Contacts of the helix formed by residues 314 - 332 (chain B) in PDB entry 3PLZ
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 ASP 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B GLU 3.9 0.2 + - - -
313B PRO* 1.3 69.2 - - - +
315B GLU* 1.3 59.3 + - - +
316B PRO* 3.2 21.7 - - - +
317B GLN* 3.0 25.6 + - + +
318B VAL* 2.9 29.2 + - - +
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Residues in contact with GLU 315 (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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313B PRO* 3.2 9.3 + - - +
314B ASP* 1.3 69.4 - - - +
316B PRO* 1.3 77.7 - - + +
318B VAL* 3.3 6.4 + - - +
319B GLN* 2.9 35.1 + - + +
397B HIS* 3.5 27.7 + - - -
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Residues in contact with PRO 316 (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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314B ASP* 3.2 12.3 - - - +
315B GLU* 1.3 100.4 - - + +
317B GLN* 1.3 55.9 + - - +
319B GLN* 3.7 9.8 - - + +
320B ALA* 2.9 31.5 + - - +
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Residues in contact with GLN 317 (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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314B ASP* 3.0 31.0 + - + +
316B PRO* 1.3 75.7 - - - +
318B VAL* 1.3 63.5 + - + +
320B ALA* 3.4 5.1 + - - +
321B LYS* 2.9 31.2 + - + +
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Residues in contact with VAL 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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2B EDO 4.1 8.7 - - - +
313B PRO* 3.9 19.3 - - + -
314B ASP 2.9 19.3 + - - +
315B GLU* 3.8 8.3 - - - +
317B GLN* 1.3 76.2 - - + +
319B GLN* 1.3 63.8 + - - +
321B LYS* 3.3 5.6 + - - +
322B ILE* 3.0 44.6 + - + +
355B SER* 3.7 28.7 - - - +
406B VAL* 4.2 11.2 - - + -
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Residues in contact with GLN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU* 2.9 29.9 + - + +
316B PRO* 3.7 8.4 - - - +
318B VAL* 1.3 77.7 - - - +
320B ALA* 1.3 58.7 + - - +
322B ILE* 3.4 2.3 + - - +
323B MET* 2.9 33.0 + - + +
404B PHE* 5.7 1.7 - - - -
406B VAL 3.6 16.3 - - - +
407B THR* 3.2 37.7 + - - +
408B GLY* 4.1 9.9 + - - -
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Residues in contact with ALA 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 PRO 2.9 18.4 + - - +
317B GLN* 3.9 5.2 - - - +
319B GLN* 1.3 74.6 - - - +
321B LYS* 1.3 60.4 + - - +
323B MET* 3.7 7.3 - - - +
324B ALA* 3.0 29.6 + - - +
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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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317B GLN* 2.9 21.5 + - + +
318B VAL* 3.6 7.2 - - - +
320B ALA* 1.3 78.3 - - - +
322B ILE* 1.3 63.8 + - + +
324B ALA* 3.4 5.8 + - - +
325B TYR* 3.1 22.3 + - - +
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Residues in contact with ILE 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 VAL* 3.0 25.9 + - + +
319B GLN* 4.0 3.1 - - - +
321B LYS* 1.3 76.0 - - + +
323B MET* 1.3 65.9 + - - +
325B TYR* 3.3 6.9 + - - +
326B LEU* 3.1 22.3 + - + +
348B MET* 3.5 31.9 - - + -
351B GLN* 4.0 35.2 - - + +
352B THR* 4.1 10.5 - - - +
355B SER* 5.4 0.7 - - - -
406B VAL* 3.7 31.9 - - + -
407B THR* 3.5 11.2 - - + -
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Residues in contact with MET 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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319B GLN* 2.9 20.7 + - + +
