Contacts of the strand formed by residues 335 - 347 (chain B) in PDB entry 1OO9
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 335 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A PHE 3.7 18.8 + - - -
155A TYR* 4.4 6.4 - + - -
156A PRO* 5.1 4.5 - - - +
329B VAL* 4.0 9.7 - - - +
330B ASN* 4.2 4.2 + - - +
332B THR* 3.2 30.3 + - + +
334B LEU* 1.3 100.2 - - + +
336B GLN* 1.3 63.0 + - - +
362B TYR* 4.3 20.3 - + + -
363B THR 3.3 23.6 - - - +
364B PRO* 3.7 19.3 - - + -
365B ALA* 4.3 1.3 - - - -
390B GLN* 3.4 24.6 + - - -
395B HIS* 3.6 33.9 - + - -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 5.8 3.8 - - - -
327B PRO* 3.9 37.9 - - + +
328B GLU* 3.8 4.8 + - - +
329B VAL* 4.0 24.1 + - + +
335B TYR* 1.3 74.4 - - - +
337B ARG* 1.3 62.8 + - - +
338B TYR* 5.2 1.6 + - - -
362B TYR* 3.7 1.3 - - - -
363B THR* 2.8 42.6 + - + +
364B PRO 4.0 5.5 + - - +
365B ALA* 3.4 30.9 + - + +
367B GLU* 5.8 2.2 + - - -
372B TYR 5.9 1.4 + - - -
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Residues in contact with ARG 337 (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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326B THR 4.2 1.7 - - - +
327B PRO* 3.6 3.7 - - - +
328B GLU* 3.1 43.0 + - + +
330B ASN* 2.3 57.0 + - + +
336B GLN* 1.3 76.7 - - - +
338B TYR* 1.3 64.6 + - - +
339B GLU 4.3 0.7 + - - -
360B PHE* 3.5 48.8 - - + -
361B VAL 3.4 9.2 - - - +
362B TYR* 2.9 41.3 + - + -
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Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 3.7 25.8 - + + -
325B GLY 3.7 18.6 - - - +
326B THR 5.1 0.2 - - - -
327B PRO* 3.7 34.3 - - + +
336B GLN* 5.1 1.9 + - + -
337B ARG* 1.3 77.2 - - - +
339B GLU* 1.3 62.9 + - - +
340B ILE* 3.5 0.7 + - + -
360B PHE* 3.3 6.0 - - - -
361B VAL* 3.0 52.8 + - + +
363B THR* 3.8 19.7 - - + -
372B TYR* 2.6 36.9 + + - -
373B PHE* 3.5 4.9 - - - -
374B HIS* 3.2 36.7 + - + -
396B ILE* 5.6 0.4 - - + -
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 3.9 0.7 - - - -
324B VAL* 2.9 44.4 + - + +
325B GLY* 3.3 19.8 + - - +
326B THR 5.4 0.2 + - - -
337B ARG 4.2 0.8 + - - -
338B TYR* 1.3 72.3 - - - +
340B ILE* 1.3 63.2 + - - +
359B ARG* 3.3 41.7 + - - +
360B PHE* 3.6 27.8 - - + -
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE* 5.2 2.5 - - + -
321B ALA* 4.3 11.4 - - + -
322B LYS 3.3 13.2 - - - +
323B PHE* 3.9 19.3 - - + -
324B VAL* 4.3 3.4 - - - +
338B TYR 4.0 0.2 - - - +
339B GLU* 1.3 79.4 - - - +
341B LYS* 1.3 60.4 + - - +
342B MET* 3.8 2.8 + - + +
358B ILE* 3.8 26.8 - - + +
359B ARG* 2.9 44.5 + - - +
360B PHE* 3.7 3.1 - - - +
361B VAL* 3.8 40.6 - - + +
385B ILE* 4.6 14.1 - - + -
394B LEU* 4.5 7.2 - - + -
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Residues in contact with LYS 341 (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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321B ALA* 3.2 5.5 - - - +
322B LYS* 2.9 56.2 + - + +
324B VAL* 3.7 21.0 - - + +
340B ILE* 1.3 71.1 - - - +
342B MET* 1.3 69.2 + - - +
343B THR* 3.5 8.8 + - + +
355B ALA* 2.7 35.4 + - - +
