Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 1QDU
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 LYS 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A PHE* 3.5 9.9 - - + +
265A PHE* 2.8 35.4 - - + +
266A THR 4.6 7.6 - - - -
267A GLY* 5.0 1.3 - - - +
273A LEU* 3.2 37.0 + - + -
274A ALA* 4.3 1.9 - - - +
275A GLY 4.2 5.5 - - - +
276A LYS 2.5 34.4 + - - +
277A PRO* 1.3 73.0 - - - +
279A VAL* 1.3 62.2 + - - +
280A PHE* 3.9 9.3 - - + -
323B ASP 5.5 0.4 - - - -
325B ALA 3.9 21.6 + - - -
326B ASP* 2.8 11.6 + - - +
327B PHE* 3.5 29.5 - - + -
328B LEU 3.0 22.4 + - - +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A CYS* 4.6 8.1 - - - -
230A PHE 2.8 15.0 + - - +
231A ILE* 3.2 14.8 - - + -
232A CYS 2.8 30.8 + - - -
277A PRO* 4.7 3.4 - - + -
278A LYS* 1.3 77.1 - - - +
280A PHE* 1.3 66.3 + - - +
281A PHE* 3.5 40.6 - - + -
328B LEU* 3.4 24.7 - - + +
366B ILE* 6.3 0.2 - - + -
394B LEU* 5.7 0.2 - - + -
398B LEU* 4.1 25.8 - - + -
400B PHE* 5.0 3.8 - - + -
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 5.2 1.3 - - + -
230A PHE* 4.1 10.3 - + - -
232A CYS* 3.2 31.0 - - + -
234A ILE* 5.5 1.6 - - + -
261A LEU* 4.3 20.0 - - + -
262A THR* 4.3 23.1 - - - +
265A PHE* 3.8 30.1 - + - -
278A LYS* 3.9 21.1 - - + -
279A VAL* 1.3 82.9 - - - +
281A PHE* 1.3 67.2 + - - +
282A ILE* 3.9 18.8 - - + -
327B PHE* 4.2 18.2 - + - -
328B LEU 2.8 11.7 + - - +
329B LEU* 4.3 7.9 - - + -
330B GLY 2.8 26.0 + - - -
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 5.9 1.1 - - + -
193A PHE* 3.8 27.4 - + - -
231A ILE* 3.9 9.4 - - + -
232A CYS 3.0 9.1 + - - -
233A CYS* 3.7 26.8 - - + +
234A ILE 3.1 23.1 + - - +
235A LEU* 4.6 2.3 - - - +
279A VAL* 3.5 28.7 - - + -
280A PHE* 1.3 76.3 - - - +
282A ILE* 1.3 66.3 + - - +
283A GLN* 4.6 0.9 - - - +
328B LEU* 5.5 0.7 - - + -
330B GLY* 3.7 7.6 - - - +
349B TYR* 3.6 18.8 - - + -
350B ILE* 5.0 5.4 - - + -
353B LEU* 3.3 39.7 - - + -
357B LEU* 5.6 1.3 - - + -
366B ILE* 4.7 12.1 - - + -
370B LEU* 4.5 14.4 - - + -
400B PHE* 6.0 2.5 - + - -
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.7 22.4 - - + +
243A ILE* 3.6 29.2 - - + -
258A ILE* 3.6 24.7 - - + -
261A LEU* 6.0 0.9 - - + -
280A PHE* 3.9 22.6 - - + -
281A PHE* 1.3 76.1 - - - +
283A GLN* 1.3 61.1 + - - +
284A ALA* 4.0 6.5 + - + +
329B LEU* 3.8 16.4 - - + -
330B GLY 3.3 7.4 + - - +
331B MET* 3.6 30.5 - - + -
332B ALA* 3.2 24.8 + - - +
349B TYR* 4.0 1.1 - - - -
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 4.0 13.4 + - - +
185A ASP* 4.3 2.2 - - - +
234A ILE 2.7 16.1 + - - +
235A LEU* 3.4 4.9 - - + -
236A SER 3.1 24.1 + - - +
282A ILE* 1.3 73.7 - - - +
284A ALA* 1.3 63.2 + - - +
332B ALA* 3.3 18.2 - - - +
339B SER* 3.3 10.0 + - - -
340B TYR 4.1 4.8 + - - -
347B THR* 2.6 42.8 + - - +
349B TYR* 4.2 8.5 - - + +
350B ILE* 3.7 33.1 - - + +
385B GLN* 5.4 0.2 - - - +
4103T ASP* 3.9 8.4 + - - -
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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