320B ALA* 3.7 7.9 - - - +
322B ILE* 1.3 76.5 - - - +
324B ALA* 1.3 56.8 + - - +
326B LEU* 3.3 9.6 + - - +
327B GLN* 3.0 49.8 + - - +
407B THR* 3.4 46.9 - - - +
408B GLY 5.1 0.9 - - - -
409B GLN* 4.5 13.9 - - + +
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Residues in contact with ALA 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 ALA 3.0 19.6 + - - +
321B LYS* 3.7 6.3 - - - +
323B MET* 1.3 76.0 - - - +
325B TYR* 1.3 62.3 + - - +
327B GLN* 3.2 16.9 + - - +
328B GLN* 3.0 24.9 + - - +
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Residues in contact with TYR 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 3.1 13.6 + - - +
322B ILE* 3.3 9.6 + - - +
324B ALA* 1.3 77.0 - - - +
326B LEU* 1.3 80.2 + - + +
328B GLN* 3.5 6.3 + - - +
329B GLU* 3.0 72.6 + - + +
347B LYS* 3.7 20.6 + - + +
348B MET* 5.6 0.2 - - + -
350B ASP* 4.7 4.0 + - - -
351B GLN* 3.5 52.0 + - + +
528B TYR 5.6 0.5 + - - -
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Residues in contact with LEU 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 ILE 3.1 13.4 + - - +
323B MET* 3.7 9.6 - - - +
325B TYR* 1.3 93.7 - - + +
327B GLN* 1.3 61.4 + - + +
329B GLU* 3.3 7.0 + - + +
330B GLN* 2.9 29.6 + - - +
333B ARG* 5.2 1.0 + - - +
339B LEU* 4.7 5.4 - - + -
344B LEU* 3.9 26.9 - - + -
347B LYS* 4.2 16.2 - - + -
348B MET* 3.3 30.1 - - + -
407B THR* 3.9 18.2 - - + +
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Residues in contact with GLN 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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323B MET* 3.0 35.9 + - - +
324B ALA* 3.2 19.9 + - - +
326B LEU* 1.3 74.6 - - + +
328B GLN* 1.3 59.6 + - - +
330B GLN* 3.3 6.4 + - - +
331B ALA* 2.9 30.2 + - - +
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Residues in contact with GLN 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 ALA 3.0 16.0 + - - +
325B TYR* 3.7 6.7 - - - +
327B GLN* 1.3 76.2 - - - +
329B GLU* 1.3 63.7 + - + +
331B ALA* 3.3 6.3 + - - +
332B ASN* 3.0 37.9 + - - +
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Residues in contact with GLU 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 TYR* 3.0 59.8 + - + +
326B LEU* 3.5 12.6 - - + +
327B GLN 3.2 0.2 - - - -
328B GLN* 1.3 76.3 - - + +
330B GLN* 1.3 61.7 + - - +
332B ASN* 3.3 11.4 + - - +
333B ARG* 3.2 33.0 + - - +
347B LYS* 2.7 32.4 + - - +
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Residues in contact with GLN 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 LEU 2.9 17.1 + - - +
327B GLN* 3.8 6.7 - - - +
329B GLU* 1.3 72.1 - - - +
331B ALA* 1.3 65.8 + - - +
332B ASN 3.4 0.2 + - - -
333B ARG* 2.9 46.7 + - - +
339B LEU* 5.0 8.1 - - - +
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Residues in contact with ALA 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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327B GLN 2.9 16.9 + - - +
328B GLN* 3.6 8.7 - - - +
329B GLU 3.3 0.2 - - - -
330B GLN* 1.3 77.0 - - - +
332B ASN* 1.3 65.8 + - - +
333B ARG 3.6 4.2 + - - +
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Residues in contact with ASN 332 (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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328B GLN* 3.0 27.0 + - - +
329B GLU* 3.3 5.4 + - - +
330B GLN 3.3 0.2 - - - -
331B ALA* 1.3 82.5 + - - +
333B ARG* 1.3 62.2 + - - +
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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