356B ALA* 4.7 4.0 - - - +
359B ARG* 4.8 17.6 - - - +
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Residues in contact with MET 342 (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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319B ILE* 3.2 38.4 - - + -
320B ARG 3.6 10.3 - - - +
321B ALA* 3.6 6.2 - - + +
340B ILE* 3.8 4.9 + - + -
341B LYS* 1.3 78.3 + - - +
343B THR* 1.4 69.8 + - - +
344B LYS 4.3 2.0 - - - +
345B MET* 3.8 19.7 - - + +
353B GLY* 3.3 30.5 - - - +
354B ASP* 3.2 30.1 - - - +
355B ALA* 3.2 30.7 + - - +
356B ALA* 5.8 0.4 - - - +
358B ILE* 4.0 26.8 + - + +
359B ARG* 6.2 0.2 - - - +
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Residues in contact with THR 343 (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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320B ARG* 2.7 25.2 + - - +
321B ALA* 4.7 0.9 - - - -
322B LYS* 3.8 27.8 - - + +
341B LYS* 3.9 13.5 - - + +
342B MET* 1.4 79.2 - - - +
344B LYS* 1.3 78.3 + - - +
345B MET 4.2 0.3 + - - -
354B ASP 4.0 13.9 - - - +
355B ALA* 4.9 2.0 - - - +
382B GLU* 2.8 28.7 + - - +
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Residues in contact with LYS 344 (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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319B ILE* 3.4 0.5 - - - -
320B ARG* 2.6 66.4 + - + +
342B MET* 4.3 2.7 - - - +
343B THR* 1.3 88.9 + - - +
345B MET* 1.3 61.3 + - - +
346B TYR* 4.0 26.4 + - + +
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Residues in contact with MET 345 (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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317B LEU* 3.8 13.2 - - + -
318B VAL 3.8 3.1 - - - -
319B ILE* 3.4 33.2 - - + -
342B MET* 3.8 14.3 - - + +
343B THR 4.2 0.8 + - - -
344B LYS* 1.3 76.7 - - - +
346B TYR* 1.3 60.9 + - - +
347B LYS 3.4 15.3 - - - +
348B GLY 3.2 28.5 - - - +
349B PHE* 3.2 46.6 - - + -
351B ALA 4.8 0.7 - - - -
352B LEU 3.2 29.2 - - - +
353B GLY* 4.8 0.7 - - - -
354B ASP* 6.3 0.2 - - - -
358B ILE* 4.6 4.5 - - + -
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Residues in contact with TYR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 4.3 7.4 - - + -
318B VAL* 2.6 24.6 + - + +
320B ARG* 3.0 42.9 + - + -
344B LYS* 4.0 20.0 + - + +
345B MET* 1.3 74.9 - - - +
347B LYS* 1.3 59.7 + - - +
349B PHE* 4.3 9.8 - - - -
384B LEU* 3.9 20.0 - - + -
405B TRP* 3.2 34.3 - + - -
416B PHE* 4.0 18.7 - - + +
417B THR* 3.8 36.8 + - + -
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Residues in contact with LYS 347 (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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312B PHE* 3.0 41.5 + - + +
313B CYS* 2.9 30.9 + - - +
315B SER 3.2 14.3 + - - +
316B ASP* 3.8 10.3 - - - +
317B LEU* 3.3 3.5 - - - -
318B VAL* 3.1 39.1 + - + -
345B MET* 3.4 18.3 + - - +
346B TYR* 1.3 81.0 - - - +
348B GLY* 1.3 65.4 + - - +
349B PHE* 3.7 5.8 - - - +
424B CYS* 5.3 2.0 - - - +
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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