Contacts of the strand formed by residues 333 - 339 (chain B) in PDB entry 5T4S
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 ARG 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B TYR* 3.3 56.2 + - + +
193B ILE 3.3 11.7 - - - +
194B ASN* 3.4 25.0 - - - +
195B LEU* 4.1 3.7 - - - +
201B TRP* 3.5 6.9 - - - -
328B ASP* 2.9 52.4 + - + +
331B ASN* 3.6 32.6 - - + +
332B ASN* 1.3 77.3 - - - +
334B ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B HIS 3.7 1.0 - - - +
192B TYR* 3.3 4.2 - - - -
193B ILE* 2.8 43.0 + - - +
195B LEU* 3.7 21.1 - - + -
201B TRP* 3.6 25.8 - - + +
203B ILE* 4.0 10.3 - - + -
225B VAL* 3.6 29.2 - - + -
325B THR* 3.5 31.2 - - + -
326B GLU 3.3 3.8 - - - +
327B PHE* 3.9 7.9 - - + -
333B ARG* 1.3 78.8 - - - +
335B GLY* 1.3 62.7 + - - +
336B PHE* 3.7 20.9 - - + -
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PHE* 3.8 9.6 - - - -
191B HIS 3.4 5.2 - - - -
192B TYR* 3.4 28.8 - - - -
324B TYR 3.7 0.3 - - - +
325B THR* 3.3 6.4 - - - +
326B GLU* 2.8 40.0 + - - +
334B ILE* 1.3 72.1 - - - +
336B PHE* 1.3 62.3 + - - -
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Residues in contact with PHE 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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189B ASN 4.2 0.9 - - - +
190B PHE* 3.4 3.2 - - - -
191B HIS* 2.9 29.5 + - - +
193B ILE* 3.6 31.9 - - + -
203B ILE* 4.2 5.4 - - + -
225B VAL* 3.9 20.9 - - + -
272B LEU* 4.0 15.9 - - + -
277B TYR* 3.5 32.3 + + + +
315B LEU* 4.8 0.2 - - + -
319B PHE* 3.5 28.9 - + - -
323B PHE* 3.9 10.8 - - + -
324B TYR 3.4 1.8 - - - -
325B THR* 3.3 34.3 - - + -
334B ILE* 3.7 17.9 - - + -
335B GLY* 1.3 77.2 - - - -
337B ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 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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186B TYR* 4.0 15.9 - - + -
187B GLU 3.8 15.9 - - - +
189B ASN 3.9 13.0 - - - +
190B PHE* 3.7 18.8 - - + -
277B TYR* 5.8 0.4 - - - -
323B PHE* 3.4 8.5 - - - -
324B TYR* 2.8 32.9 + - - +
336B PHE* 1.3 76.1 - - - +
338B LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 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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164B ARG* 5.9 1.1 - - - +
186B TYR* 3.3 2.6 - - - -
187B GLU* 2.8 59.2 + - + +
322B LYS* 3.7 42.4 - - + +
323B PHE* 4.1 16.4 - - + -
337B ALA* 1.3 70.5 - - - +
339B ALA* 1.3 69.1 - - - +
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Residues in contact with ALA 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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161B TYR* 4.2 13.5 - - + -
164B ARG* 4.9 10.7 + - - +
185B HIS 3.4 9.9 - - - +
187B GLU* 5.0 2.3 - - - +
320B ILE 4.3 1.6 - - - +
321B ARG 3.4 18.8 - - - +
322B LYS 2.8 20.6 + - - +
323B PHE 4.3 0.2 - - - -
324B TYR* 3.6 19.1 - - + +
337B ALA 3.2 2.4 + - - -
338B LEU* 1.3 82.9 - - - +
340B ARG* 1.3 63.9 + - - +
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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