9 - - + +
218E ALA* 4.1 10.8 - - + +
221E LEU* 3.9 34.3 - - + +
222E ASP 4.7 1.1 - - - +
225E PHE* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E TYR* 3.3 26.2 - - + +
130E LYS* 4.1 16.2 - - + -
134E PHE* 5.2 0.2 - - + -
145E GLY 3.0 18.2 + - - +
146E GLN* 3.2 21.3 + - - +
148E LEU* 1.3 75.0 - - - +
150E LEU* 1.3 58.9 + - - +
152E TYR* 3.0 4.5 + - - +
153E VAL* 2.9 32.9 + - + +
221E LEU* 4.3 17.7 - - + -
225E PHE* 4.0 24.4 - - + -
301E GSH 3.4 38.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E TYR* 4.1 15.3 - - + -
146E GLN* 3.0 46.6 + - + +
147E LEU* 3.8 11.4 - - + +
149E ILE* 1.3 77.8 - - - +
151E THR* 1.3 57.3 + - - +
154E TYR* 2.8 61.8 + - + +
155E GLY* 3.0 6.9 + - - -
164E ILE* 4.1 15.8 - - + +
166E LEU* 4.8 3.1 - - + -
169E LEU* 3.9 31.0 - - + -
174E LEU* 4.4 8.7 - - + -
177E SER* 6.1 0.4 - - - +
301E GSH 4.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LEU* 2.4 36.1 + - - +
148E LEU* 3.5 9.1 - - - -
150E LEU* 1.3 73.1 - - - +
152E TYR* 1.3 59.3 + - - +
155E GLY* 3.1 23.5 - - - +
162E ILE* 3.7 22.7 - - + -
164E ILE* 4.3 7.4 - - - +
208E VAL* 3.6 32.9 - - + +
211E LEU* 4.2 13.5 - - + -
214E LEU* 4.1 4.5 - - + +
236E LEU* 3.5 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E LEU* 2.9 54.6 + - + +
149E ILE 3.6 2.9 - - - +
151E THR* 1.3 81.2 - - - +
153E VAL* 1.3 61.7 + - - +
155E GLY 4.3 6.1 - - - +
211E LEU* 3.4 27.0 - - + +
215E LYS* 3.7 10.2 - - + +
222E ASP* 5.2 2.8 + - - -
225E PHE* 3.6 27.1 - + + -
232E THR* 3.8 37.4 + - - +
233E TRP* 3.2 41.9 + + - -
236E LEU* 4.3 14.2 - - + +
237E ASN* 2.8 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E LYS* 3.1 51.0 + - + -
149E ILE* 2.9 31.0 + - + +
152E TYR* 1.3 77.6 - - - +
154E TYR* 1.3 87.2 + - + +
155E GLY 5.3 0.4 - - - -
225E PHE* 4.4 12.1 - - + -
232E THR* 4.8 11.7 - - + +
301E GSH 4.5 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ILE* 3.3 38.0 - - + +
62E TYR* 3.5 24.5 - + - +
63E TYR 4.6 0.2 - - - -
64E LYS* 3.5 43.1 - - + +
150E LEU* 2.8 43.0 + - + +
153E VAL* 1.3 99.3 - - + +
155E GLY* 1.3 61.9 + - - +
156E LYS* 4.9 0.5 - - - +
163E LYS 3.5 1.4 - - - +
164E ILE* 4.4 3.1 - - + -
165E THR* 3.3 37.4 + - - +
166E LEU* 3.8 29.8 - - + -
301E GSH 4.4 4.9 + - - -
----------------------------------------------------------
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