Contacts of the helix formed by residues 150 - 169 (chain B) in PDB entry 4EMX
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 TYR 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B TYR 3.1 4.0 + - - -
149B PHE* 1.3 74.4 - - + +
151B ALA* 1.3 65.2 + - - +
152B PRO* 3.8 13.2 - - + -
153B GLU* 3.2 28.4 - - + +
154B LEU 3.0 18.0 + - - -
192B SER* 5.0 2.0 - - - +
196B GLN* 3.6 38.9 - - + +
241B VAL* 3.5 13.7 - - + +
242B HIS* 3.5 24.5 + + - -
245B CYS* 3.7 22.0 - - - -
253B CYS* 3.9 4.7 - - - -
257B ARG* 3.2 29.5 + - - -
291B ALA* 5.9 1.3 - - + -
603B CL 2.8 30.4 - - + +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.8 19.7 - - + -
25B ILE* 4.0 9.1 - - + +
149B PHE 3.0 8.0 + - - +
150B TYR* 1.3 71.1 - - - +
152B PRO* 1.4 69.1 - - + +
154B LEU* 3.0 27.1 + - - +
155B LEU* 3.3 8.1 + - - +
245B CYS* 4.0 11.8 - - - -
250B LEU* 3.8 29.6 - - + +
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Residues in contact with PRO 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.3 0.9 - - + -
150B TYR* 3.8 11.4 - - + -
151B ALA* 1.4 95.5 - - + +
153B GLU* 1.3 55.3 + - - +
155B LEU* 3.1 36.3 + - + +
156B PHE* 3.3 6.6 + - - +
245B CYS* 3.7 11.2 - - - -
253B CYS* 4.0 7.9 - - - -
254B ALA* 4.1 22.9 - - + +
257B ARG* 3.4 48.0 + - - +
284B LEU* 4.3 5.9 - - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PHE* 4.3 0.9 - - + -
150B TYR* 3.2 34.5 + - + +
152B PRO* 1.3 78.5 - - - +
154B LEU* 1.3 57.5 + - - +
156B PHE* 3.1 19.5 + - - +
157B PHE* 2.8 41.9 + - + -
192B SER* 3.5 14.9 + - - +
195B LYS* 5.7 2.3 + - - -
257B ARG* 2.8 29.9 + - - +
288B HIS* 2.9 43.4 + - - +
291B ALA* 5.9 2.9 - - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.6 31.2 - - + -
138B TYR* 4.3 13.5 - - + +
139B LEU* 3.8 29.1 - - + +
142B ILE* 4.1 30.1 - - + -
143B ALA* 4.4 7.4 - - + +
149B PHE* 3.7 31.4 - - + -
150B TYR 3.0 4.0 + - - +
151B ALA* 3.0 13.9 + - - +
153B GLU* 1.3 71.8 - - - +
155B LEU* 1.3 64.0 + - - +
157B PHE* 4.0 6.3 - - + -
158B ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 6.2 0.2 - - + -
18B ASN* 3.9 29.8 - - + +
21B ALA* 3.6 30.1 - - + -
22B LEU* 3.9 30.1 - - + -
25B ILE* 4.0 19.1 - - + -
139B LEU* 5.0 2.7 - - + -
151B ALA 3.3 7.0 + - - +
152B PRO* 3.1 19.6 + - + +
154B LEU* 1.3 75.4 - - - +
156B PHE* 1.3 56.2 + - - +
158B ALA* 3.3 7.3 + - + +
159B LYS* 2.9 29.6 + - - +
254B ALA* 5.0 2.9 - - + -
284B LEU* 4.0 21.3 - - + +
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PRO 3.3 7.0 + - - +
153B GLU* 3.1 19.7 + - - +
155B LEU* 1.3 77.5 - - - +
157B PHE* 1.3 68.3 + + - +
159B LYS* 3.3 12.4 + - + +
160B ARG* 3.1 61.8 + - + +
284B LEU* 4.1 21.7 - - + +
285B GLU* 3.8 34.1 - - + -
288B HIS* 3.4 47.6 - + + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B TYR* 3.7 18.8 + - - +
149B PHE* 3.7 22.0 - + - -
153B GLU* 2.8 55.5 + - + -
154B LEU* 3.5 8.9 + - + +
155B LEU 3.4 0.2 - - - -
156B PHE* 1.3 81.2 - + - +
158B ALA* 1.3 52.7 + - - +
160B ARG* 3.1 9.1 + - - +
161B TYR* 2.8 34.3 + - - +
185B LEU* 3.6 29.6 - - + +
188B GLU* 3.7 52.9 - - + -
189B GLY* 4.0 2.5 - - - -
192B SER* 3.7 6.1 - - - -
288B HIS* 5.2 4.5 - + - -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.2 20.5 - - + +
138B TYR* 3.7 17.4 - - + -
139B LEU* 3.8 23.3 - - + -
154B LEU 3.1 15.3 + - - +
155B LEU* 3.4 11.0 - - - +
157B PHE* 1.3 74.6 - - - +
159B LYS* 1.3 64.7 + - - +
161B TYR* 3.2 0.4 + - - -
162B LYS* 2.9 20.6 + - - +
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU 2.9 12.7 + - - +
156B PHE* 3.5 25.4 - - + +
158B ALA* 1.3 77.6 - - - +
160B ARG* 1.3 58.4 + - + +
162B LYS* 3.5 10.7 + - + +
163B ALA* 3.1 27.0 + - + +
