Contacts of the strand formed by residues 359 - 365 (chain B) in PDB entry 3THY
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 LEU 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328B SER* 3.5 17.7 - - - +
329B THR* 5.3 2.2 - - + -
357B SER 3.8 1.4 + - - -
358B TYR* 1.3 71.4 - - - +
360B LEU* 1.3 61.8 + - - +
382B VAL 3.6 1.7 - - - +
383B GLY* 3.2 4.1 - - - -
384B VAL* 2.8 52.5 + - + +
386B PRO* 4.8 2.0 - - + -
416B GLU* 3.7 35.9 - - + +
417B LEU 4.3 0.4 - - - -
418B LEU* 4.1 18.4 - - + +
497B ILE* 3.7 26.0 - - + -
500B TYR* 3.7 28.5 - - + -
501B LEU* 4.0 9.4 - - + -
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Residues in contact with LEU 360 (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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358B TYR* 3.9 1.1 - - + -
359B LEU* 1.3 74.4 - - - +
361B CYS* 1.3 59.9 + - - +
362B ILE* 4.0 11.7 + - + +
381B ILE* 3.9 30.3 - - + -
382B VAL 3.5 18.6 - - - +
383B GLY* 4.0 1.1 - - - -
405B LEU* 5.3 1.1 - - + -
409B MET* 4.0 24.5 - - + +
412B LEU* 4.0 25.8 - - + -
414B PRO* 3.5 28.3 - - + -
416B GLU 3.0 7.3 + - - -
417B LEU* 3.3 25.2 - - + +
418B LEU* 3.0 20.6 + - - +
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Residues in contact with CYS 361 (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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359B LEU 4.1 0.8 + - - -
360B LEU* 1.3 72.8 - - - +
362B ILE* 1.3 61.3 + - - +
381B ILE* 3.3 6.2 - - - +
382B VAL 2.8 35.1 + - - +
418B LEU* 3.3 41.3 - - + -
454B PHE* 3.7 20.2 - - - -
493B SER* 3.5 25.8 - - - +
496B ALA* 3.9 0.2 - - - -
497B ILE* 3.5 25.1 - - + -
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Residues in contact with ILE 362 (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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360B LEU* 4.1 13.2 - - + +
361B CYS* 1.3 78.1 - - - +
363B SER* 1.3 65.4 + - - +
364B GLU* 5.7 1.1 - - - +
379B ILE* 4.3 15.5 - - + -
380B GLY 3.8 2.2 - - - -
381B ILE* 4.0 18.6 - - + -
405B LEU* 4.1 32.3 - - + -
409B MET* 4.6 6.3 - - - -
417B LEU* 4.1 23.3 - - + -
418B LEU 3.2 7.7 + - - -
419B LEU* 3.8 18.2 - - + -
420B PRO* 3.3 27.4 - - - +
423B LEU* 4.5 12.2 - - + +
427B THR* 5.2 2.0 - - + -
431B ILE* 4.9 5.4 - - + -
454B PHE* 4.1 1.4 - - - -
493B SER* 4.5 0.9 - - - -
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Residues in contact with SER 363 (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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362B ILE* 1.3 78.2 - - - +
364B GLU* 1.3 66.3 + - - +
379B ILE* 3.4 5.7 - - - +
380B GLY 2.7 38.3 + - - +
420B PRO* 5.0 2.7 - - - -
423B LEU* 5.4 0.2 - - - -
454B PHE* 4.1 15.3 + - - +
489B PRO* 3.0 27.2 + - - +
492B CYS* 3.5 12.0 - - - +
493B SER* 3.6 17.7 - - - -
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Residues in contact with GLU 364 (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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362B ILE* 5.7 1.8 - - - +
363B SER* 1.3 81.6 + - - +
365B ASN* 1.3 68.3 + - - +
377B ILE* 3.3 24.5 - - + +
378B PHE 3.2 13.5 - - - +
379B ILE* 3.5 18.0 - - + +
420B PRO* 6.1 0.2 - - - +
423B LEU* 3.5 21.9 - - + +
424B SER* 2.9 35.4 + - - -
427B THR* 3.4 17.2 + - - +
489B PRO* 4.4 3.8 - - - +
492B CYS* 5.9 1.4 - - - +
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Residues in contact with ASN 365 (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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364B GLU* 1.3 81.2 - - - +
366B LYS* 1.3 72.6 + - - +
377B ILE* 3.2 23.3 - - - +
378B PHE* 3.0 37.7 + - - +
488B LYS* 4.3 24.0 - - - +
489B PRO* 4.8 9.4 - - + -
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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