Contacts of the helix formed by residues 153 - 167 (chain B) in PDB entry 1M6X
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 SER 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLY 3.6 1.1 + - - -
152B GLU* 1.3 74.3 - - - +
154B ILE* 1.3 67.0 + - - +
155B TRP* 3.5 8.0 + - - +
156B GLU* 2.9 39.1 + - - +
157B ILE* 2.8 25.4 + - - +
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Residues in contact with ILE 154 (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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148B LEU* 3.7 40.4 - - + -
153B SER* 1.3 73.3 - - - +
155B TRP* 1.3 61.0 + - + +
157B ILE* 3.0 10.1 + - + +
158B THR* 2.7 31.8 + - - +
186B PHE* 3.7 33.7 - - + -
310B LEU* 4.1 23.8 - - + +
314B PHE* 4.2 35.4 - - + +
317B MET* 5.8 2.5 - - - -
346C GLN* 4.9 9.2 - - - +
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Residues in contact with TRP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 3.3 6.3 + - - +
154B ILE* 1.3 79.2 - - + +
156B GLU* 1.3 64.4 + - + +
158B THR* 3.2 16.0 + - + -
159B GLU* 3.0 24.4 + - - +
183B LEU* 4.6 1.3 - - + -
186B PHE* 4.0 25.7 - + - -
187B ILE* 4.2 12.8 - - + -
235B ALA* 5.3 4.3 - - + -
239B ILE* 3.9 37.0 - - + -
241B PRO* 5.9 1.1 - - + -
314B PHE* 4.9 22.5 - + - -
357B LEU 5.2 1.6 + - - -
358B VAL* 3.1 34.8 + - + +
360B ARG* 3.4 58.0 - - + +
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Residues in contact with GLU 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 GLY 4.6 0.9 - - - +
152B GLU* 3.2 23.8 - - + +
153B SER* 2.9 41.9 + - - +
155B TRP* 1.3 76.5 - - + +
157B ILE* 1.3 63.4 + - - +
159B GLU* 3.3 8.1 + - - +
160B LYS* 3.1 28.7 + - - +
293B TYR* 4.8 0.7 - - - -
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Residues in contact with ILE 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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147B LEU* 3.9 42.4 - - + +
148B LEU* 3.9 17.7 - - + -
152B GLU* 3.8 25.4 - - + +
153B SER 2.8 23.3 + - - +
154B ILE* 3.3 9.9 - - + +
156B GLU* 1.3 76.3 - - - +
158B THR* 1.3 62.6 + - - +
160B LYS* 3.2 2.9 + - - +
161B ILE* 3.0 41.2 + - + +
293B TYR* 3.6 21.5 - - + +
310B LEU* 4.5 7.4 - - + -
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Residues in contact with THR 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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154B ILE* 2.7 29.1 + - - +
155B TRP* 3.2 19.2 + - + -
157B ILE* 1.3 75.6 - - - +
159B GLU* 1.3 56.8 + - - +
161B ILE 3.4 0.3 + - - -
162B LEU* 2.8 34.8 + - + +
182B PHE* 3.4 33.7 - - + -
183B LEU* 4.5 11.9 - - + -
186B PHE* 3.9 32.3 - - + -
239B ILE* 5.4 1.1 - - + -
310B LEU* 4.7 3.9 - - - +
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Residues in contact with GLU 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 TRP 3.0 12.5 + - - +
156B GLU* 3.7 10.8 - - - +
157B ILE 3.3 0.2 - - - -
158B THR* 1.3 75.7 - - - +
160B LYS* 1.3 60.0 + - - +
162B LEU* 3.3 5.9 + - - +
163B ASN* 2.8 55.3 + - - +
238B ARG* 3.1 53.8 + - - +
239B ILE* 4.0 26.5 - - + +
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Residues in contact with LYS 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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152B GLU* 2.5 32.9 + - - +
156B GLU* 3.1 15.5 + - - +
157B ILE 3.2 3.6 + - - +
