Contacts of the strand formed by residues 334 - 341 (chain B) in PDB entry 2AR0
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 CYS 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ILE* 4.0 22.7 - - - -
330B LEU* 2.8 40.0 + - + +
331B MSE 3.3 2.6 - - - +
333B LYS* 1.3 81.3 - - - +
335B HIS* 1.3 61.3 + - - +
336B LEU 3.6 0.4 - - - +
359B PHE* 3.8 27.8 - - + -
360B THR 3.1 13.5 - - - +
361B LYS* 4.3 9.4 - - - -
362B GLY 3.9 1.1 - - - +
373B CYS* 3.1 14.0 - - - +
374B THR* 2.8 16.5 + - - -
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Residues in contact with HIS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B CYS* 1.3 71.7 - - - +
336B LEU* 1.3 61.5 + - - +
337B HIS* 3.2 31.9 + - + +
359B PHE* 3.8 2.7 - - - -
360B THR* 2.7 32.0 + - - +
362B GLY 3.2 18.8 + - - +
363B THR* 4.3 9.8 - - + -
364B VAL* 5.9 0.8 + - - +
373B CYS* 2.9 29.2 - - + +
374B THR* 3.6 5.8 - - - -
375B ASP* 3.0 23.6 + - - -
376B ASP 4.9 3.0 + - - -
412B HIS 4.8 2.0 + - - -
413B GLY 5.5 0.2 - - - -
414B LEU* 4.2 24.3 - - + +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.4 15.9 - - + -
331B MSE 4.6 9.2 - - + -
334B CYS 3.6 1.6 + - - +
335B HIS* 1.3 71.7 - - - +
337B HIS* 1.3 59.7 + - - +
338B THR 4.1 3.8 - - - +
339B ILE* 4.0 19.5 - - + -
357B LEU* 3.9 19.7 - - + -
358B PHE 3.3 18.4 - - - +
359B PHE* 3.4 26.6 - - + +
374B THR* 3.0 33.3 + - + +
376B ASP 3.8 3.3 - - - +
377B VAL* 3.6 13.6 - - + +
465B LEU* 3.6 34.5 - - + -
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG* 6.4 0.4 - - + -
335B HIS* 3.3 31.4 + - + +
336B LEU* 1.3 76.3 - - - +
338B THR* 1.3 91.9 + - - +
358B PHE* 3.1 24.5 + - + +
359B PHE* 3.6 12.1 - - - -
360B THR* 4.3 4.0 + - - -
376B ASP 3.9 8.1 - - - +
377B VAL* 4.3 2.5 - - - -
378B TRP* 2.8 32.3 + - + +
407B TYR* 3.3 20.7 + - - -
411B PRO 4.8 2.5 - - - -
412B HIS* 3.8 22.8 + - - -
413B GLY* 3.8 22.8 + - - +
417B ARG* 3.6 6.8 + - - +
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Residues in contact with THR 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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336B LEU* 3.8 2.0 - - - +
337B HIS* 1.3 92.6 - - - +
339B ILE* 1.3 72.1 + - - +
357B LEU* 3.7 0.2 - - - -
358B PHE* 2.9 43.8 + - + +
378B TRP 3.2 8.7 - - - +
403B PHE* 3.9 30.7 - - + -
407B TYR* 3.9 11.9 - - + -
417B ARG* 2.7 28.6 + - - -
449B TRP* 4.0 11.0 - - + -
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Residues in contact with ILE 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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317B LEU* 4.8 5.8 - - + -
336B LEU* 4.0 13.0 - - + -
338B THR* 1.3 83.3 - - - +
340B LEU* 1.3 66.8 + - - +
341B ARG* 4.6 11.9 - - + -
355B ASN* 4.6 9.6 - - + -
356B VAL 3.6 3.6 - - - +
357B LEU* 3.8 29.6 - - + -
377B VAL* 3.8 23.8 - - + -
378B TRP 2.7 11.6 + - - +
379B VAL* 3.2 16.0 - - + +
380B TYR* 2.8 26.2 + - - +
465B LEU* 4.2 27.4 - - + +
467B ILE* 5.4 0.9 - - + -
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Residues in contact with LEU 340 (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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157B LEU* 4.9 3.1 - - + -
160B THR* 5.9 1.6 - - + -
161B ILE* 6.4 0.7 - - + -
338B THR 4.2 0.4 - - - -
339B ILE* 1.3 72.0 - - - +
341B ARG* 1.3 60.8 + - - +
342B LEU* 3.5 23.5 + - + -
355B ASN* 3.0 7.0 - - - +
356B VAL* 2.8 51.8 + - + +
358B PHE* 4.0 12.3 - - + -
380B TYR* 3.8 33.2 - - + +
382B LEU* 4.2 14.6 - - + -
400B LEU* 4.2 11.0 - - + -
403B PHE* 3.7 38.8 - - + -
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Residues in contact with ARG 341 (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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314B ASP* 2.8 42.8 + - - -
317B LEU* 3.5 12.8 - - - +
339B ILE* 4.6 5.6 - - + +
340B LEU* 1.3 72.3 - - - +
342B LEU* 1.3 65.7 + - - +
355B ASN* 2.5 26.0 - - - +
379B VAL* 3.9 19.3 - - + -
380B TYR 3.1 15.9 + - - +
381B ASP* 4.5 11.0 - - - +
382B LEU* 3.1 25.6 + - - +
383B ARG* 3.5 19.1 + - + +
465B LEU 5.6 0.9 - - - -
466B ASP* 2.9 22.8 + - - -
467B ILE 3.1 36.1 + - - +
468B SER* 4.4 7.0 - - - +
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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