Contacts of the strand formed by residues 274 - 280 (chain D) 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 PHE 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D HIS* 3.2 39.7 - + - +
126D ILE 3.6 9.2 - - - +
127D THR* 4.2 4.7 - - - -
154D TRP* 3.7 8.1 - - - -
185D TYR* 3.9 11.2 - + - -
186D SER* 3.1 7.1 + - - -
187D GLN* 3.0 76.7 + - + +
243D TYR* 4.7 0.4 - + - -
270D HIS 4.7 2.7 - - - -
271D GLU 3.5 20.4 - - - -
273D SER* 1.3 79.6 - - - +
275D PHE* 1.3 63.3 + - - +
222F LEU 5.6 0.4 - - - -
223F MET* 3.8 20.6 - - + -
245F GLY 3.0 30.3 - - - -
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Residues in contact with PHE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D HIS* 3.3 2.1 - - - -
126D ILE* 2.7 53.2 + - + +
154D TRP* 3.7 33.2 - + + -
169D LEU* 5.3 0.2 - - + -
172D GLY 4.5 2.2 - - - -
174D LEU* 3.1 38.6 - - + -
184D ILE* 3.9 19.3 - - + -
185D TYR* 3.1 25.4 - - - -
186D SER* 3.9 1.6 - - - +
210D ILE* 5.0 2.2 - - + -
256D ILE* 3.5 29.8 - - + -
257D PHE* 4.2 8.3 - - - -
258D VAL* 3.5 28.0 - - + -
274D PHE* 1.3 79.5 - - - +
276D GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 276 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D ALA 3.1 17.0 - - - -
174D LEU* 4.4 9.0 - - - -
184D ILE* 3.7 4.0 - - - +
185D TYR* 2.9 47.7 + - - +
275D PHE* 1.3 78.3 - - - +
277D ALA* 1.3 64.4 + - - +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ALA* 3.3 1.9 - - - -
124D ALA* 2.8 32.2 + - - +
167D LEU* 4.9 7.5 - - + +
174D LEU* 4.6 12.2 - - + +
182D TYR* 4.5 12.8 - - + -
183D TYR 3.0 15.0 - - - +
184D ILE* 3.8 19.7 - - + -
185D TYR* 3.8 3.2 - - - -
256D ILE* 4.7 6.3 - - + -
276D GLY* 1.3 77.6 - - - +
278D PHE* 1.3 63.1 + - - +
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Residues in contact with PHE 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D VAL 3.5 6.3 - - - +
123D ALA* 3.5 20.4 - - + -
182D TYR* 3.5 7.5 - - - -
183D TYR* 2.9 67.7 + + + +
185D TYR* 4.3 3.1 - + - -
277D ALA* 1.3 77.5 - - - +
279D LEU* 1.3 81.9 + - - +
280D VAL* 3.8 16.8 - - + -
278E PHE* 4.0 7.9 - + - -
183F TYR* 4.0 19.7 - + + -
247F ILE* 3.4 19.1 - - + -
278F PHE* 3.9 33.9 - + - -
280F VAL* 3.8 17.5 - - + -
281F GLY 5.8 0.4 - - - +
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D VAL* 3.2 35.6 + - + +
178D GLU* 3.7 23.1 - - - +
179D LYS 4.4 2.5 - - - +
180D GLY* 4.0 14.4 - - - -
181D PHE 3.3 15.5 - - - +
182D TYR* 3.4 33.2 - - + +
278D PHE* 1.3 93.0 - - - +
280D VAL* 1.3 62.7 + - - +
281F GLY 5.7 8.8 - - - -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D PHE* 2.8 50.3 + - + +
183D TYR* 3.8 27.1 - - + -
247D ILE* 3.4 18.6 - - + -
278D PHE* 3.8 12.1 - - + +
279D LEU* 1.3 87.2 - - - +
281D GLY* 1.3 62.0 + - - +
121E ARG* 3.8 7.3 + - - +
123E ALA* 4.5 7.6 - - + -
278E PHE* 4.1 24.7 - - + -
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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