Contacts of the strand formed by residues 255 - 260 (chain J) in PDB entry 1DU3
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 255 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLU* 3.1 28.5 + - + +
174J LEU 3.3 7.4 - - - +
175J VAL* 3.9 26.0 - - + -
176J ILE 5.0 0.2 - - - +
212J LYS* 3.1 2.3 - - - -
213J TYR* 2.6 88.4 + - + +
214J THR 5.4 1.8 + - - -
253J ASN 3.6 12.6 - - - +
254J ASP* 1.3 84.2 - - - +
256J ILE* 1.3 64.4 + - - +
257J PHE* 4.7 1.8 - - - -
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Residues in contact with ILE 256 (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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173J GLU* 3.3 1.6 - - - -
174J LEU* 2.9 63.0 + - + +
176J ILE* 4.3 18.6 - - + -
184J ILE* 4.6 13.5 - - + -
210J ILE* 5.0 5.4 - - + -
211J TYR 3.2 9.0 - - - +
212J LYS* 4.1 15.5 - - + -
222J LEU* 4.5 5.8 - - + -
250J LEU* 4.0 26.5 - - + -
254J ASP* 5.6 0.2 - - + -
255J ARG* 1.3 82.4 - - - +
257J PHE* 1.3 66.3 + - - +
275J PHE* 3.5 22.8 - - + -
277J ALA* 4.8 4.3 - - + -
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Residues in contact with PHE 257 (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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146J ALA* 4.0 16.6 - - + -
150J LYS* 3.4 30.5 - - + -
172J GLY 3.9 7.9 - - - +
173J GLU* 3.7 22.2 - - + -
210J ILE* 3.3 7.4 - - - +
211J TYR* 2.9 75.9 + + + +
213J TYR* 3.3 40.4 - + - -
219J PRO* 4.1 4.9 - - + -
255J ARG 4.7 0.7 - - - -
256J ILE* 1.3 80.1 - - - +
258J VAL* 1.3 69.5 + - - +
259J SER* 4.3 6.1 - - - -
275J PHE* 4.1 9.2 - - - -
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Residues in contact with VAL 258 (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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150J LYS* 3.4 2.9 - - - -
151J ILE* 2.8 45.7 + - + +
154J TRP* 3.8 16.5 - - + +
172J GLY 4.9 0.2 + - - -
186J SER* 3.9 22.7 - - - +
188J THR* 4.3 1.1 - - + -
208J GLN* 3.9 20.6 - - + -
209J TYR 3.4 3.1 - - - +
210J ILE* 4.2 4.9 - - + -
257J PHE* 1.3 81.2 - - - +
259J SER* 1.3 64.7 + - - +
260J VAL* 4.3 0.9 - - + -
275J PHE* 3.5 41.6 - - + -
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Residues in contact with SER 259 (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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146J ALA* 4.6 3.3 - - - +
147J LEU 2.5 28.6 + - - -
148J GLY 3.4 0.5 - - - -
149J ARG 3.2 21.7 + - - -
150J LYS* 3.4 4.3 + - - -
209J TYR* 2.8 29.9 + - - -
211J TYR* 3.8 24.0 - - - -
257J PHE* 4.3 3.9 - - - -
258J VAL* 1.3 75.1 - - - +
260J VAL* 1.3 70.3 + - - +
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Residues in contact with VAL 260 (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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95H ASP* 4.9 0.3 - - - +
148J GLY* 3.5 4.1 - - - -
149J ARG* 2.8 45.1 + - - +
151J ILE* 3.8 29.8 - - + -
188J THR* 4.2 18.8 - - + +
190J PHE* 4.3 5.2 - - + -
207J VAL 3.3 13.9 - - - +
208J GLN* 4.0 9.2 - - + -
209J TYR* 4.6 0.9 - - - -
258J VAL* 4.3 1.1 - - + -
259J SER* 1.3 87.2 + - - +
261J THR* 1.3 73.5 + - - +
263J GLU* 3.9 18.0 + - + -
266J ILE* 4.1 9.4 - - + -
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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