Contacts of the helix formed by residues 317 - 331 (chain B) in PDB entry 1WBB
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 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B ASP* 4.7 1.5 + - - +
315B VAL* 3.4 12.8 - - + +
316B ARG* 1.3 75.1 - - - +
318B THR* 1.3 65.7 + - - +
319B ARG* 3.3 40.7 + - - +
320B VAL* 3.2 29.0 + - + +
321B LEU* 3.4 13.2 + - - +
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Residues in contact with THR 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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316B ARG 3.1 11.6 + - - +
317B ASP* 1.3 72.1 + - - +
319B ARG* 1.3 58.7 + - - +
320B VAL 3.3 0.2 - - - -
321B LEU* 3.6 11.4 - - + +
322B LEU* 2.7 46.3 + - - +
572B PHE* 3.9 41.3 - - + -
635B TYR* 4.6 5.4 - - + +
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Residues in contact with ARG 319 (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 ASP* 3.3 27.5 + - - +
318B THR* 1.3 81.3 + - - +
320B VAL* 1.3 61.8 + - + +
322B LEU* 3.3 10.1 + - + +
323B GLU* 3.1 29.1 + - - +
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Residues in contact with VAL 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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315B VAL* 4.5 14.4 - - + -
317B ASP* 3.2 29.0 + - + +
319B ARG* 1.3 78.4 - - + +
321B LEU* 1.3 62.0 + - - +
323B GLU* 3.4 14.3 + - + +
324B ARG* 3.1 50.0 + - + +
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Residues in contact with LEU 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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315B VAL* 3.5 20.4 - - + +
317B ASP 3.5 15.7 - - - +
318B THR* 3.2 15.2 + - - +
319B ARG 3.2 0.4 - - - -
320B VAL* 1.3 75.6 - - - +
322B LEU* 1.3 60.3 + - - +
324B ARG* 3.1 5.9 + - - +
325B GLN* 2.9 34.1 + - - +
572B PHE* 3.9 22.0 - - + -
634B ALA 3.8 0.7 - - - +
635B TYR* 3.5 50.7 - - + +
636B ILE 3.6 3.6 - - - -
637B GLY* 3.3 33.4 - - - +
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Residues in contact with LEU 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 THR* 2.7 37.2 + - - +
319B ARG* 3.7 8.5 - - + +
321B LEU* 1.3 73.9 - - - +
323B GLU* 1.3 57.0 + - - +
325B GLN* 3.6 21.1 - - - +
326B GLN* 3.2 48.6 + - + +
572B PHE* 4.3 16.6 - - + -
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Residues in contact with GLU 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 ARG* 3.1 19.9 + - - +
320B VAL* 3.5 14.9 - - + +
321B LEU 3.1 0.4 - - - -
322B LEU* 1.3 75.2 - - - +
324B ARG* 1.3 64.4 + - + +
326B GLN* 3.5 12.1 + - - +
327B THR* 2.8 30.6 + - - -
389B PRO* 4.0 26.3 - - + +
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Residues in contact with ARG 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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310B TRP* 3.5 56.6 + - + +
313B MET 5.7 1.0 + - - -
315B VAL* 3.8 16.9 - - - +
320B VAL* 3.1 33.7 + - + +
321B LEU* 3.1 8.3 + - - +
323B GLU* 1.3 79.3 - - + +
325B GLN* 1.3 57.7 + - - +
327B THR* 3.5 6.8 + - - -
328B ILE* 3.0 35.1 + - + +
551B GLU* 5.5 2.8 + - - +
555B LEU* 4.2 19.5 - - + +
636B ILE* 2.8 35.3 + - - +
637B GLY* 3.7 13.9 - - - +
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Residues in contact with GLN 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 LEU* 2.9 18.5 + - - +
322B LEU* 3.6 25.7 - - - +
324B ARG* 1.3 75.6 - - - +
326B GLN* 1.3 64.5 + - + +
328B ILE* 3.0 5.9 + - - +
329B GLY 3.0 18.4 + - - -
569B CYS* 3.4 29.0 - - - -
570B PRO* 3.2 32.0 + - - +
572B PHE* 3.3 26.6 - - - -
634B ALA 4.7 4.0 + - - -
637B GLY* 3.7 16.4 - - - +
638B SER 4.9 1.4 + - - +
639B TYR* 3.7 16.2 + - + -
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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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322B LEU* 3.2 32.1 + - + +
323B GLU* 3.9 14.5 - - - +
324B ARG 3.5 0.2 - - - -
325B GLN* 1.3 79.4 - - + +
327B THR* 1.3 56.5 + - - +
329B GLY* 3.3 2.6 + - - +
330B ALA* 2.9 30.5 + - - +
387B SER* 4.3 8.5 - - - +
389B PRO* 5.4 6.3 - - + +
639B TYR* 5.6 0.2 - - - -
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Residues in contact with THR 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 GLU 2.8 21.7 + - - -
324B ARG* 3.5 5.8 - - - -
326B GLN* 1.3 77.3 - - - +
328B ILE* 1.3 57.0 + - - +
330B ALA* 3.4 1.8 + - - +
331B LEU* 3.0 54.1 + - + +
387B SER* 3.7 8.6 + - - -
389B PRO* 3.4 25.1 - - + +
390B VAL* 3.5 12.6 - - + +
393B LEU* 5.3 0.9 - - + -
555B LEU* 3.4 32.5 - - + +
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Residues in contact with ILE 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 ARG* 3.0 17.7 + - + +
325B GLN* 3.0 4.2 + - - +
327B THR* 1.3 75.0 - - - +
329B GLY* 1.3 61.3 + - - +
332B GLN* 3.7 9.2 + - - +
555B LEU* 3.8 26.9 - - + +
558B LEU* 3.6 28.9 - - + +
559B ALA* 3.3 37.6 - - - +
562B ALA* 4.4 4.0 - - + -
637B GLY 3.3 26.5 - - - +
638B SER* 4.0 9.9 - - - -
639B TYR* 3.6 28.9 - - + +
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Residues in contact with GLY 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 GLN 3.0 10.7 + - - -
326B GLN* 3.3 4.0 + - - -
328B ILE* 1.3 77.3 - - - +
330B ALA* 1.3 62.6 + - - +
332B GLN* 3.5 21.9 + - - +
639B TYR* 3.6 18.4 - - - -
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Residues in contact with ALA 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 GLN 2.9 16.9 + - - +
327B THR 3.4 3.1 + - - +
329B GLY* 1.3 76.9 - - - +
331B LEU* 1.3 57.9 + - - +
332B GLN 3.3 0.9 + - - -
333B ASP* 4.6 1.4 + - - +
334B PHE* 3.3 24.9 - - - -
385B VAL* 3.6 16.4 - - + +
386B ASP* 3.5 26.7 - - + +
387B SER* 3.9 7.6 - - - -
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Residues in contact with LEU 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 THR* 3.0 43.2 + - + +
328B ILE 4.0 0.6 + - - -
329B GLY 3.3 0.2 - - - -
330B ALA* 1.3 76.2 - - - +
332B GLN* 1.3 65.9 + - - +
333B ASP 3.3 2.2 - - - -
334B PHE* 3.1 15.9 + - + -
335B THR* 3.5 12.1 + - - -
338B LEU* 3.8 27.8 - - + -
382B LEU* 4.1 14.6 - - + -
385B VAL* 4.3 7.6 - - + -
390B VAL* 3.8 20.6 - - + -
552B LEU* 5.0 5.6 - - + -
555B LEU* 4.2 12.6 - - + -
556B VAL* 4.1 20.6 - - + +
559B ALA* 4.2 11.7 - - + -
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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