Contacts of the helix formed by residues 320 - 331 (chain B) in PDB entry 5KYT
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 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B PRO 3.9 3.2 + - - -
319B LEU* 1.3 76.7 - - - +
321B LYS* 1.3 54.7 + - - +
322B GLU* 3.4 6.2 + - - +
323B VAL* 3.1 36.5 + - - +
324B GLY* 2.7 35.0 + - - -
456B SER* 3.4 27.8 + - - -
459B LEU* 5.3 6.3 - - - -
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Residues in contact with LYS 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 LEU 3.2 6.3 + - - -
320B SER* 1.3 71.1 + - - +
322B GLU* 1.3 78.7 + - - +
324B GLY* 3.7 1.4 - - - -
325B GLU* 2.9 52.6 + - + +
359B PRO* 4.1 21.4 + - + +
360B GLY* 3.8 29.2 - - - +
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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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320B SER* 3.2 3.2 + - - +
321B LYS* 1.3 95.6 + - + +
323B VAL* 1.3 62.4 + - + +
325B GLU* 3.3 6.9 + - - +
326B ALA* 2.8 32.8 + - - +
456B SER* 3.2 22.4 + - - +
460B GLN* 6.2 4.9 - - + -
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Residues in contact with VAL 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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292B PHE* 3.7 35.7 - - + +
293B SER* 6.0 0.2 - - - -
296B ALA* 5.3 7.6 - - + -
319B LEU* 4.9 2.9 - - + -
320B SER* 3.1 29.2 + - - +
322B GLU* 1.3 77.8 - - + +
324B GLY* 1.3 54.8 + - - +
326B ALA* 3.2 5.1 + - - +
327B VAL* 2.8 40.4 + - + +
459B LEU* 5.2 16.4 - - + -
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Residues in contact with GLY 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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292B PHE* 4.5 3.8 - - - -
319B LEU* 4.1 12.9 - - - +
320B SER 2.7 21.4 + - - -
321B LYS* 3.7 1.8 - - - -
323B VAL* 1.3 72.9 - - - +
325B GLU* 1.3 56.8 + - - +
327B VAL 4.0 0.2 - - - -
328B ALA* 3.0 27.2 + - - +
335B GLY* 6.1 0.2 - - - -
336B ILE* 3.3 26.0 + - - +
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Residues in contact with GLU 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 LYS* 2.9 41.6 + - + +
322B GLU* 4.0 5.6 - - - +
324B GLY* 1.3 74.0 - - - +
326B ALA* 1.3 65.6 + - - +
328B ALA* 3.4 7.0 + - - +
329B LYS* 3.1 22.3 + - - +
335B GLY* 6.1 0.4 - - - -
359B PRO* 3.9 25.4 - - + +
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Residues in contact with ALA 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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296B ALA* 4.7 12.2 - - - +
322B GLU 2.8 17.9 + - - +
323B VAL* 3.6 7.0 - - + +
325B GLU* 1.3 77.0 - - - +
327B VAL* 1.3 62.9 + - + +
329B LYS* 3.2 15.0 + - - +
330B ARG* 3.2 13.0 + - - +
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Residues in contact with VAL 327 (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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292B PHE* 3.6 54.1 - - + +
295B PHE* 4.5 8.3 - - + +
296B ALA* 4.1 17.5 - - - +
312B ILE* 4.7 7.0 - - + -
323B VAL* 2.8 24.8 + - + +
324B GLY 4.2 1.6 - - - +
326B ALA* 1.3 70.2 - - + +
328B ALA* 1.3 67.3 + - - +
330B ARG* 3.3 7.2 + - - +
331B PHE* 3.1 45.9 + - + -
336B ILE* 4.8 0.9 - - + -
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Residues in contact with ALA 328 (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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324B GLY 3.0 20.5 + - - +
325B GLU* 3.6 8.7 - - - +
326B ALA 3.2 0.2 - - - -
327B VAL* 1.3 77.5 - - - +
329B LYS* 1.3 59.1 + - - +
331B PHE* 3.2 3.6 + - - -
332B HIS 2.9 4.9 + - - -
333B LEU* 2.8 48.3 + - - +
334B PRO 4.7 0.7 - - - -
335B GLY* 3.9 22.9 - - - +
336B ILE* 4.0 10.1 - - + +
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Residues in contact with LYS 329 (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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325B GLU 3.1 13.6 + - - +
326B ALA* 3.2 9.4 + - - +
328B ALA* 1.3 75.2 - - - +
330B ARG* 1.3 55.8 + - - +
332B HIS* 2.7 33.0 + - - +
333B LEU 4.5 3.8 - - - -
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Residues in contact with ARG 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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295B PHE 4.9 4.0 - - - +
296B ALA 5.1 4.0 - - - +
297B LYS* 6.3 0.7 - - - -
301B ILE* 3.9 36.0 - - + +
302B ASP* 5.2 4.0 - - - +
326B ALA 3.2 9.0 + - - +
327B VAL* 3.7 10.5 - - - +
329B LYS* 1.3 78.8 - - - +
331B PHE* 1.3 61.1 + - + +
332B HIS* 3.5 11.6 + - - -
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Residues in contact with PHE 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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273B PHE* 5.7 0.7 - + - -
274B LEU* 4.0 22.2 - - + -
277B LEU* 4.1 11.2 - - + -
295B PHE* 4.0 28.3 - + + -
301B ILE* 4.0 17.5 - - + -
306B LEU* 3.3 42.3 - - + +
309B LEU* 3.7 17.7 - - + +
312B ILE* 3.4 28.9 - - + -
327B VAL* 3.1 39.7 + - + +
328B ALA 4.0 2.2 - - - +
330B ARG* 1.3 76.2 - - + +
332B HIS* 1.3 73.0 + - - +
333B LEU* 3.5 13.9 + - + +
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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