Contacts of the helix formed by residues 151 - 177 (chain E) in PDB entry 5X11
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 151 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E LEU* 4.6 14.3 - - + +
145E MET* 4.1 12.8 - - + +
149E SER* 3.2 9.6 + - - +
150E PRO* 1.3 78.2 - - + +
152E PHE* 1.3 63.7 + - - +
153E GLY 3.3 2.7 - - - -
154E HIS* 3.1 22.3 + - + +
155E TYR* 3.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E MET* 4.1 10.1 - - + -
146E SER* 3.5 24.2 - - - +
147E PHE* 3.6 47.1 - + + +
149E SER* 3.1 18.9 + - - +
150E PRO 3.3 1.4 - - - -
151E ASP* 1.3 76.8 - - - +
153E GLY* 1.3 64.3 + - - +
155E TYR* 3.1 32.4 + + - +
156E LEU* 3.1 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ARG* 5.9 5.4 - - - -
150E PRO 4.9 1.8 + - - -
151E ASP 3.3 1.0 - - - -
152E PHE* 1.3 77.3 - - - +
154E HIS* 1.3 62.5 + - - +
156E LEU* 3.1 22.2 + - - +
157E VAL* 3.2 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLU* 3.3 46.6 + - + +
138E LEU* 4.0 21.7 - - + +
151E ASP* 3.1 18.5 + - - +
153E GLY* 1.3 75.2 - - - +
155E TYR* 1.3 56.0 + - - +
157E VAL* 3.2 11.3 - - - +
158E LEU* 3.0 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E TYR* 4.1 7.4 + + - -
138E LEU* 4.0 13.4 - - + +
139E MET* 3.7 32.5 - - + +
145E MET* 3.7 40.2 - - + -
151E ASP 3.1 2.2 + - - -
152E PHE* 3.1 33.6 + + - +
154E HIS* 1.3 78.7 - - - +
156E LEU* 1.3 58.7 + - + +
158E LEU* 3.8 0.8 - - - +
159E THR* 2.8 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PHE* 3.1 51.0 + - + +
153E GLY* 3.1 14.0 + - - +
155E TYR* 1.3 82.0 - - + +
157E VAL* 1.3 61.3 + - + +
159E THR* 3.1 6.2 + - - +
160E LYS* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLU* 3.8 36.7 - - + +
30E LEU* 4.7 18.8 - - + +
33E PHE* 3.2 35.2 - - + -
153E GLY 3.2 10.9 + - - +
154E HIS* 3.2 17.3 - - - +
156E LEU* 1.3 79.4 - - + +
158E LEU* 1.3 56.1 + - - +
160E LYS* 4.5 0.7 - - - -
161E ALA* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLU* 4.8 10.8 - - + -
131E LEU* 4.1 36.1 - - + +
134E SER* 3.9 25.1 - - - +
135E TYR* 4.1 16.6 - - + +
138E LEU* 3.8 18.8 - - + -
154E HIS* 3.0 45.3 + - + +
155E TYR* 3.8 4.0 - - - +
157E VAL* 1.3 74.4 - - - +
159E THR* 1.3 60.7 + - - +
161E ALA* 3.3 4.0 + - + +
162E LEU* 2.8 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E TYR* 3.7 18.8 - - + +
155E TYR* 2.8 60.7 + - + +
156E LEU* 3.1 13.9 + - - +
158E LEU* 1.3 73.3 - - - +
160E LYS* 1.3 56.2 + - - +
162E LEU* 3.4 9.0 - - + +
163E GLU* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.5 26.3 - - + -
156E LEU 3.0 19.3 + - - +
157E VAL* 3.9 1.1 - - - +
159E THR* 1.3 74.8 + - - +
161E ALA* 1.3 65.4 + - - +
163E GLU* 3.3 8.2 + - + +
164E ARG* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLN* 4.0 26.9 - - + +
33E PHE* 3.6 11.6 - - + -
131E LEU* 3.5 26.8 - - + +
157E VAL 2.9 21.3 + - - +
158E LEU* 3.6 5.4 - - + +
160E LYS* 1.3 76.8 - - - +
162E LEU* 1.3 62.2 + - - +
164E ARG* 3.3 9.6 + - - +
165E GLU* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LEU* 3.6 23.6 - - + -
131E LEU* 4.0 20.4 - - + +
132E GLN* 3.6 25.1 - - - +
135E TYR* 3.6 47.8 - - + -
158E LEU* 2.8 16.1 + - + +
159E THR* 3.4 7.6 - - + +
161E ALA* 1.3 77.3 - - - +
163E GLU* 1.3 62.8 + - - +
164E ARG 3.3 0.2 + - - -
165E GLU* 3.3 3.3 + - - +
166E LYS* 3.0 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E THR 2.8 19.5 + - - +
160E LYS* 3.9 9.2 - - + +
162E LEU* 1.3 72.7 - - - +
164E ARG* 1.3 56.5 + - - +
166E LYS* 3.3 9.8 + - - +
167E ASN* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLN* 3.1 51.1 + - - +
33E PHE* 3.3 31.3 - - + -
124E ARG* 5.8 0.6 - - - +
160E LYS* 3.0 24.7 + - - +
161E ALA* 3.4 7.7 + - - +
162E LEU 3.2 0.2 - - - -
