Contacts of the strand formed by residues 184 - 189 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23J ALA 3.6 4.5 - - - -
25J ARG* 3.4 11.9 + - - +
167J SER* 5.5 3.1 - - - +
170J MET* 3.7 41.3 - - + -
171J LEU* 3.8 28.7 - - + -
174J VAL* 5.8 2.0 - - + -
181J GLY* 6.1 0.4 - - - -
183J GLY* 1.4 79.1 - - - +
185J ILE* 1.4 64.8 + - - +
186J VAL* 3.8 23.6 - - + -
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Residues in contact with ILE 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ALA* 3.0 22.5 - - - +
23J ALA* 3.1 17.7 + - + +
25J ARG* 4.1 23.3 - - + -
40J LYS 6.3 0.7 - - - +
41J ILE* 3.7 24.7 - - + +
184J VAL* 1.4 75.0 - - - +
186J VAL* 1.4 63.7 + - - +
187J HIS* 3.3 29.6 - - + +
196J THR* 3.7 19.1 - - - +
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Residues in contact with VAL 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J ILE 3.5 9.4 - - - +
22J ALA* 3.9 6.5 - - + -
163J PHE* 4.6 17.0 - - + -
166J ILE* 3.8 26.0 - - + -
167J SER* 4.1 17.5 - - - +
170J MET* 5.8 0.2 - - + -
184J VAL* 3.8 19.7 - - + -
185J ILE* 1.4 82.0 - - - +
187J HIS* 1.3 57.3 + - - +
188J ILE* 3.9 22.1 + - + +
195J THR 2.7 23.7 - - - +
196J THR* 3.3 14.0 + - - +
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Residues in contact with HIS 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J VAL 3.4 4.2 - - - +
20J ALA* 3.5 0.5 - - - -
21J ILE* 2.9 42.9 + - + +
41J ILE* 3.7 37.1 - - + +
49J TYR* 4.2 21.5 - + + -
185J ILE* 3.3 36.9 - - + +
186J VAL* 1.3 72.2 - - - +
188J ILE* 1.3 60.4 + - - +
189J ILE* 3.6 0.9 - - + -
194J ILE* 4.3 13.7 - - + -
195J THR 3.4 4.3 - - - -
196J THR* 3.1 27.8 + - - -
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Residues in contact with ILE 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J CYS* 3.5 28.7 - - + -
19J VAL 3.6 3.8 - - - +
20J ALA* 4.2 11.0 - - + -
159J PRO* 3.5 21.3 - - + +
162J LEU* 4.1 7.9 - - + -
163J PHE* 3.3 58.3 - - + +
186J VAL* 3.9 11.2 - - + +
187J HIS* 1.3 77.0 - - - +
189J ILE* 1.4 61.6 + - - +
190J GLU* 3.4 6.2 + - - +
193J LYS* 3.7 10.2 - - - +
194J ILE* 3.9 6.9 - - - +
195J THR* 3.6 20.5 + - - +
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Residues in contact with ILE 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ASN 4.2 1.9 - - - +
18J CYS* 3.3 9.5 - - - -
19J VAL* 2.9 41.6 + - + +
21J ILE* 5.0 2.9 - - + -
48J LEU 4.8 4.7 - - - +
49J TYR* 3.1 48.2 - - + +
109J ALA 3.3 25.8 - - - +
110J GLY* 3.4 11.0 - - - -
111J LEU* 3.7 30.8 - - + +
187J HIS 4.8 3.1 - - - +
188J ILE* 1.4 71.1 - - - +
190J GLU* 1.4 60.9 + - - +
194J ILE* 4.2 16.8 - - + -
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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