Contacts of the helix formed by residues 329 - 337 (chain B) in PDB entry 5M8N
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 GLU 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ALA* 3.9 4.3 - - - +
254B GLY* 3.1 24.4 - - - +
326B ARG* 3.6 22.7 - - - +
327B LEU 4.4 2.4 - - - +
328B PRO* 1.3 75.7 - - - +
330B PRO* 1.3 71.9 - - + +
331B GLN* 3.1 31.1 + - - +
332B ASP* 2.9 33.9 + - - +
333B VAL 4.0 1.6 + - - -
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Residues in contact with PRO 330 (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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252B ALA* 3.2 25.1 - - + +
253B THR* 3.9 18.6 - - + +
329B GLU* 1.3 87.9 - - + +
331B GLN* 1.3 68.5 + - - +
332B ASP 3.3 0.7 + - - -
333B VAL* 3.4 12.7 + - + +
334B ALA 3.5 6.2 + - - -
469B PRO* 3.6 21.4 - - + +
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Residues in contact with GLN 331 (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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329B GLU* 3.1 25.8 + - - +
330B PRO* 1.3 84.8 - - - +
332B ASP* 1.3 58.5 + - - +
333B VAL 3.4 0.2 - - - -
334B ALA* 3.5 10.6 - - + +
335B GLN* 2.7 56.7 + - + +
469B PRO* 5.3 1.1 - - - -
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Residues in contact with ASP 332 (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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328B PRO* 3.8 7.1 - - - +
329B GLU* 2.9 37.4 + - - +
331B GLN* 1.3 86.2 - - - +
333B VAL* 1.3 64.3 + - - +
335B GLN* 3.9 5.9 + - - +
336B CYS* 3.0 27.5 + - - +
365B PRO* 3.7 34.7 - - + +
375B SER* 5.5 0.7 - - - -
376B LEU* 3.9 19.3 + - + +
379B LEU* 5.3 2.8 - - - +
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Residues in contact with VAL 333 (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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252B ALA* 3.3 34.1 - - + -
330B PRO* 3.4 8.9 + - + +
331B GLN 3.4 0.4 - - - -
332B ASP* 1.3 75.5 - - - +
334B ALA* 1.3 60.7 + - - +
336B CYS* 3.6 7.1 - - - -
337B LEU* 3.2 31.2 + - + +
376B LEU* 4.3 11.0 - - + -
406B PHE* 4.3 9.9 - - + -
410B VAL* 4.0 15.3 - - + -
468B TRP* 3.4 39.0 - - + -
469B PRO* 5.0 5.2 - - + -
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Residues in contact with ALA 334 (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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330B PRO 3.5 1.6 + - - -
331B GLN* 3.1 15.1 + - + +
333B VAL* 1.3 78.9 - - - +
335B GLN* 1.3 65.1 + - + +
337B LEU* 3.6 11.7 + - - +
338B GLU* 2.9 25.1 + - - +
417B ARG* 4.7 3.1 + - - +
469B PRO* 3.8 32.1 - - + +
470B SER 5.4 6.1 - - - +
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Residues in contact with GLN 335 (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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331B GLN* 2.7 49.5 + - + +
332B ASP* 3.9 7.8 + - - +
334B ALA* 1.3 74.8 - - + +
336B CYS* 1.3 62.2 + - - +
338B GLU* 3.1 25.3 + - - +
339B VAL* 3.9 5.4 + - - +
364B ASP* 5.0 0.2 - - - +
365B PRO* 3.3 23.1 - - + +
366B THR* 3.1 35.3 + - + +
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Residues in contact with CYS 336 (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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332B ASP 3.0 16.2 + - - +
333B VAL* 3.6 14.8 - - - -
335B GLN* 1.3 76.3 - - - +
337B LEU* 1.3 61.5 + - - +
338B GLU 3.1 4.5 + - - -
339B VAL* 3.2 17.5 + - - +
355B PHE* 3.3 26.0 - - + -
358B THR* 3.7 26.0 - - + -
359B VAL* 4.2 3.8 - - - +
365B PRO 3.2 7.4 + - - +
376B LEU* 3.9 14.4 - - + -
410B VAL* 3.9 27.4 - - - -
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Residues in contact with LEU 337 (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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333B VAL* 3.2 27.1 + - + +
334B ALA* 4.1 3.8 - - - +
335B GLN 3.2 1.6 - - - -
336B CYS* 1.3 81.9 - - - +
338B GLU* 1.3 58.1 + - - +
355B PHE* 4.4 4.5 - - + -
410B VAL* 3.5 16.2 - - + +
413B GLU* 3.6 20.9 - - + -
414B TRP* 3.5 39.9 - - + +
417B ARG* 2.8 38.6 + - - +
418B TYR* 3.3 22.1 + - - -
468B TRP* 4.1 21.3 - - + -
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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