Contacts of the strand formed by residues 276 - 283 (chain B) in PDB entry 1W1J
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 TYR 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TRP* 3.7 20.9 - + + -
275B GLY* 1.3 74.8 - - - +
277B GLN* 1.3 73.8 + - - +
278B SER* 3.6 17.2 - - - -
356B ALA* 3.9 12.8 - - + -
357B LEU 3.7 9.2 - - - -
358B TYR* 3.8 16.6 - + - -
364B ARG* 3.9 10.9 + - - +
399B ASP* 2.8 32.8 + - - -
402B MET* 3.2 38.4 + - - +
403B GLN* 3.3 33.9 - - + -
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TYR* 1.3 87.5 - - - +
278B SER* 1.3 80.3 + - - +
279B TYR* 4.1 0.4 - - + -
356B ALA* 3.4 1.2 - - - -
357B LEU* 2.8 43.6 + - + +
364B ARG* 4.3 21.8 + - - +
385B PHE* 3.7 40.2 - - + +
386B PRO* 3.5 24.0 - - - +
399B ASP* 5.1 1.0 + - - -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TYR* 3.6 17.2 - - - -
277B GLN* 1.3 95.0 + - - +
279B TYR* 1.3 67.6 + - - +
355B GLY 3.6 11.2 - - - -
356B ALA* 3.9 2.7 - - - -
385B PHE* 4.0 1.4 - - - -
386B PRO* 3.7 12.5 - - - +
395B LEU* 4.3 3.8 - - - +
399B ASP* 2.2 45.6 + - - +
402B MET* 4.0 7.9 - - - -
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLN 4.1 4.3 - - - -
278B SER* 1.3 83.0 + - - +
280B LEU* 1.3 62.9 + - - +
281B ILE* 3.8 26.7 - - + -
305B LEU* 3.3 30.0 - - - +
353B PHE* 4.0 5.1 - + - -
354B TYR* 3.4 6.1 - - - +
355B GLY* 3.1 48.7 + - - +
356B ALA* 3.3 26.2 + - - -
357B LEU* 4.1 13.0 - - + -
368B TRP* 3.5 41.3 - + + -
371B ILE* 4.0 8.8 - - + +
384B TYR 3.3 13.7 - - - +
385B PHE* 4.2 6.5 - + + +
395B LEU* 3.6 13.9 - - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 1.3 76.2 - - - +
281B ILE* 1.3 86.0 + - - +
282B THR* 3.8 9.4 - - + -
348B LEU* 3.8 23.6 - - + -
352B ASN* 3.9 10.5 - - + -
353B PHE 3.5 7.4 - - - +
354B TYR* 3.9 28.0 - - + +
382B LYS 3.5 0.9 - - - +
383B PHE* 3.5 5.4 - - - +
384B TYR* 2.9 53.3 + - + +
389B THR* 4.7 5.8 - - + -
393B SER* 6.5 0.4 - - - -
395B LEU* 3.6 27.1 - - + -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B TYR* 3.8 22.0 - - + -
280B LEU* 1.3 83.4 - - - +
282B THR* 1.3 62.2 + - - +
283B LEU* 4.0 3.4 + - + +
352B ASN* 3.7 0.7 - - - -
353B PHE* 2.8 66.3 + - + +
368B TRP* 4.6 0.4 - - + -
371B ILE* 4.0 8.3 - - + -
375B PHE* 3.8 27.8 - - + -
381B VAL* 3.7 26.7 - - + -
382B LYS 3.5 2.9 - - - +
383B PHE* 3.8 29.8 - - + -
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B LEU* 3.8 11.9 - - + -
281B ILE* 1.3 75.0 - - - +
283B LEU* 1.3 62.3 - - - +
284B PRO* 3.7 4.9 - - - +
347B ASN 4.0 10.3 + - - +
348B LEU* 4.0 2.2 - - - -
349B GLY* 3.8 11.9 - - - +
352B ASN* 3.2 25.1 - - - +
380B GLY 5.4 0.3 + - - -
381B VAL* 3.4 22.0 - - - +
382B LYS* 3.1 33.3 + - - +
384B TYR* 3.6 21.7 + - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 4.2 4.0 - - + +
282B THR* 1.3 78.6 - - - +
284B PRO* 1.3 71.5 - - + +
285B LYS 3.6 3.1 + - - +
288B ASP* 4.1 14.4 - - + +
292B ALA* 3.9 19.5 - - + -
311B ILE* 4.6 4.7 - - + -
349B GLY* 3.9 2.7 - - - -
350B ARG 2.9 21.1 + - - -
351B TRP* 3.1 40.2 + - + +
352B ASN 4.5 0.2 - - - +
353B PHE* 4.3 20.2 - - + -
375B PHE* 3.9 21.3 - - + -
378B ILE* 3.8 30.1 - - + -
381B VAL* 4.5 6.3 - - + -
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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
------------------------------------------------------------
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