Contacts of the helix formed by residues 317 - 324 (chain B) in PDB entry 2Y48
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 SER 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B LEU* 1.3 75.1 - - - +
318B GLN* 1.3 66.6 + - - +
319B GLU* 3.2 23.8 + - - +
320B ASP* 2.8 41.2 + - - +
321B VAL* 3.1 13.0 + - - +
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Residues in contact with GLN 318 (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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396A LEU* 3.2 56.1 + - + +
316B LEU 3.9 1.6 + - - -
317B SER* 1.3 72.7 - - - +
319B GLU* 1.3 62.0 + - - +
321B VAL* 3.3 18.5 + - - +
322B GLU* 3.1 42.2 + - - +
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Residues in contact with GLU 319 (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* 3.2 13.6 + - - +
318B GLN* 1.3 79.6 - - - +
320B ASP* 1.3 73.0 + - - +
322B GLU* 3.5 15.1 + - - +
323B ALA* 3.3 21.7 + - + +
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Residues in contact with ASP 320 (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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418A LEU* 3.8 18.1 - - + +
421A LYS* 2.6 33.8 + - + +
315B PHE 6.1 0.2 - - - -
317B SER* 2.8 32.0 + - - +
319B GLU* 1.3 84.8 - - - +
321B VAL* 1.3 64.0 + - - +
323B ALA* 3.5 6.6 + - - +
324B VAL* 3.3 29.1 + - - +
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Residues in contact with VAL 321 (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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392A LEU* 4.5 7.2 - - + -
396A LEU* 3.8 25.4 - - + -
398A PHE* 4.1 31.2 - - + -
414A VAL* 4.0 24.6 - - + +
418A LEU* 3.9 18.4 - - + -
316B LEU* 4.7 1.8 - - + -
317B SER 3.1 18.4 + - - +
318B GLN* 3.3 9.4 + - - +
320B ASP* 1.3 77.6 - - - +
322B GLU* 1.3 60.7 + - + +
323B ALA 3.2 1.0 + - - -
324B VAL* 3.2 10.6 + - - +
325B SER* 2.9 20.1 + - - -
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Residues in contact with GLU 322 (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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318B GLN* 3.1 48.1 - - - +
319B GLU* 3.5 12.4 - - - +
320B ASP 3.4 0.2 - - - -
321B VAL* 1.3 75.8 - - + +
323B ALA* 1.3 57.5 + - - +
325B SER* 3.2 16.1 + - - -
326B ALA* 3.2 22.0 + - - +
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Residues in contact with ALA 323 (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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421A LYS* 6.0 2.2 - - - +
319B GLU* 3.3 15.7 + - + +
320B ASP* 3.8 10.3 - - - +
321B VAL 3.1 1.0 - - - -
322B GLU* 1.3 79.8 - - - +
324B VAL* 1.3 62.6 + - + +
325B SER 3.2 2.8 + - - -
326B ALA* 4.2 4.6 + - - +
330B ALA* 3.6 21.7 - - - +
334B VAL* 5.0 11.0 - - + +
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Residues in contact with VAL 324 (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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414A VAL* 4.6 12.0 - - + +
417A GLN* 3.7 35.5 - - + +
418A LEU* 3.7 17.7 - - + -
421A LYS* 5.2 9.4 - - + -
320B ASP 3.3 16.8 + - - +
321B VAL 3.2 5.7 + - - +
323B ALA* 1.3 81.7 - - + +
325B SER* 1.3 57.9 + - - +
326B ALA 3.9 0.2 - - - -
327B ASN 4.7 2.6 - - - +
330B ALA* 4.1 9.4 - - - +
331B ALA* 3.7 25.4 + - - +
334B VAL* 4.4 21.5 - - + -
335B LEU* 6.5 0.2 - - + -
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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