Contacts of the helix formed by residues 319 - 326 (chain B) in PDB entry 2XWU
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 HIS 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B ILE* 3.3 31.2 + - + -
269B GLN 5.2 2.7 - - - -
272B ALA* 4.2 2.0 - - + -
273B GLN* 3.9 37.8 - - + +
279B LEU* 3.3 40.3 - - + +
315B LEU* 3.2 19.5 + - + +
316B GLY 4.0 1.8 - - - -
318B ASN* 1.3 99.4 + - + +
320B SER* 1.3 64.2 + - - +
321B ARG* 3.4 3.1 - - - -
322B ALA* 4.0 12.9 - - + +
323B LEU* 2.9 34.2 + - + +
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Residues in contact with SER 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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316B GLY 3.1 19.9 + - - -
317B GLU 4.1 0.4 + - - -
318B ASN 3.7 1.8 - - - -
319B HIS* 1.3 76.5 - - - +
321B ARG* 1.3 64.7 + - - +
323B LEU* 3.8 1.7 - - - +
324B LEU* 2.9 30.8 + - - +
333B PHE* 4.1 17.2 - - - -
363B PHE* 4.6 5.4 - - - -
366B THR* 3.7 17.7 - - - -
367B LEU* 4.9 4.0 - - - -
370B ASP* 3.1 16.6 - - - -
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Residues in contact with ARG 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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319B HIS* 5.5 0.7 - - - -
320B SER* 1.3 75.4 - - - +
322B ALA* 1.3 62.3 + - + +
324B LEU* 3.1 7.5 + - - +
325B ASP* 2.7 42.0 + - - +
369B ASP* 5.3 4.0 + - - -
370B ASP* 3.0 44.6 + - + +
373B SER* 3.3 34.7 + - - -
374B PHE* 4.8 8.5 - - + -
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Residues in contact with ALA 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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273B GLN* 5.9 6.3 - - + +
276B VAL* 5.3 14.3 - - + +
279B LEU* 5.4 3.6 - - + -
319B HIS* 3.4 21.4 + - + +
320B SER 3.3 0.4 - - - -
321B ARG* 1.3 84.4 - - + +
323B LEU* 1.3 64.1 + - + +
325B ASP* 3.3 23.2 + - - +
326B GLN* 3.5 13.3 + - - +
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Residues in contact with LEU 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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276B VAL* 4.9 3.1 - - + +
279B LEU* 4.3 20.0 - - + -
280B LEU* 3.8 32.1 - - + +
283B ILE* 4.0 17.3 - - + -
315B LEU* 4.3 20.4 - - + +
316B GLY* 4.9 0.4 - - - -
319B HIS* 2.9 34.7 + - + +
320B SER 3.8 0.9 - - - +
322B ALA* 1.3 76.2 - - - +
324B LEU* 1.3 63.6 + - - +
326B GLN* 3.4 23.3 + - + +
329B HIS* 5.6 1.0 - - - +
330B TRP* 5.6 1.4 + - - -
333B PHE* 3.7 40.7 - - + +
336B LEU* 5.0 0.2 - - + -
382B TYR* 4.7 0.5 + - - -
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Residues in contact with LEU 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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320B SER* 2.9 25.8 + - - +
321B ARG 3.5 4.3 - - - +
323B LEU* 1.3 74.3 - - - +
325B ASP* 1.3 65.9 + - - +
326B GLN 3.5 0.2 + - - -
327B VAL 3.9 1.7 + - - -
333B PHE* 3.6 30.5 - - + -
367B LEU* 4.2 14.8 - - + -
370B ASP* 3.6 30.7 - - + +
371B ILE* 4.6 3.8 - - + -
374B PHE* 3.6 20.6 - - + -
378B LYS* 3.7 3.9 + - - -
382B TYR* 2.8 57.0 + - + +
386B TYR* 4.3 7.0 - - + -
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Residues in contact with ASP 325 (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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321B ARG* 2.7 30.5 + - - +
322B ALA* 3.5 14.6 - - - +
323B LEU 3.2 0.4 - - - -
324B LEU* 1.3 78.5 - - - +
326B GLN* 1.3 64.9 + - + +
327B VAL* 2.9 14.7 + - - +
374B PHE* 3.7 20.3 - - - -
378B LYS* 4.0 12.8 + - - +
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Residues in contact with GLN 326 (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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276B VAL* 4.9 16.8 - - + +
280B LEU* 4.5 20.9 - - + -
322B ALA 3.5 11.8 + - - +
323B LEU* 3.4 17.7 + - + +
324B LEU 3.2 1.5 - - - -
325B ASP* 1.3 79.1 - - - +
327B VAL* 1.3 64.0 + - - +
328B GLU* 3.3 2.9 - - - -
329B HIS* 3.2 29.3 + - + +
330B TRP 3.9 2.4 + - - -
382B TYR* 4.7 0.5 + - - -
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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