Contacts of the strand formed by residues 200 - 206 (chain F) in PDB entry 5U0A
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 GLU 200 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E THR 2.6 29.3 - - - +
28E VAL* 3.6 15.8 - - - +
29E VAL* 4.2 7.9 + - + +
37E ARG* 3.3 11.8 + - - +
14F TYR* 2.9 39.8 - - + +
198F THR* 3.4 6.6 + - + +
199F VAL* 1.3 72.5 - - - +
201F VAL* 1.3 67.9 + - - +
202F ASP 3.6 0.7 + - - -
225F GLN* 3.7 0.2 - - - -
226F PHE* 2.9 42.0 + - - +
227F SER* 4.7 4.0 - - - -
228F ALA 5.3 0.2 + - - -
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Residues in contact with VAL 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG* 4.6 2.1 + - - -
199F VAL* 3.8 2.5 + - + +
200F GLU* 1.3 78.0 - - - +
202F ASP* 1.3 62.1 + - - +
203F PHE 4.1 1.3 + - - +
223F ALA* 4.1 16.6 - - + +
224F GLY 3.8 5.4 - - - +
225F GLN* 4.2 9.2 - - + +
174L ARG* 4.2 24.2 - - + +
175L HIS* 3.8 28.0 - - + +
178L ARG* 3.5 30.5 - - - +
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Residues in contact with ASP 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LYS* 3.5 14.5 + - - +
37E ARG* 3.0 25.6 + - - +
41E GLN* 3.9 16.8 + - - +
190E HIS* 4.2 5.5 - - - -
14F TYR* 2.9 24.2 + - - +
200F GLU 3.6 0.8 + - - -
201F VAL* 1.3 70.3 - - - +
203F PHE* 1.3 73.3 + - - +
204F PHE* 3.6 6.1 + - - +
223F ALA* 4.0 1.8 - - - -
224F GLY 2.8 38.1 + - - +
226F PHE* 3.8 14.7 - - + -
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Residues in contact with PHE 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ASP* 4.4 6.3 - - + +
21E ASP* 3.2 56.5 - - + +
26E LYS* 3.2 26.1 + - - +
201F VAL* 4.0 4.0 + - - +
202F ASP* 1.3 75.0 + - - +
204F PHE* 1.3 59.3 + - - +
205F THR* 3.3 28.7 - - + -
221F MET* 3.5 29.6 - - + -
222F ASN 3.0 27.8 - - - -
223F ALA* 3.8 6.7 - - + +
33K G 4.3 16.5 + + - +
178L ARG* 3.9 29.2 - - + +
31M A 5.3 2.2 - + - -
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Residues in contact with PHE 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLN* 3.8 17.7 - - - +
202F ASP* 3.8 8.3 - - - +
203F PHE* 1.3 77.9 - - - +
205F THR* 1.3 67.7 + - - +
220F HIS* 4.6 4.5 - + - -
222F ASN* 2.9 59.5 + - + +
223F ALA 3.9 0.7 - - - -
224F GLY* 3.3 33.9 - - - -
226F PHE* 6.2 1.1 - + - -
31K G 3.2 68.0 - + - +
33K G 3.4 11.7 - - - +
32M C 5.5 0.4 - - - -
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Residues in contact with THR 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F PHE* 3.3 35.7 - - + -
204F PHE* 1.3 74.4 - - - +
206F ALA* 1.3 55.7 + - - +
218F SER* 3.8 8.8 - - - -
220F HIS 3.3 12.3 - - - -
221F MET* 3.7 10.8 - - + -
31K G 2.4 23.7 + - - -
32K U 3.0 47.6 - - - +
33K G 2.8 26.0 + - - +
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Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 5.3 4.7 - - - -
116E LEU* 4.8 10.1 - - + -
205F THR* 1.3 70.1 - - - +
207F VAL* 1.3 56.0 + - - +
218F SER* 4.3 1.8 - - - -
219F GLY* 2.5 36.5 + - - -
220F HIS* 2.9 32.1 + - + -
31K G 3.7 34.8 - - + +
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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