Contacts of the strand formed by residues 182 - 186 (chain X) in PDB entry 6JM9
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 HIS 182 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159X PHE* 3.5 18.6 - - + +
170X VAL* 3.7 17.2 - - + +
173X VAL* 3.6 26.1 - - + +
174X ALA* 3.3 30.7 + - + -
177X THR 3.6 14.4 + - - -
178X ASN* 3.9 1.0 - - - -
179X CYS* 3.2 45.5 + - + -
181X HIS* 1.3 77.2 - - - +
183X TYR* 1.3 61.4 + - - +
214X ALA* 4.1 6.6 - - + +
215X GLU 3.5 23.2 + - - +
216X TYR* 3.5 3.9 - - + +
217X THR* 3.2 24.4 + - - +
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Residues in contact with TYR 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158X LEU* 4.6 8.9 - - + +
159X PHE* 2.9 22.9 + - - +
160X VAL* 3.6 23.4 - - + -
161X ASP 3.0 23.2 + - - -
170X VAL* 3.4 16.8 - - - +
181X HIS* 3.3 47.7 + + + -
182X HIS* 1.3 72.6 - - - +
184X GLY* 1.3 60.8 + - - +
217X THR* 3.3 27.8 - - - -
219X GLU* 3.0 35.2 - - - +
228X TRP* 5.0 3.8 - + + -
231X ARG* 4.1 15.5 + - - -
235X THR* 5.3 1.3 - - - -
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Residues in contact with GLY 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161X ASP 3.8 1.8 - - - -
164X SER* 3.4 24.2 - - - -
170X VAL* 4.0 0.9 - - - -
183X TYR* 1.3 76.4 - - - +
185X VAL* 1.4 58.8 + - - -
195X ALA* 6.6 0.2 - - - -
217X THR 3.4 7.5 + - - -
218X LEU* 3.7 14.0 - - - +
219X GLU* 2.9 33.7 + - - +
228X TRP* 5.4 0.4 - - - -
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Residues in contact with VAL 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X VAL* 4.8 0.9 - - + -
161X ASP 3.2 13.2 + - - +
162X LEU* 3.9 6.7 - - + -
163X GLY 3.0 19.6 + - - -
164X SER* 3.2 5.0 + - - -
184X GLY* 1.4 71.1 - - - -
186X GLU* 1.3 66.5 + - - +
219X GLU 3.5 4.3 - - - +
221X GLY* 3.9 6.1 - - - -
222X ASP 3.6 39.0 - - - +
223X PHE* 3.6 18.1 - - + +
228X TRP* 3.7 46.4 - - + +
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Residues in contact with GLU 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLY 4.3 0.3 + - - -
163X GLY 3.9 0.2 - - - -
164X SER* 3.8 3.1 - - - +
165X GLY* 2.9 50.1 + - - +
185X VAL* 1.3 77.6 - - - +
187X LYS* 1.4 54.0 + - - +
188X ALA* 3.0 17.8 + - - +
191X PRO* 3.9 9.2 - - + -
192X ALA* 3.7 32.1 - - + +
195X ALA* 5.7 0.9 - - + -
219X GLU 3.7 6.3 + - - +
221X GLY 2.7 27.6 + - - +
223X PHE* 4.3 0.2 - - - -
500X SAM 2.2 59.3 + - - +
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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
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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