Contacts of the helix formed by residues 155 - 168 (chain B) in PDB entry 4O6M
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 ILE 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B TRP* 4.9 8.3 - - + -
151B ILE* 2.9 36.2 + - + +
154B GLU* 1.3 92.9 - - + +
156B ASN* 1.3 77.2 + - - +
157B ARG 3.5 1.3 - - - -
158B LYS* 3.4 18.8 + - - +
159B VAL* 3.7 12.0 + - + +
208B GLN* 4.6 7.4 - - - +
212B ILE* 6.0 2.0 - - + -
306B LEU* 5.7 4.9 - - + -
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Residues in contact with ASN 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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151B ILE* 3.1 22.5 + - - +
152B ALA* 3.7 18.0 - - + +
155B ILE* 1.3 84.6 - - - +
157B ARG* 1.3 59.7 + - + +
159B VAL* 3.1 6.8 + - - +
160B SER* 3.0 28.8 + - - +
208B GLN* 2.9 26.3 + - - +
211B SER* 3.3 26.9 + - - +
212B ILE* 3.9 23.5 - - + +
302B ASP* 4.1 7.7 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.8 30.2 - - + +
136B LYS* 3.7 12.3 - - - +
148B ASP* 2.8 42.1 + - - +
152B ALA* 2.8 28.6 + - - +
153B ARG* 4.1 10.8 - - - +
156B ASN* 1.3 70.2 - - + +
158B LYS* 1.3 67.5 + - + +
160B SER* 3.3 4.7 - - - -
161B LEU* 3.0 34.4 + - + +
215B GLY* 3.0 28.7 + - - -
219B GLU* 2.8 41.5 + - - +
222B ARG* 3.9 4.0 - - - +
422B C5P 2.9 27.9 + - - -
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Residues in contact with LYS 158 (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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153B ARG 3.9 14.7 + - - +
154B GLU* 3.4 40.6 + - - +
155B ILE 3.4 8.5 - - - +
156B ASN 3.2 0.4 - - - -
157B ARG* 1.3 79.9 - - + +
159B VAL* 1.3 60.9 + - + +
161B LEU* 4.6 4.9 - - + +
162B ARG* 3.2 26.2 + - - +
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 4.0 14.8 - - + +
156B ASN 3.1 5.9 + - - +
158B LYS* 1.3 80.2 - - + +
160B SER* 1.3 66.4 + - - +
161B LEU 3.3 0.2 - - - -
162B ARG* 3.1 17.8 + - + +
163B ILE* 3.2 22.0 + - + +
209B LEU* 6.5 0.9 - - + -
212B ILE* 3.7 31.6 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASN* 3.0 16.8 + - - +
157B ARG* 3.3 9.0 + - - -
159B VAL* 1.3 77.0 - - - +
161B LEU* 1.3 57.4 + - - +
163B ILE* 3.0 5.9 + - - +
164B SER* 2.8 27.4 + - - -
212B ILE* 3.4 30.6 + - - -
215B GLY* 4.5 0.7 - - - -
216B CYS* 3.7 14.3 - - - -
219B GLU* 2.7 34.0 + - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.2 51.7 - - + +
132B SER* 4.6 4.7 - - - -
134B LEU* 4.1 11.7 - - + -
135B ILE* 4.2 19.7 - - + -
157B ARG* 3.0 29.6 + - + +
158B LYS* 4.6 6.3 - - + +
160B SER* 1.3 76.7 + - - +
162B ARG* 1.3 63.3 + - - +
164B SER* 3.5 2.3 + - - -
165B ARG* 3.0 27.7 + - - +
219B GLU* 3.7 30.1 - - + +
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Residues in contact with ARG 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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127B GLU* 5.5 0.4 + - - -
128B LYS* 6.0 2.6 - - - +
131B LEU* 4.1 14.3 - - - +
158B LYS 3.2 20.9 - - - +
159B VAL* 3.1 8.9 + - + +
161B LEU* 1.3 79.8 - - - +
163B ILE* 1.3 64.3 + - + +
165B ARG* 3.4 50.6 + - - +
166B LEU* 3.5 25.7 + - - +
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Residues in contact with ILE 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 VAL* 3.2 29.1 + - + +
160B SER* 3.0 13.3 + - - +
162B ARG* 1.3 76.6 - - + +
164B SER* 1.3 64.5 + - - +
166B LEU* 3.0 12.9 + - + +
167B LEU* 3.0 38.8 + - + +
209B LEU* 5.9 3.4 - - + -
212B ILE* 4.4 9.4 - - + -
213B ILE* 4.4 15.9 - - + -
216B CYS* 3.9 9.6 - - - -
403B MPG 4.5 7.0 - - + -
404B MPG 4.0 25.4 - - + -
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Residues in contact with SER 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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131B LEU* 5.0 6.1 - - - -
134B LEU* 5.3 0.7 - - - -
160B SER 2.8 14.4 + - - -
161B LEU* 3.8 5.6 - - - -
162B ARG 3.4 0.2 - - - -
163B ILE* 1.3 73.1 - - - +
165B ARG* 1.3 57.0 - - - +
167B LEU* 3.1 5.1 + - - -
168B ALA* 2.8 32.5 + - - +
216B CYS* 3.7 14.7 + - - +
219B GLU* 2.6 38.1 + - - +
220B ILE* 3.6 18.3 - - - +
223B LEU* 4.4 5.1 - - - +
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Residues in contact with ARG 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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17B LEU* 4.0 24.2 - - + +
127B GLU* 2.7 29.7 + - - -
131B LEU* 4.1 13.4 - - + +
161B LEU 3.0 17.4 + - - +
162B ARG* 3.4 45.3 + - - +
164B SER* 1.3 78.2 - - - +
166B LEU* 1.3 80.4 + - + +
168B ALA* 3.6 12.7 + - - +
169B ASP* 4.4 3.8 + - - +
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Residues in contact with LEU 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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162B ARG 3.5 15.7 - - - +
163B ILE* 3.0 10.8 + - + +
165B ARG* 1.3 99.6 - - + +
167B LEU* 1.3 60.6 + - - +
168B ALA 3.5 0.7 + - - -
169B ASP* 3.7 11.8 + - - +
170B THR* 3.9 10.7 - - - +
404B MPG 4.1 44.6 - - + +
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Residues in contact with LEU 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 ILE* 3.0 38.9 + - + +
164B SER* 3.8 7.0 - - - +
166B LEU* 1.3 72.7 - - - +
168B ALA* 1.3 65.2 + - - +
169B ASP 3.1 3.1 - - - -
170B THR* 2.8 27.3 + - - +
172B VAL* 4.3 18.6 + - + +
177B ILE* 4.2 22.9 - - + -
216B CYS* 4.6 7.4 - - + -
220B ILE* 3.9 13.0 - - + +
224B LYS* 4.3 1.4 + - - -
402B MPG 4.2 20.2 - - + -
403B MPG 4.3 20.6 - - + -
404B MPG 4.1 19.5 - - + -
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Residues in contact with ALA 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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17B LEU* 3.7 23.3 - - + +
18B GLY* 3.5 16.5 - - - -
164B SER 2.8 16.4 + - - +
165B ARG 3.6 9.0 - - - +
166B LEU 3.3 0.8 - - - -
167B LEU* 1.3 77.2 - - - +
169B ASP* 1.3 56.8 + - - +
170B THR 3.2 0.4 - - - -
220B ILE* 4.1 7.4 - - - -
223B LEU* 3.7 23.8 - - + -
224B LYS* 3.1 23.9 + - + +
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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
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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