Contacts of the strand formed by residues 341 - 348 (chain B) in PDB entry 5WY8
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 GLY 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B PRO* 3.8 13.2 - - - +
242B PRO* 3.9 2.4 - - - +
337B GLU* 3.5 2.0 - - - +
338B ASN* 3.0 33.7 + - - +
339B GLY 3.4 0.4 - - - -
340B ASN* 1.3 81.0 - - - +
342B ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 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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241B PRO* 4.3 2.6 - - - +
242B PRO* 5.0 0.2 - - - -
282B TYR* 4.7 10.1 + - - -
335B TYR* 4.2 27.8 + - + -
336B VAL 3.1 15.0 - - - +
337B GLU* 3.6 25.5 + - + -
341B GLY* 1.3 74.8 - - - +
343B ARG* 1.3 77.3 + - - +
344B HIS* 4.3 17.9 + - + -
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Residues in contact with ARG 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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241B PRO* 4.0 22.2 - - + +
242B PRO 3.0 29.6 + - - +
243B LYS* 4.7 2.6 - - - +
244B LEU* 4.0 17.2 - - + +
249B GLU* 2.6 47.8 + - - +
334B CYS 3.8 0.7 - - - +
335B TYR* 3.4 3.8 - - - +
336B VAL* 2.9 43.9 + - + +
342B ARG* 1.3 81.2 - - - +
344B HIS* 1.3 64.4 + - - +
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Residues in contact with HIS 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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244B LEU* 3.9 2.2 - - - -
249B GLU* 3.8 15.0 + - - +
333B SER* 4.9 4.5 - - - -
334B CYS 3.1 7.9 - - - +
335B TYR* 3.4 45.1 - + + -
342B ARG* 4.3 12.6 - - + -
343B ARG* 1.3 75.7 - - - +
345B ALA* 1.3 62.0 + - - +
412B ZN 1.9 37.7 - - - -
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Residues in contact with ALA 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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244B LEU* 3.7 11.1 - - + +
247B PRO* 3.2 35.9 - - + +
248B MET 3.7 4.7 - - - +
249B GLU* 3.7 17.9 - - - +
251B LYS 5.3 0.4 - - - +
333B SER* 3.2 2.7 - - - -
334B CYS* 2.8 32.5 + - - +
344B HIS* 1.3 75.5 - - - +
346B SER* 1.3 60.9 + - - +
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Residues in contact with SER 346 (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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247B PRO* 4.5 2.2 - - - +
251B LYS 4.0 6.0 + - - +
252B LEU* 3.8 27.2 - - - +
253B THR* 3.9 8.7 + - - -
331B ASN* 4.8 10.1 + - - -
332B TYR 3.1 9.9 - - - -
333B SER* 3.2 24.5 - - - -
345B ALA* 1.3 74.8 - - - +
347B VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 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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246B TYR* 5.0 10.1 - - + +
247B PRO* 3.6 22.2 - - + -
252B LEU* 3.9 3.6 - - - -
253B THR* 3.2 31.0 - - - +
255B GLN* 5.6 6.1 - - + +
265B LEU* 3.6 37.9 - - + -
266B THR 6.0 0.2 - - - +
283B TRP* 4.5 6.5 - - + -
330B GLY 4.0 0.2 - - - +
331B ASN* 3.5 4.7 - - - +
332B TYR* 2.8 40.9 + - + +
346B SER* 1.3 74.7 - - - +
348B LEU* 1.3 66.3 + - - +
349B LEU 5.3 0.2 - - - +
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Residues in contact with LEU 348 (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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252B LEU* 3.7 18.8 - - + -
253B THR 3.1 4.9 + - - -
254B ILE* 3.8 24.4 - - + +
255B GLN* 2.6 37.1 + - - +
330B GLY* 3.4 29.4 - - - +
331B ASN* 3.3 22.4 - - - +
347B VAL* 1.3 78.3 - - - +
349B LEU* 1.3 66.9 + - - +
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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