282B PRO* 4.1 26.7 - - - +
284B LEU* 4.6 23.3 - - + +
285B GLU* 5.7 4.2 - - + +
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B PHE* 3.1 55.4 + - + +
157B PHE* 3.1 10.9 + - - +
159B LYS* 1.3 76.3 - - + +
161B TYR* 1.3 61.7 + - - +
163B ALA* 3.9 6.8 - - + +
164B ALA* 3.1 28.4 + - - +
181B LYS 5.2 1.0 + - - -
184B GLU* 4.1 15.4 + - - +
185B LEU* 3.6 32.3 - - + +
188B GLU* 2.8 42.2 + - - -
288B HIS* 5.1 1.8 + - - -
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B MET* 4.0 10.8 - - + +
134B PHE* 3.5 40.0 + + - -
135B LEU* 4.0 12.1 - - + -
138B TYR* 3.4 59.4 - + + +
157B PHE 2.8 15.8 + - - +
158B ALA 3.5 4.3 - - - +
160B ARG* 1.3 77.8 - - - +
162B LYS* 1.3 61.6 + - - +
164B ALA* 3.4 4.0 + - - +
165B PHE* 3.2 45.0 + + - -
182B LEU* 4.1 22.2 - - + -
185B LEU* 3.9 12.7 - - + +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 4.8 12.2 + - - +
127B PHE* 4.0 9.3 - - + -
131B GLU* 4.4 19.6 + - + +
132B GLU* 5.2 6.9 + - - -
135B LEU* 3.7 31.9 - - + -
158B ALA 2.9 15.7 + - - +
159B LYS* 3.7 9.2 - - + +
161B TYR* 1.3 78.9 - - - +
163B ALA* 1.3 58.0 + - - +
165B PHE* 3.2 3.6 + - - +
166B THR* 2.7 42.0 + - - +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS* 3.1 18.4 + - + +
160B ARG* 4.1 7.4 - - + +
161B TYR 3.4 0.2 - - - -
162B LYS* 1.3 76.9 - - - +
164B ALA* 1.3 57.1 + - - +
166B THR* 3.7 8.3 - - - -
167B GLU* 2.9 32.8 + - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG 3.1 17.9 + - - +
161B TYR* 3.6 7.2 - - - +
162B LYS 3.2 0.2 - - - -
163B ALA* 1.3 74.9 - - - +
165B PHE* 1.3 58.8 + - - +
168B CYS* 3.1 34.9 + - - +
178B LEU* 3.4 14.0 - - + +
181B LYS* 4.0 35.9 - - + +
182B LEU* 4.5 7.0 - - + -
185B LEU* 5.1 1.6 - - + -
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B MET* 3.6 37.7 - - + -
127B PHE* 3.5 41.8 - + + -
128B HIS* 5.1 0.2 - - - -
134B PHE* 3.7 20.2 - + - -
161B TYR* 3.2 52.2 + + - -
162B LYS 3.2 2.5 + - - +
164B ALA* 1.3 73.6 - - - +
166B THR* 1.3 69.5 + - - +
169B CYS* 3.1 44.5 + - - +
178B LEU* 3.5 27.8 - - + -
182B LEU* 4.0 12.1 - - + -
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PHE* 3.7 18.2 - - + -
128B HIS* 5.8 1.3 - - - -
131B GLU* 5.1 2.4 + - - -
162B LYS* 2.7 38.1 + - - +
163B ALA* 3.3 9.3 + - - -
165B PHE* 1.3 75.6 - - - +
167B GLU* 1.3 62.1 + - - +
169B CYS* 4.3 0.7 + - - +
170B GLN* 4.0 16.1 - - - +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ALA 2.9 16.7 + - - +
164B ALA 4.7 0.2 - - - +
166B THR* 1.3 77.0 - - - +
168B CYS* 1.3 65.4 + - - +
170B GLN* 3.2 20.0 + - - +
171B ALA* 3.7 4.3 + - - -
177B CYS* 4.1 11.2 - - - -
181B LYS* 2.8 29.4 + - - +
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B CYS* 4.9 0.2 - - - -
164B ALA 3.1 23.3 + - - +
167B GLU* 1.3 71.0 - - - +
169B CYS* 1.3 58.5 + - - +
170B GLN 3.0 4.9 - - - -
171B ALA* 2.8 24.4 + - - +
174B LYS* 3.6 12.5 - - - +
177B CYS* 2.1 62.8 - - + -
178B LEU* 3.6 21.3 - - + -
181B LYS* 3.8 17.0 - - - -
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Residues in contact with CYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B CYS* 2.0 55.2 - - + -
127B PHE* 4.6 3.4 - - - -
128B HIS* 3.7 24.5 + - + +
165B PHE* 3.1 41.9 + - - +
166B THR 5.0 0.7 - - - +
168B CYS* 1.3 74.7 - - - +
170B GLN* 1.3 65.7 + - - +
174B LYS* 3.4 21.3 - - - +
178B LEU* 5.0 1.3 - - - -
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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
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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) + - + + + + + -
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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