Contacts of the strand formed by residues 336 - 343 (chain B) in PDB entry 1RY7
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 GLU 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289B LYS* 3.3 7.9 - - - +
290B HIS* 2.9 65.8 + - + +
297B LYS* 3.8 10.4 + - - -
335B GLY* 1.3 73.4 - - - -
337B TYR* 1.3 62.8 + - - +
351B SER* 3.1 23.6 - - - -
352B ALA 3.3 17.9 - - - +
353B TRP* 3.2 46.4 - - + +
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Residues in contact with TYR 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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260B PRO* 4.4 2.1 - - - +
273B PHE* 3.6 26.7 - + + -
287B TRP* 4.6 8.1 - - + -
288B LEU 3.5 5.8 - - - +
289B LYS* 4.1 14.8 - - + +
309B LEU* 4.1 16.2 - - + -
324B LEU* 3.4 21.1 - - + -
326B LEU* 3.1 46.7 - - + +
333B ASP* 2.8 40.4 + - - +
335B GLY 3.8 12.3 - - - -
336B GLU* 1.3 80.6 - - - +
338B THR* 1.3 61.9 + - - +
351B SER* 3.1 2.5 - - - -
352B ALA* 2.7 42.4 + - + +
354B LEU* 4.6 4.0 - - + -
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Residues in contact with THR 338 (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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287B TRP* 3.3 11.7 - - - -
288B LEU* 2.8 49.2 + - + +
290B HIS* 2.6 29.0 + - + +
337B TYR* 1.3 72.7 - - - +
339B CYS* 1.3 67.3 + - - +
340B LEU* 3.9 6.7 - - + +
349B HIS* 4.0 17.5 - - + +
350B HIS 2.9 18.2 - - - +
351B SER* 2.5 17.6 + - - +
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Residues in contact with CYS 339 (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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255B LEU* 4.1 13.2 - - + -
260B PRO* 4.1 8.2 - - + +
275B CYS* 2.7 45.3 - - - -
277B VAL* 5.1 1.3 - - - -
285B ILE* 4.0 20.9 - - - -
286B GLN 3.5 4.9 - - - -
287B TRP* 4.0 15.4 - - + -
338B THR* 1.3 71.3 - - - +
340B LEU* 1.3 59.3 + - - +
341B ALA* 3.7 3.1 + - - -
349B HIS* 3.3 6.1 - - - +
350B HIS 3.0 28.1 + - - +
351B SER* 4.7 0.2 - - - +
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Residues in contact with LEU 340 (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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284B HIS 3.6 2.8 - - - +
285B ILE* 4.5 0.2 - - - -
286B GLN* 2.9 51.5 + - + +
288B LEU* 3.7 31.9 - - + -
338B THR* 3.9 3.3 - - + -
339B CYS* 1.3 70.4 - - - +
341B ALA* 1.3 60.2 + - - +
342B GLY 3.4 6.2 + - - -
347B PHE* 3.2 42.9 - - + -
348B SER 3.6 12.8 - - - +
349B HIS* 3.9 12.8 - - + +
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Residues in contact with ALA 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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253B PRO* 3.3 25.5 - - + +
255B LEU* 3.6 22.4 - - + -
277B VAL* 4.3 1.1 - - + -
285B ILE* 3.5 29.4 - - + -
339B CYS* 3.7 5.0 + - - -
340B LEU* 1.3 68.8 - - - +
342B GLY* 1.3 63.6 + - - +
347B PHE* 4.4 0.7 - - - -
348B SER 3.0 32.2 + - - +
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Residues in contact with GLY 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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66A VAL* 4.0 4.7 - - - -
253B PRO* 3.4 1.2 - - - +
283B PRO* 3.2 5.7 - - - +
284B HIS* 3.1 38.3 + - - -
340B LEU 3.4 2.4 + - - -
341B ALA* 1.3 73.7 - - - +
343B ASN* 1.3 66.2 + - - +
347B PHE* 3.4 30.7 - - - -
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Residues in contact with ASN 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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66A VAL* 3.3 20.3 - - - +
251B HIS 3.4 18.2 + - - -
252B ARG 4.1 0.4 - - - -
253B PRO* 3.0 21.7 - - + +
279B SER* 3.2 21.2 + - - +
281B ALA* 3.2 32.8 + - - +
282B GLN 4.2 6.7 - - - +
342B GLY* 1.3 74.9 - - - +
344B SER* 1.3 86.5 + - - +
345B ILE* 2.5 26.3 + - - +
346B GLY* 3.2 12.3 + - - +
347B PHE* 4.9 0.2 - - - -
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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