Contacts of the helix formed by residues 353 - 360 (chain B) in PDB entry 3R2A
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 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B ILE* 3.7 21.1 - - + -
314B SER* 3.4 27.1 - - - +
349B VAL* 2.7 20.7 + - + +
352B GLU* 1.3 80.1 - - - +
354B VAL* 1.3 60.4 + - - +
355B SER 3.6 0.2 - - - -
356B LYS* 4.2 0.5 - - - +
357B MET* 2.9 44.2 + - + +
421B ARG* 4.4 16.5 - - + +
424B ALA* 4.5 3.6 - - + +
425B LEU* 3.8 31.0 - - + +
428B ILE* 3.6 28.5 - - + -
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B SER* 3.6 28.5 - - - +
317B SER* 4.3 13.5 - - - +
318B ILE* 4.2 22.4 - - + +
323B GLY 5.7 0.4 - - - +
324B ILE* 6.2 0.9 - - + -
349B VAL* 2.7 30.1 + - + +
350B LEU* 3.7 21.1 - - + +
353B LEU* 1.3 69.8 - - - +
355B SER* 1.3 59.0 + - - +
357B MET* 2.7 7.7 + - - +
358B ARG* 2.5 49.4 + - - +
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Residues in contact with SER 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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350B LEU* 2.6 28.1 + - - +
351B THR* 3.9 10.6 - - - -
354B VAL* 1.3 78.5 - - - +
356B LYS* 1.3 55.1 + - - +
358B ARG* 3.2 15.1 + - - +
359B ASP* 2.4 49.7 + - - +
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Residues in contact with LYS 356 (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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378A PRO* 5.0 8.2 + - - -
379A ASP* 3.7 20.1 + - - +
386A PRO* 5.9 2.2 - - - +
390A GLU* 3.3 41.3 + - - +
351B THR 4.0 13.2 + - - +
352B GLU 3.9 5.8 - - - +
353B LEU 3.9 0.2 + - - -
354B VAL 3.1 0.4 - - - -
355B SER* 1.3 78.8 - - - +
357B MET* 1.3 67.5 + - - +
359B ASP* 3.4 18.1 + - + +
360B MET* 3.2 20.7 + - - +
417B LYS* 5.8 6.5 - - - -
421B ARG* 3.7 40.4 - - - +
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Residues in contact with MET 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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311B ALA* 4.0 15.0 - - + +
314B SER* 3.6 27.1 - - - -
315B HIS* 3.7 14.1 - - - -
318B ILE* 4.6 8.5 - - + +
353B LEU* 2.9 30.7 + - + +
354B VAL* 2.7 9.3 + - - +
356B LYS* 1.3 79.4 - - - +
358B ARG* 1.3 59.4 + - - +
360B MET* 3.4 18.2 - - - +
362B MET* 3.4 43.5 + - + +
367B LEU* 3.7 28.9 - - + -
370B LEU* 5.1 4.5 - - + -
421B ARG* 5.3 8.2 - - + +
425B LEU* 6.0 2.0 - - + -
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Residues in contact with ARG 358 (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 SER 3.5 1.8 + - - -
318B ILE* 2.6 65.2 + - + +
320B VAL 2.7 23.6 + - - -
321B LYS* 4.9 2.5 - - - +
322B ASP* 4.7 11.5 + - - +
354B VAL* 2.5 31.3 + - - +
355B SER* 3.6 14.9 + - - +
357B MET* 1.3 70.6 - - - +
359B ASP* 1.3 59.4 + - - +
360B MET 3.0 4.9 - - - -
361B GLN* 2.5 36.7 + - - +
362B MET 5.1 0.4 - - - +
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Residues in contact with ASP 359 (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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355B SER* 2.4 42.2 + - - +
356B LYS* 4.0 15.2 + - + +
357B MET 3.4 0.4 - - - -
358B ARG* 1.3 80.3 + - - +
360B MET* 1.3 57.8 + - + +
361B GLN* 3.5 10.3 + - - +
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Residues in contact with MET 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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356B LYS* 3.2 18.6 - - - +
357B MET* 3.4 11.0 - - - +
359B ASP* 1.3 78.8 - - - +
361B GLN* 1.3 71.2 + - - +
362B MET* 3.2 14.4 - - + +
411B GLN* 5.9 4.3 + - - +
414B ARG* 2.8 48.2 + - + +
417B LYS* 4.3 33.9 - - + +
418B LEU* 3.6 40.6 - - + +
421B ARG* 4.9 12.8 - - - -
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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