Contacts of the strand formed by residues 194 - 199 (chain J) in PDB entry 1U8R
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 ARG 194 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164J ALA* 6.1 1.8 - - + -
165J VAL 3.5 9.6 - - - +
166J VAL* 4.4 12.4 - - + +
192J ASN 4.4 0.2 - - - -
193J ALA* 1.3 72.3 - - - +
195J VAL* 1.3 63.2 + - - +
209J ILE* 5.5 1.4 - - - +
210J PRO* 4.1 16.7 - - + +
230J VAL* 3.5 37.9 + - - +
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Residues in contact with VAL 195 (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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164J ALA* 3.7 1.4 - - - +
165J VAL* 2.9 41.9 + - + +
167J VAL* 4.0 26.0 - - + -
189J VAL* 5.2 3.1 - - + -
193J ALA* 4.1 4.0 - - + +
194J ARG* 1.3 77.3 - - - +
196J THR* 1.3 67.0 + - - +
197J VAL* 4.8 2.0 - - + -
207J ILE* 3.3 33.7 - - + -
208J VAL 2.8 31.2 - - - +
209J ILE* 3.7 15.5 - - + -
210J PRO* 4.6 2.9 - - - -
227J VAL* 6.1 0.2 - - + -
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Residues in contact with THR 196 (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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162J PRO* 4.6 9.0 - - + +
163J VAL 3.0 20.0 - - - +
164J ALA* 3.7 16.6 - - + -
195J VAL* 1.3 81.3 - - - +
197J VAL* 1.3 62.0 + - - +
206J THR 3.7 0.2 - - - +
207J ILE* 3.4 3.3 - - - +
208J VAL* 2.7 60.9 + - - +
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Residues in contact with VAL 197 (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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154J LEU* 3.8 21.3 - - + -
157J LEU* 3.2 32.6 - - + +
162J PRO* 3.5 2.0 - - - +
163J VAL* 2.9 34.0 + - - +
165J VAL* 3.9 17.0 - - + -
195J VAL* 4.8 2.0 - - + -
196J THR* 1.3 79.6 - - - +
198J GLU* 1.3 60.4 - - - +
205J VAL* 4.0 10.8 - - + -
206J THR 3.2 5.4 - - - +
207J ILE* 3.9 29.2 - - + -
208J VAL* 5.9 0.4 - - - -
227J VAL* 5.8 1.1 - - + -
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Residues in contact with GLU 198 (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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160J GLY 2.7 28.9 - - - +
161J SER 4.7 0.9 - - - -
162J PRO* 3.0 36.7 - - + +
197J VAL* 1.3 76.0 - - - +
199J THR* 1.3 72.9 - - - +
200J THR 3.3 0.9 + - - -
205J VAL* 3.6 3.8 - - - -
206J THR* 2.9 41.1 + - - +
208J VAL* 5.9 3.6 - - + -
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Residues in contact with THR 199 (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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154J LEU 5.3 0.5 + - - -
157J LEU* 3.3 25.4 + - - +
158J PRO 3.8 2.9 + - - -
159J ALA* 3.5 37.4 - - + +
160J GLY 5.3 1.0 + - - -
198J GLU* 1.3 81.8 - - - +
200J THR* 1.3 74.4 + - - +
201J PRO* 4.7 0.5 - - - +
203J GLY* 5.0 7.0 - - - -
204J GLY 3.8 13.1 + - - +
205J VAL* 4.5 6.1 - - + +
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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