163E GLU* 1.3 77.5 - - - +
165E GLU* 1.3 71.9 + - - +
167E ASN* 3.5 4.1 + - - +
168E TYR* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLN* 5.4 2.0 - - - +
124E ARG* 3.1 55.8 + - - +
127E LYS* 3.8 13.4 - - + +
128E LEU* 3.9 29.2 - - + +
131E LEU* 3.6 26.5 - - + -
161E ALA 3.2 5.0 + - - +
162E LEU 4.0 2.2 - - - +
164E ARG* 1.3 91.0 + - - +
166E LYS* 1.3 66.7 + - - +
168E TYR* 3.6 2.1 - - - +
169E VAL* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LEU* 3.7 26.2 - - + +
132E GLN* 3.9 27.0 + - - +
162E LEU* 3.0 25.9 + - + +
163E GLU* 3.5 10.8 - - - +
165E GLU* 1.3 76.5 - - - +
167E ASN* 1.3 62.4 + - - +
169E VAL* 3.7 2.9 - - - +
170E SER* 3.0 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E GLU* 2.8 34.9 + - - +
164E ARG* 4.1 4.1 - - - +
166E LYS* 1.3 75.4 - - - +
168E TYR* 1.3 60.5 + - - +
170E SER* 3.7 8.1 - - - -
171E TRP* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ASP* 2.9 33.3 + - - -
98E PHE* 3.7 20.6 - + - +
99E MET* 4.0 8.0 - - + +
120E GLN* 4.4 3.4 - - - -
124E ARG* 3.3 50.6 + - - -
164E ARG* 3.0 25.8 + - + +
165E GLU* 3.2 9.2 + - - +
167E ASN* 1.3 74.1 - - - +
169E VAL* 1.3 59.6 + - - +
171E TRP* 3.4 13.9 + + - +
172E LEU* 2.9 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LEU* 3.8 16.4 - - + -
124E ARG* 4.0 31.9 - - + +
125E LYS* 4.0 11.9 - - + +
128E LEU* 3.9 22.2 - - + -
165E GLU* 2.9 20.4 + - - +
166E LYS 3.7 4.7 - - - +
168E TYR* 1.3 76.3 - - - +
170E SER* 1.3 53.0 + - - +
172E LEU* 3.2 6.9 + - - +
173E GLU* 2.8 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E LYS 3.0 18.2 + - - -
167E ASN* 3.7 10.8 - - - -
169E VAL* 1.3 75.9 - - - +
171E TRP* 1.3 62.4 + - - +
173E GLU* 3.5 15.7 + - - +
174E SER* 3.1 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E PHE* 4.2 9.6 - + - -
99E MET* 3.5 42.0 - - + -
102E ALA* 4.7 3.8 - - + -
117E PHE* 3.9 31.0 - + - -
167E ASN 2.9 19.6 + - - +
168E TYR* 3.6 11.7 - + - +
170E SER* 1.3 75.7 - - - +
172E LEU* 1.3 81.7 + - + +
174E SER* 3.0 18.9 + - - -
175E ILE* 3.0 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E PHE* 3.7 23.6 - - + -
117E PHE* 3.6 31.4 - - + +
120E GLN* 3.8 21.5 - - + -
121E LEU* 3.9 27.4 - - + -
124E ARG* 3.9 9.9 - - + -
168E TYR* 2.9 41.5 + - + +
169E VAL* 3.5 5.2 - - - +
171E TRP* 1.3 83.2 - - + +
173E GLU* 1.3 61.4 + - - +
175E ILE* 3.3 5.0 + - - +
176E LEU* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LEU* 3.9 23.8 - - + +
125E LYS* 5.6 2.1 - - - +
169E VAL* 2.8 38.1 + - - +
170E SER* 3.7 14.1 + - - +
172E LEU* 1.3 72.9 - - - +
174E SER* 1.3 62.2 + - - +
176E LEU* 3.4 6.6 + - - +
177E ALA* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E SER 3.1 13.1 + - - -
171E TRP* 3.0 15.5 + - - -
173E GLU* 1.3 77.0 - - - +
175E ILE* 1.3 67.3 + - - +
177E ALA* 3.3 19.8 + - - +
178E MET* 3.5 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ILE* 5.6 2.5 - - + -
117E PHE* 3.7 26.2 - - + -
171E TRP* 3.0 58.9 + - + +
172E LEU 3.3 4.9 + - - +
174E SER* 1.3 78.1 - - - +
176E LEU* 1.3 60.7 + - - +
178E MET* 2.9 34.0 + - + +
179E ILE* 3.2 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E SER* 3.8 26.7 - - - +
117E PHE* 4.1 15.9 - - + +
118E THR* 3.6 33.7 - - + +
121E LEU* 3.9 27.6 - - + -
172E LEU 3.1 16.7 + - - +
173E GLU* 3.7 6.1 - - - +
175E ILE* 1.3 77.0 - - - +
177E ALA* 1.3 56.6 + - - +
178E MET 3.1 0.2 - - - -
179E ILE* 2.9 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E GLU 3.1 12.6 + - - +
174E SER* 3.4 13.9 - - - +
175E ILE 3.2 0.4 - - - -
176E LEU* 1.3 75.3 - - - +
178E MET* 1.3 60.0 + - + +
179E ILE 3.3 4.5 - - - +
----------------------------------------------------------
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