Contacts of the strand formed by residues 353 - 357 (chain B) in PDB entry 3EE6
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 THR 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B HIS 2.9 20.3 + - - +
320B VAL* 3.3 23.9 - - + +
321B HIS 2.9 28.6 + - - +
351B GLY 4.7 0.9 - - - +
352B LEU* 1.3 71.4 - - - +
354B LEU* 1.3 61.5 + - - +
355B LEU* 3.7 17.0 - - - +
386B THR* 5.2 2.3 + - - -
485B LEU* 4.2 12.9 - - + +
489B ASN* 4.1 9.6 - - - +
500B LEU* 4.9 4.7 - - + -
501B GLY 2.8 30.5 - - - +
502B PHE* 5.0 1.3 - - - +
503B LEU* 5.1 3.7 - - - +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TRP* 4.5 17.5 - - + -
311B LEU* 4.6 5.4 - - + -
321B HIS* 3.6 24.7 - - + +
323B VAL* 5.3 0.7 - - + -
344B LEU* 3.9 27.8 - - + +
347B ALA* 3.5 24.7 - - + -
352B LEU* 3.6 27.5 + - + +
353B THR* 1.3 80.9 + - - +
355B LEU* 1.3 60.9 + - - +
356B PHE* 4.4 7.4 - - + -
384B TYR 5.1 3.8 - - - +
385B VAL* 4.0 15.4 - - + -
386B THR* 3.1 28.1 + - - -
502B PHE* 5.9 0.8 - - - +
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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
----------------------------------------------------------
320B VAL* 3.8 17.7 - - + -
321B HIS 2.9 20.1 + - - +
322B THR* 4.3 5.2 - - + -
323B VAL* 2.8 33.1 + - - +
353B THR* 3.7 23.8 - - - +
354B LEU* 1.3 76.3 - - - +
356B PHE* 1.3 62.1 + - - +
386B THR* 3.2 19.3 - - + +
388B VAL* 4.0 17.7 - - + -
478B THR* 3.7 15.2 - - + +
481B PHE* 4.1 12.6 - - + -
482B GLY* 4.1 11.9 - - - +
485B LEU* 3.9 21.5 - - + -
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Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE* 3.6 31.6 - + - -
307B TRP* 4.5 5.4 - + - -
323B VAL* 3.4 44.4 - - + -
325B TYR* 3.9 18.4 - - + -
344B LEU* 4.7 7.2 - - + -
354B LEU* 4.4 10.1 - - + -
355B LEU* 1.3 77.6 - - - +
357B ALA* 1.3 66.8 + - - +
379B PRO* 3.8 21.1 - - + -
380B ALA* 4.7 9.0 - - - -
385B VAL* 3.5 42.4 - - + -
386B THR 3.0 6.1 + - - -
387B THR* 3.3 4.2 - - - +
388B VAL* 2.8 25.3 + - - -
478B THR* 3.8 4.3 - - - -
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Residues in contact with ALA 357 (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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323B VAL 3.3 12.7 + - - +
324B SER* 4.4 9.4 - - - +
325B TYR 4.8 9.8 - - - +
356B PHE* 1.3 76.0 - - - +
358B SER* 1.3 63.9 + - - +
359B GLY* 3.2 2.6 + - - +
377B THR* 5.0 1.7 - - - +
380B ALA* 4.0 10.9 - - - +
387B THR* 4.4 0.2 - - - -
388B VAL 3.8 1.6 - - - -
474B THR* 3.5 26.9 - - - +
475B SER* 4.0 8.3 - - - +
478B THR* 3.2 19.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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