Contacts of the strand formed by residues 331 - 337 (chain B) in PDB entry 1YQZ
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 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B PRO* 3.7 33.4 - - + +
197B ASP* 5.5 5.3 + - + +
198B GLU* 3.7 33.0 - - + -
327B LYS* 3.4 7.0 - - - +
328B PHE 2.9 29.8 + - - +
330B ASP* 1.3 82.4 - - - +
332B THR* 1.3 63.5 + - - +
333B PHE* 3.5 21.0 - - + -
367B PRO* 5.5 4.8 - - + +
387B VAL* 4.2 2.2 - - + -
388B GLY* 3.8 26.0 - - - -
389B LYS* 3.5 39.5 + - + +
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Residues in contact with THR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TYR* 2.6 33.2 + - + +
325B ILE* 3.6 27.4 - - + -
326B VAL 3.6 3.8 - - - -
330B ASP 5.4 0.2 + - - -
331B TYR* 1.3 72.4 - - - +
333B PHE* 1.3 67.2 + - - +
334B ALA 4.1 0.4 - - - +
386B ALA 3.8 0.5 - - - +
387B VAL* 3.3 7.6 - - - +
388B GLY 3.0 35.4 + - - -
389B LYS 4.7 6.2 + - - -
390B GLU* 6.0 0.6 - - - -
392B ALA* 3.8 22.6 - - + +
393B ASP* 4.3 4.2 + - - +
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Residues in contact with PHE 333 (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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184B ASN* 3.8 17.7 - - - +
187B MET* 4.0 10.1 - - + -
191B MET 4.0 7.9 - - - -
192B ASN* 3.8 17.5 - - - -
194B PRO* 3.9 14.1 - - + -
195B ILE* 3.5 27.4 - - + -
324B ASN* 4.9 1.9 - - - +
325B ILE* 3.3 2.5 - - - -
326B VAL* 2.9 49.4 + - + +
328B PHE* 3.8 22.0 - + + -
331B TYR* 3.5 31.6 - - + -
332B THR* 1.3 74.0 - - - +
334B ALA* 1.3 60.1 + - - +
386B ALA 3.7 4.3 - - - -
387B VAL* 3.7 28.7 - - + -
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Residues in contact with ALA 334 (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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418A ALA* 5.1 0.9 - - + -
187B MET* 3.2 8.2 - - - +
324B ASN* 3.2 12.6 - - - +
325B ILE* 3.8 21.5 - - + -
332B THR* 4.1 3.8 - - + -
333B PHE* 1.3 74.1 - - - +
335B SER* 1.3 61.8 + - - +
385B ALA* 3.4 0.2 - - - -
386B ALA 2.9 35.8 + - - +
392B ALA 4.4 4.9 - - - +
393B ASP* 4.9 0.2 - - - -
396B ILE* 3.7 26.5 - - + +
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Residues in contact with SER 335 (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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186B LEU 3.0 18.4 + - - -
187B MET* 4.2 4.0 - - - +
323B ASN* 3.2 3.8 - - - +
324B ASN* 2.9 54.8 + - - -
334B ALA* 1.3 76.9 - - - +
336B VAL* 1.3 62.1 + - - +
383B ARG* 3.9 22.7 + - - -
384B ALA 3.2 13.5 - - - -
385B ALA* 4.1 5.4 - - - +
396B ILE* 3.9 4.9 - - - -
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Residues in contact with VAL 336 (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 LEU* 3.7 25.6 - - + +
322B GLY 3.8 5.6 - - - -
323B ASN* 3.9 18.6 - - + +
335B SER* 1.3 76.4 - - - +
337B GLY* 1.3 65.4 + - - +
383B ARG* 3.2 7.0 - - - +
384B ALA* 2.9 47.0 + - + +
396B ILE* 3.7 28.7 - - + +
399B LEU* 4.6 0.7 - - + -
400B SER* 4.1 12.3 - - - +
403B MET* 3.8 22.7 - - - -
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Residues in contact with GLY 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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283B TYR* 3.8 9.9 + - - -
285B HIS* 3.8 4.9 - - - -
321B LEU 2.7 27.2 + - - +
322B GLY* 4.5 5.2 - - - +
336B VAL* 1.3 76.5 - - - +
338B VAL* 1.3 68.5 + - - +
339B LYS* 3.7 1.9 + - - +
382B LEU 3.4 11.4 - - - -
383B ARG* 4.6 1.7 + - - -
403B MET* 3.7 11.7 - - - -
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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