Contacts of the helix formed by residues 320 - 330 (chain B) in PDB entry 5H1Y
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 THR 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B ILE* 4.7 1.3 - - - -
264B CYS 3.5 14.1 - - - +
265B PRO 4.1 2.7 - - - +
266B SER* 3.5 35.2 - - - +
267B ARG 4.0 2.2 - - - +
270B ALA* 4.8 0.7 - - + -
297B CYS 3.2 4.1 + - - +
298B ILE* 3.5 16.9 - - + +
319B ALA* 1.3 77.3 - - - +
321B PRO* 1.3 74.3 - - - +
322B GLY 4.9 0.2 - - - -
323B ARG* 3.0 42.6 + - - +
324B LEU* 3.2 20.3 + - - +
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Residues in contact with PRO 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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263B ILE* 3.8 17.5 - - + -
264B CYS 3.2 15.7 - - - +
265B PRO* 4.8 0.2 - - + -
320B THR* 1.3 89.1 - - + +
322B GLY* 1.3 63.9 + - - +
323B ARG 3.3 0.3 + - - -
324B LEU* 3.3 1.7 + - + -
325B MET* 3.0 26.8 + - - +
349B MET* 4.0 8.3 - - - -
354B PHE* 3.9 37.9 - - + -
357B ASP* 4.2 20.0 - - + -
358B ILE* 4.6 4.7 - - + -
361B ILE* 3.7 18.1 - - + +
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Residues in contact with GLY 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 THR* 3.5 1.0 - - - -
321B PRO* 1.3 80.1 - - - +
323B ARG* 1.3 69.2 + - - +
325B MET* 3.8 8.7 - - - +
326B ASP* 3.1 23.7 + - - +
354B PHE* 5.6 4.9 - - - -
357B ASP* 4.2 14.0 + - - -
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Residues in contact with ARG 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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265B PRO 5.7 1.0 + - - -
266B SER* 5.9 0.4 - - - +
267B ARG* 2.8 42.5 - - - +
297B CYS* 3.8 22.4 - - - +
298B ILE* 3.4 4.9 - - - +
299B GLY* 3.2 26.5 - - - +
306B GLN* 5.8 1.1 - - - +
320B THR* 3.0 34.0 + - - +
321B PRO 3.2 0.8 - - - -
322B GLY* 1.3 81.4 - - - +
324B LEU* 1.3 63.0 + - - +
326B ASP* 3.4 6.9 + - - +
327B LEU* 3.1 28.3 + - + +
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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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261B LEU* 3.5 37.5 - - + -
263B ILE* 4.1 10.1 - - + -
297B CYS* 3.8 10.0 - - - -
317B MET* 4.0 25.1 - - - -
319B ALA* 4.1 9.0 - - + -
320B THR 3.2 16.8 + - - +
321B PRO 3.9 2.9 - - - +
323B ARG* 1.3 74.3 - - - +
325B MET* 1.3 66.1 + - - +
327B LEU* 3.1 1.6 + - - -
328B LEU* 2.8 41.0 + - + +
333B VAL* 4.0 18.6 - - + -
335B LEU* 5.0 3.4 - - + -
361B ILE* 4.0 20.0 - - + -
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Residues in contact with MET 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 PRO 3.0 15.6 + - - +
322B GLY* 3.8 10.1 - - - +
324B LEU* 1.3 76.8 - - - +
326B ASP* 1.3 58.3 + - + +
328B LEU* 3.4 10.8 + - - +
329B GLN* 2.9 57.9 + - + +
357B ASP* 3.5 48.5 - - - +
360B THR* 4.1 24.2 - - + -
361B ILE* 4.3 9.1 - - + +
364B TYR* 6.0 0.9 - - + -
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Residues in contact with ASP 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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322B GLY 3.1 16.9 + - - +
323B ARG* 3.4 8.7 - - - +
325B MET* 1.3 80.3 - - - +
327B LEU* 1.3 65.5 + - - +
329B GLN* 3.2 11.2 + - - +
330B LYS* 2.9 70.3 + - - +
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Residues in contact with LEU 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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297B CYS* 3.6 11.4 - - - -
303B VAL* 5.1 13.5 - - + -
306B GLN* 3.4 33.9 - - - +
307B MET* 4.2 11.0 - - + -
323B ARG* 3.1 15.8 + - + +
324B LEU 3.1 2.2 + - - +
326B ASP* 1.3 87.4 - - - +
328B LEU* 1.3 62.0 + - - +
330B LYS* 3.5 5.2 + - + +
331B LYS 3.2 2.3 + - - -
332B MET* 2.8 49.8 + - + -
333B VAL* 3.4 28.9 + - + -
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Residues in contact with LEU 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 LEU* 2.8 37.2 + - + +
325B MET* 3.6 4.9 - - - +
327B LEU* 1.3 76.8 - - - +
329B GLN* 1.3 61.6 + - - +
331B LYS* 3.1 19.8 + - - +
333B VAL* 3.5 33.7 - - + +
334B SER* 4.3 3.1 - - - -
335B LEU* 3.8 31.2 - - + +
361B ILE* 4.3 13.7 - - + -
364B TYR* 3.7 54.1 - - + -
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Residues in contact with GLN 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 MET* 2.9 47.8 + - + +
326B ASP* 3.7 9.2 - - - +
328B LEU* 1.3 75.5 - - - +
330B LYS* 1.3 60.4 + - + +
331B LYS* 3.3 15.0 + - - +
360B THR* 4.3 12.7 - - - +
364B TYR* 3.4 23.2 + - + +
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Residues in contact with LYS 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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326B ASP* 2.9 50.3 + - - +
327B LEU* 4.1 4.7 - - + +
328B LEU 3.2 0.4 - - - -
329B GLN* 1.3 78.7 - - + +
331B LYS* 1.3 73.1 + - - +
332B MET* 3.2 32.9 + - + +
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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