Contacts of the helix formed by residues 359 - 375 (chain B) in PDB entry 3PLA
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 ILE 359 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B ASN* 2.7 14.5 + - - +
347B ILE* 5.0 2.0 - - + -
351B VAL* 3.9 26.9 - - + -
357B ARG* 3.6 33.9 - - + +
358B PHE* 1.3 78.6 - - - +
360B GLY* 1.3 60.6 + - - +
361B ASP 3.2 7.2 + - - -
362B GLN* 3.4 34.7 - - + +
363B LEU* 3.5 37.3 + - + +
62D PRO* 4.7 20.9 - - + -
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Residues in contact with GLY 360 (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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264B ASN* 3.0 13.0 + - - -
267B ALA* 3.9 10.2 - - - +
268B LEU* 5.2 0.7 - - - +
358B PHE* 3.7 20.9 - - - -
359B ILE* 1.3 77.2 - - - +
361B ASP* 1.3 61.9 + - - +
362B GLN 3.6 0.2 - - - -
363B LEU* 3.9 10.3 - - - +
364B ASN* 3.2 34.7 + - - -
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Residues in contact with ASP 361 (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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267B ALA* 5.7 0.2 - - - +
358B PHE* 3.4 25.9 - - + -
359B ILE 3.2 1.6 - - - -
360B GLY* 1.3 77.3 - - - +
362B GLN* 1.3 70.1 + - - +
364B ASN* 3.4 8.1 + - - +
365B GLU* 3.0 28.5 + - - +
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Residues in contact with GLN 362 (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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358B PHE* 5.0 1.6 + - - -
359B ILE* 3.4 42.7 + - + +
361B ASP* 1.3 80.5 - - - +
363B LEU* 1.3 57.4 + - + +
365B GLU* 3.0 13.5 + - - +
366B GLN* 2.7 55.1 + - + +
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Residues in contact with LEU 363 (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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264B ASN* 4.8 2.7 - - + -
268B LEU* 4.1 17.9 - - + +
344B LYS* 4.1 16.5 - - + +
347B ILE* 4.7 12.3 - - + -
348B ALA* 3.8 39.9 - - + +
359B ILE* 3.5 44.9 + - + +
360B GLY* 3.9 10.3 - - - +
361B ASP 3.3 0.2 - - - -
362B GLN* 1.3 79.3 - - + +
364B ASN* 1.3 56.6 + - - +
366B GLN* 3.5 21.7 + - - +
367B LEU* 3.0 28.9 + - - +
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Residues in contact with ASN 364 (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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267B ALA* 3.0 32.4 + - - +
268B LEU* 3.9 19.6 - - - +
323B TYR* 4.7 5.0 + - - -
360B GLY 3.2 20.2 + - - +
361B ASP* 3.6 7.4 + - - +
362B GLN 3.3 0.2 - - - -
363B LEU* 1.3 78.7 - - - +
365B GLU* 1.3 57.5 + - - +
367B LEU* 3.3 3.5 + - - +
368B LYS* 2.8 66.5 + - - +
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Residues in contact with GLU 365 (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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361B ASP* 3.0 15.3 + - - +
362B GLN* 3.0 15.9 + - - +
364B ASN* 1.3 74.2 - - - +
366B GLN* 1.3 65.6 + - + +
368B LYS* 3.4 6.8 + - - +
369B LYS* 3.0 41.1 + - - +
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Residues in contact with GLN 366 (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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344B LYS* 2.8 42.5 + - - +
347B ILE* 5.7 0.2 - - - +
362B GLN* 2.7 43.1 + - + +
363B LEU* 3.8 17.8 - - - +
365B GLU* 1.3 72.3 - - + +
367B LEU* 1.3 62.4 + - - +
369B LYS* 3.3 14.7 + - + +
370B ARG* 3.1 21.8 + - - +
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Residues in contact with LEU 367 (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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268B LEU* 3.8 21.8 - - + -
