Contacts of the helix formed by residues 334 - 346 (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 PHE 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ALA 3.3 26.9 - - - -
331B LEU* 3.1 8.6 + - - +
333B ASP* 1.3 92.4 - - + +
335B THR* 1.3 63.6 + - - +
336B ALA 3.6 1.8 - - - -
337B GLY* 3.6 5.0 + - - +
338B LEU* 3.2 42.1 + - + +
381B GLN* 3.8 23.5 - - + +
384B THR* 3.8 32.3 - - + -
385B VAL* 3.7 26.5 - - + -
386B ASP 5.5 0.2 - - - -
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Residues in contact with THR 335 (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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331B LEU 3.5 7.0 + - - -
332B GLN* 3.7 15.0 - - - +
333B ASP 3.5 1.8 - - - -
334B PHE* 1.3 75.2 - - - +
336B ALA* 1.3 73.9 + - + +
338B LEU* 3.3 1.1 + - - +
339B GLN* 3.2 32.0 + - - +
556B VAL* 3.3 34.8 + - - +
559B ALA* 4.8 0.5 - - - +
560B GLU* 3.3 33.4 + - + +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASP 5.3 0.6 + - - -
334B PHE 3.6 0.2 - - - -
335B THR* 1.3 86.5 - - + +
337B GLY* 1.3 57.7 + - - +
339B GLN* 5.5 1.3 - - - -
340B PRO* 3.0 29.0 - - - +
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 3.6 6.2 + - - +
335B THR 3.2 0.4 - - - -
336B ALA* 1.3 81.9 - - - +
338B LEU* 1.3 60.6 + - - +
340B PRO* 3.7 6.2 - - - +
341B VAL* 3.9 7.8 - - - +
381B GLN* 2.9 29.6 + - - +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 3.8 11.2 - - + -
334B PHE* 3.2 29.4 + - + +
335B THR 3.3 3.1 + - - +
337B GLY* 1.3 75.7 - - - +
339B GLN* 1.3 61.4 + - - +
341B VAL* 3.1 6.9 + - - +
342B LEU* 2.8 34.3 + - + +
378B LEU* 4.3 14.7 - - + +
381B GLN* 2.9 38.5 + - + +
382B LEU* 3.7 29.2 - - + -
552B LEU* 4.8 0.9 - - + -
556B VAL* 3.6 35.0 - - + -
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Residues in contact with GLN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B CYS* 3.6 22.4 + - - +
298B THR* 5.1 0.6 - - - +
299B VAL* 3.8 24.9 - - + +
335B THR* 3.2 15.3 + - - +
336B ALA* 5.4 1.1 - - - -
338B LEU* 1.3 79.6 - - - +
340B PRO* 1.3 64.6 - - + +
342B LEU* 4.3 6.5 - - + -
343B ARG* 2.9 30.6 + - - +
553B ASP* 5.1 2.4 + - - +
556B VAL* 3.6 24.3 + - + +
557B ASN* 4.0 22.0 + - - +
560B GLU* 4.2 20.9 + - - +
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Residues in contact with PRO 340 (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 ALA* 3.0 24.7 - - - +
337B GLY 3.7 4.5 - - - +
338B LEU 3.5 2.9 - - - -
339B GLN* 1.3 94.3 - - + +
341B VAL* 1.3 62.0 + - + +
343B ARG* 3.5 18.9 - - + +
344B GLN* 3.6 15.4 + - - +
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Residues in contact with VAL 341 (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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337B GLY 3.9 6.7 - - - +
338B LEU 3.1 7.2 + - - +
340B PRO* 1.3 77.1 - - + +
342B LEU* 1.3 67.4 + - - +
344B GLN* 3.2 17.7 + - - +
345B VAL* 3.6 3.6 + - - +
374B GLN* 3.6 36.7 - - + +
377B GLU* 3.8 25.6 - - + -
378B LEU* 3.5 30.3 - - + -
381B GLN* 3.9 12.1 - - - +
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Residues in contact with LEU 342 (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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299B VAL* 3.8 14.6 - - + -
300B THR* 3.3 11.8 - - + +
338B LEU* 2.8 23.5 + - + +
339B GLN* 3.9 2.5 - - + +
341B VAL* 1.3 74.6 - - - +
343B ARG* 1.3 66.8 - - - +
345B VAL* 2.9 24.0 + - + +
378B LEU* 4.2 11.4 - - + -
549B LEU* 3.7 46.0 - - + +
552B LEU* 3.7 26.9 - - + +
553B ASP* 4.1 22.2 - - + +
556B VAL* 4.5 13.2 - - + -
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Residues in contact with ARG 343 (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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128B ARG* 5.7 0.8 - - - +
298B THR 4.1 5.5 + - - -
299B VAL* 3.1 66.5 + - + +
339B GLN 2.9 19.0 + - - +
340B PRO* 3.5 11.2 - - - +
341B VAL 3.2 0.2 - - - -
342B LEU* 1.3 76.1 - - - +
344B GLN* 1.3 74.5 + - - +
345B VAL 3.2 0.9 + - - -
346B GLY* 3.3 14.7 + - - -
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Residues in contact with GLN 344 (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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340B PRO 3.6 13.4 + - - +
341B VAL* 3.2 9.3 + - - +
342B LEU 3.2 0.2 - - - -
343B ARG* 1.3 90.8 - - - +
345B VAL* 1.3 63.2 + - - +
346B GLY* 3.4 1.8 + - - -
367B ARG 5.0 1.2 - - - +
370B HIS* 2.7 53.2 + - + +
371B ALA* 4.4 3.3 - - - +
374B GLN* 3.8 20.6 - - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 4.7 2.0 - - + -
302B MET* 3.7 20.2 - - + -
341B VAL 3.6 2.9 + - - +
342B LEU* 2.9 16.3 + - + +
344B GLN* 1.3 78.0 - - - +
346B GLY* 1.3 59.0 - - - +
347B ASP 4.0 0.2 + - - -
348B LEU* 4.0 9.9 + - + +
351B ILE* 5.7 1.9 - - - +
367B ARG* 4.8 2.6 - - - +
371B ALA* 3.4 33.4 - - + +
374B GLN* 3.8 26.7 - - + -
375B LEU* 5.1 0.4 - - + -
378B LEU* 4.3 4.9 - - + -
549B LEU* 3.7 42.6 - - + -
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 3.5 24.2 - - - +
301B PRO* 4.3 5.6 - - - -
302B MET* 3.6 8.8 - - - +
342B LEU 3.9 2.0 + - - -
343B ARG 3.3 12.6 + - - -
344B GLN 3.3 4.0 - - - -
345B VAL* 1.3 82.3 - - - +
347B ASP* 1.3 57.4 + - - -
348B LEU 3.0 7.9 + - - -
351B ILE* 6.2 0.2 - - - -
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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