159B GLU* 1.3 79.3 - - - +
161B ILE* 1.3 64.8 + - - +
163B ASN* 3.0 8.0 + - - +
164B SER* 2.9 22.6 + - - -
292B PRO* 4.9 9.4 - - + +
293B TYR* 3.2 33.7 - - + +
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Residues in contact with ILE 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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147B LEU* 5.9 0.9 - - + -
157B ILE* 3.0 34.9 + - + +
158B THR 3.7 3.8 - - - +
160B LYS* 1.3 74.4 - - - +
162B LEU* 1.3 64.8 + - - +
164B SER* 2.5 27.2 + - - +
165B PHE* 3.4 14.5 - - + -
182B PHE* 3.8 39.5 - - + -
287B LEU* 4.2 15.5 - - + -
292B PRO* 4.1 5.8 - - + -
293B TYR* 3.9 17.3 - - + -
296B PHE* 3.8 26.2 - - + -
306B ILE* 4.6 1.3 - - + -
310B LEU* 4.3 8.5 - - + -
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Residues in contact with LEU 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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158B THR* 2.8 18.9 + - + +
159B GLU* 3.4 6.1 - - - +
161B ILE* 1.3 79.3 - - - +
163B ASN* 1.3 63.1 + - - +
165B PHE* 3.4 14.6 + - + -
179B GLN* 3.0 64.5 + - + +
182B PHE* 3.8 17.2 - - + -
183B LEU* 4.5 8.5 - - + -
239B ILE* 3.8 28.7 - - + -
244B TYR* 3.3 38.1 - - + +
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Residues in contact with ASN 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 GLU* 2.8 42.6 + - - +
160B LYS* 3.6 6.2 - - - +
162B LEU* 1.3 77.9 - - - +
164B SER* 1.3 53.8 + - - +
165B PHE 2.7 7.3 + - - -
166B GLU* 2.7 41.9 + - + +
167B TYR* 4.1 5.3 + - + -
179B GLN* 4.4 2.2 - - - +
239B ILE* 5.2 1.4 - - - +
244B TYR* 4.8 6.5 + - - -
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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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160B LYS 2.9 7.3 + - - -
161B ILE 2.5 20.3 + - - -
163B ASN* 1.3 75.9 - - - +
165B PHE* 1.3 65.1 + - - +
167B TYR 4.9 0.2 - - - -
168B THR* 3.0 30.1 + - - +
287B LEU* 4.9 0.3 - - - +
290B ASN* 3.6 13.5 + - - +
292B PRO* 3.6 39.6 - - - +
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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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161B ILE* 3.4 37.7 - - + -
162B LEU* 3.4 13.7 - - - +
163B ASN 2.7 2.8 + - - -
164B SER* 1.3 75.9 - - - +
166B GLU* 1.3 69.5 + - - +
167B TYR 3.1 3.7 + - - -
168B THR* 3.5 3.8 - - - -
169B SER* 2.9 32.6 + - - +
175B LYS* 3.6 4.0 - - + +
178B TYR* 3.5 36.3 - + + -
179B GLN* 4.0 16.8 - - + -
182B PHE* 4.6 5.6 - - + -
283B TYR* 3.6 28.9 - + - -
286B ALA* 4.1 2.7 - - + -
287B LEU* 3.9 39.0 - - + -
290B ASN* 3.9 13.5 - - - -
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Residues in contact with GLU 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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163B ASN* 2.7 26.1 + - + +
165B PHE* 1.3 77.2 - - - +
167B TYR* 1.3 91.1 + - + +
169B SER* 5.1 1.4 + - - +
175B LYS* 3.1 42.8 + - - +
179B GLN* 3.7 17.1 + - - +
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Residues in contact with TYR 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 ASN* 4.1 5.1 + - + -
164B SER 4.8 0.8 + - - -
165B PHE 3.2 0.2 - - - -
166B GLU* 1.3 107.7 - - + +
168B THR* 1.3 64.7 + - + +
169B SER 3.7 4.4 - - - +
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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