Contacts of the strand formed by residues 354 - 358 (chain B) in PDB entry 5XA0
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 SER 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B GLU* 2.9 31.7 + - - +
318B VAL 4.0 0.6 + - - -
319B ASP* 2.4 47.7 + - - +
353B TYR* 1.3 74.3 - - - +
355B LEU* 1.3 64.8 + - - +
356B VAL* 4.3 5.0 + - - +
417B LYS* 3.5 7.4 - - - +
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Residues in contact with LEU 355 (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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262B VAL* 4.0 10.7 - - - +
314B LEU* 4.2 24.5 - - + -
315B ALA 3.1 10.1 - - - +
316B ALA* 3.2 34.1 - - + +
353B TYR* 4.2 9.9 - - + +
354B SER* 1.3 82.8 + - - +
356B VAL* 1.3 66.3 + - - +
368B PHE* 4.7 2.9 - - + -
397B THR* 6.2 1.1 - - + -
399B VAL* 3.8 29.2 - - + -
417B LYS* 2.7 54.7 - - - +
419B GLY* 5.0 7.0 - - - -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLN 5.0 1.6 - - - +
261B HIS* 3.7 31.4 - - + +
262B VAL* 3.3 10.1 - - - +
315B ALA 3.0 21.7 + - - +
317B GLU* 5.4 8.9 - - + +
319B ASP* 5.7 4.7 - - - +
354B SER* 5.2 7.4 - - - +
355B LEU* 1.3 79.5 - - - +
357B SER* 1.3 73.1 + - - +
358B VAL* 3.7 4.8 - - + +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B CYS* 3.0 29.4 - - - -
260B GLN* 4.7 10.0 + - - -
261B HIS* 4.6 5.4 - - - +
262B VAL* 2.8 18.5 - - - +
312B HIS* 3.5 27.7 + - - +
313B TYR 3.9 3.6 - - - -
314B LEU 4.0 7.8 + - - -
356B VAL* 1.3 86.6 - - - +
358B VAL* 1.3 62.4 + - - +
359B PRO* 4.8 0.5 - - - +
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 3.2 5.9 - - - -
313B TYR* 2.6 60.1 + - + +
315B ALA* 3.4 29.6 - - + -
356B VAL* 3.7 4.0 - - + +
357B SER* 1.3 84.1 - - - +
359B PRO* 1.3 66.7 - - + +
360B GLU 3.4 18.4 - - - +
363B ASP* 4.4 18.4 - - + +
366B SER* 4.9 1.3 - - - +
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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