Contacts of the strand formed by residues 184 - 189 (chain X) in PDB entry 5A0Q
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 VAL 184 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X ALA 3.6 4.7 - - - -
25X ARG* 3.4 12.4 + - - +
167X SER* 5.5 2.9 - - - +
170X MET* 3.7 41.1 - - + -
171X LEU* 3.8 28.7 - - + -
174X VAL* 5.8 1.6 - - + -
181X GLY* 6.1 0.7 - - - -
183X GLY* 1.4 78.1 - - - +
185X ILE* 1.4 64.6 + - - +
186X VAL* 3.8 23.1 - - + -
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Residues in contact with ILE 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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22X ALA* 3.0 23.6 - - - +
23X ALA* 3.1 18.6 + - + +
25X ARG* 4.1 22.9 - - + -
40X LYS 6.3 0.9 - - - +
41X ILE* 3.7 25.1 - - + +
184X VAL* 1.4 73.5 - - - +
186X VAL* 1.4 64.4 + - - +
187X HIS* 3.3 29.8 - - + +
196X THR* 3.7 19.7 - - - +
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Residues in contact with VAL 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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21X ILE 3.5 10.3 - - - +
22X ALA* 3.9 7.2 - - + -
163X PHE* 4.6 17.0 - - + -
166X ILE* 3.8 26.9 - - + -
167X SER* 4.1 17.5 - - - +
184X VAL* 3.8 19.7 - - + -
185X ILE* 1.4 81.8 - - - +
187X HIS* 1.3 56.8 + - - +
188X ILE* 3.9 22.2 - - + +
195X THR 2.7 23.6 - - - +
196X THR* 3.3 15.5 + - - +
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Residues in contact with HIS 187 (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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19X VAL 3.4 4.0 - - - +
20X ALA* 3.5 0.5 - - - -
21X ILE* 2.9 42.8 + - + +
41X ILE* 3.7 37.8 - - + +
49X TYR* 4.2 22.0 - + + -
185X ILE* 3.3 36.5 - - + +
186X VAL* 1.3 72.4 - - - +
188X ILE* 1.3 61.2 + - - +
189X ILE 3.6 0.9 - - - -
194X ILE* 4.3 13.7 - - + -
195X THR 3.4 4.3 - - - -
196X THR* 3.1 27.4 + - - -
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Residues in contact with ILE 188 (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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18X CYS* 3.5 28.0 - - + -
19X VAL 3.6 3.6 - - - -
20X ALA* 4.2 11.2 - - + -
159X PRO* 3.5 21.1 - - + +
162X LEU* 4.1 8.3 - - + -
163X PHE* 3.3 58.1 - - + +
186X VAL* 3.9 11.7 - - + -
187X HIS* 1.3 76.9 - - - +
189X ILE* 1.4 61.2 + - - +
190X GLU* 3.4 5.9 + - - +
193X LYS 3.7 10.4 - - - +
194X ILE* 3.9 7.8 - - - +
195X THR* 3.6 20.7 + - - +
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Residues in contact with ILE 189 (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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17X ASN 4.2 2.1 - - - +
18X CYS* 3.3 8.8 - - - -
19X VAL* 2.9 43.0 + - + +
21X ILE* 5.0 3.1 - - + -
48X LEU 4.8 4.5 - - - +
49X TYR* 3.1 48.7 - - + +
109X ALA 3.3 25.1 - - - +
110X GLY* 3.4 9.9 - - - -
111X LEU* 3.7 31.7 - - + +
187X HIS 4.8 3.1 - - - +
188X ILE* 1.4 70.2 - - - +
190X GLU* 1.4 60.6 + - - +
194X ILE* 4.2 16.2 - - + -
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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