323B TYR* 3.3 27.6 - - + +
337B ILE 4.9 0.9 - - - +
340B ALA* 3.8 16.8 - - + +
341B LEU* 3.7 45.5 - - + +
344B LYS* 4.3 11.4 - - + +
363B LEU 3.0 18.9 + - - +
364B ASN* 3.6 7.0 - - - +
366B GLN* 1.3 77.0 - - - +
368B LYS* 1.3 57.7 + - + +
370B ARG* 3.1 7.4 + - + +
371B ILE* 2.9 44.3 + - + +
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Residues in contact with LYS 368 (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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323B TYR* 5.1 7.9 - - - +
364B ASN* 2.8 52.7 + - - +
365B GLU* 4.1 5.4 - - - +
367B LEU* 1.3 70.9 - - + +
369B LYS* 1.3 59.3 + - - +
371B ILE* 3.9 14.5 - - + +
372B ASP* 3.0 38.6 + - - +
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Residues in contact with LYS 369 (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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365B GLU* 3.0 31.8 + - + +
366B GLN* 3.4 16.1 - - + +
368B LYS* 1.3 74.1 - - - +
370B ARG* 1.3 65.6 + - - +
372B ASP* 3.4 6.8 + - - +
373B GLU* 3.2 37.7 + - - +
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Residues in contact with ARG 370 (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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336B LYS* 4.2 18.4 + - - +
339B ARG* 4.8 8.7 - - - +
340B ALA* 3.9 26.9 - - + +
344B LYS* 6.4 2.0 - - - -
366B GLN 3.1 10.9 + - - +
367B LEU* 3.4 10.5 - - - +
369B LYS* 1.3 79.4 - - - +
371B ILE* 1.3 60.8 + - - +
373B GLU* 3.6 28.9 + - - +
374B ILE* 3.1 61.5 + - - +
377B LYS* 5.2 7.5 - - - +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B TYR* 4.4 5.6 - - + +
325B ALA* 4.4 23.1 - - + -
337B ILE* 4.2 27.4 - - + -
340B ALA* 5.7 0.7 - - + -
367B LEU* 2.9 48.8 + - + +
368B LYS* 3.9 13.0 - - + +
370B ARG* 1.3 75.9 - - + +
372B ASP* 1.3 64.3 + - - +
374B ILE* 3.1 9.7 + - + +
375B LYS* 2.9 49.9 + - + +
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Residues in contact with ASP 372 (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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368B LYS* 3.0 23.4 + - - +
369B LYS* 3.4 7.1 + - - +
371B ILE* 1.3 80.6 - - - +
373B GLU* 1.3 62.6 + - + +
375B LYS* 3.5 7.1 + - - +
376B GLU* 3.3 32.0 + - - +
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Residues in contact with GLU 373 (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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369B LYS* 3.2 28.8 + - - +
370B ARG* 3.6 29.3 + - - +
372B ASP* 1.3 73.0 - - + +
374B ILE* 1.3 67.9 + - - +
376B GLU* 3.1 21.6 + - - +
377B LYS* 4.2 15.8 + - - +
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Residues in contact with ILE 374 (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 GLN* 3.8 42.3 + - + +
336B LYS* 3.6 38.6 + - + +
337B ILE* 3.7 24.9 - - + +
340B ALA* 5.0 1.8 - - + -
370B ARG* 3.1 48.2 + - + +
371B ILE* 3.1 10.7 + - + +
373B GLU* 1.3 77.7 - - - +
375B LYS* 1.3 62.1 + - + +
376B GLU 3.3 1.2 + - - -
377B LYS* 4.1 18.8 + - - +
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Residues in contact with LYS 375 (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 ALA* 4.7 4.9 + - - +
328B THR* 5.6 2.2 - - - -
329B SER* 3.0 32.5 + - - +
330B PRO* 5.3 1.8 - - + +
333B GLN* 3.3 27.7 + - - +
337B ILE* 4.6 1.8 - - - -
371B ILE* 2.9 37.2 + - + +
372B ASP* 3.9 8.7 - - - +
373B GLU 3.1 0.6 - - - -
374B ILE* 1.3 79.2 - - + +
376B GLU* 1.3 60.0 + - + +
377B LYS 3.4 7.0 + - - +
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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