Contacts of the helix formed by residues 373 - 384 (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 GLN 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B ARG* 3.1 29.9 + - + +
370B HIS* 3.5 31.9 + - - +
371B ALA 3.1 0.2 - - - -
372B PHE* 1.3 77.8 - - - +
374B GLN* 1.3 67.5 + - - +
375B LEU 3.6 0.2 + - - -
376B PRO* 3.6 12.3 - - - +
377B GLU* 4.7 3.3 + - - +
404B ARG* 3.7 34.6 + - + +
408B GLU* 3.0 29.4 + - - +
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Residues in contact with GLN 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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341B VAL* 3.6 41.6 - - + +
344B GLN* 3.8 19.1 - - + +
345B VAL* 3.8 16.2 - - + -
370B HIS* 3.0 44.4 + - - +
371B ALA* 3.5 9.2 - - - +
372B PHE 3.2 0.8 - - - -
373B GLN* 1.3 85.5 + - - +
375B LEU* 1.3 63.1 + - - +
376B PRO 3.5 0.7 - - - -
377B GLU* 3.2 9.5 + - - +
378B LEU* 3.0 24.8 + - + +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B VAL* 5.1 0.4 - - + -
371B ALA 3.8 10.3 - - - +
372B PHE* 3.2 18.8 + - + +
374B GLN* 1.3 76.7 - - - +
376B PRO* 1.3 65.2 - - + +
378B LEU* 3.3 6.6 + - + +
379B ARG* 2.9 34.7 + - - +
397B MET* 3.6 36.2 - - + +
398B GLY 3.6 17.7 - - - +
399B GLU* 3.3 28.5 - - - +
400B PHE* 3.8 16.6 - - + -
545B SER* 4.7 1.6 - - - +
549B LEU* 4.1 19.5 - - + -
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Residues in contact with PRO 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PHE 3.5 10.8 - - - +
373B GLN 3.6 11.4 - - - +
375B LEU* 1.3 93.6 - - + +
377B GLU* 1.3 61.6 + - - +
379B ARG* 3.2 11.3 + - + +
380B ALA* 3.0 25.2 + - - +
399B GLU* 5.3 5.6 - - + +
404B ARG* 4.3 19.5 - - - +
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Residues in contact with GLU 377 (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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341B VAL* 3.8 20.9 - - + -
373B GLN 5.1 2.5 - - - +
374B GLN* 3.2 13.4 + - - +
376B PRO* 1.3 78.9 - - - +
378B LEU* 1.3 62.1 + - - +
380B ALA* 3.7 8.3 + - - +
381B GLN* 2.7 55.3 + - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 4.3 20.9 - - + +
341B VAL* 3.5 28.9 - - + -
342B LEU* 4.2 20.2 - - + -
345B VAL* 4.3 6.1 - - + -
374B GLN* 3.0 27.7 + - + +
375B LEU* 3.7 7.6 - - + +
377B GLU* 1.3 74.4 - - - +
379B ARG* 1.3 63.6 + - - +
381B GLN* 4.6 3.4 - - - +
382B LEU* 3.0 32.6 + - + +
397B MET* 3.8 16.6 - - - -
549B LEU* 3.8 30.3 - - + -
552B LEU* 5.1 4.0 - - + -
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Residues in contact with ARG 379 (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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375B LEU 2.9 20.2 + - - +
376B PRO* 3.2 11.9 + - + +
378B LEU* 1.3 75.4 - - - +
380B ALA* 1.3 63.0 + - - +
382B LEU 3.7 0.2 + - - -
383B GLU* 3.2 9.7 + - - +
394B ARG* 3.0 79.6 + - - +
395B GLU* 4.9 12.1 + - - +
397B MET* 3.7 18.4 - - + +
398B GLY 4.4 2.9 + - - +
399B GLU* 3.5 42.1 + - - +
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Residues in contact with ALA 380 (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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376B PRO 3.0 14.8 + - - +
377B GLU* 3.8 13.2 - - - +
379B ARG* 1.3 75.8 - - - +
381B GLN* 1.3 64.0 + - + +
383B GLU* 3.2 26.2 + - - +
384B THR* 4.4 3.3 + - - -
394B ARG* 5.3 0.4 - - - +
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Residues in contact with GLN 381 (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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334B PHE* 3.8 28.3 - - + +
337B GLY* 2.9 44.1 + - - -
338B LEU* 2.9 22.8 - - + +
341B VAL* 3.9 8.0 - - - +
377B GLU* 2.7 46.9 + - - +
378B LEU* 4.0 3.6 - - - +
380B ALA* 1.3 79.8 - - + +
382B LEU* 1.3 61.2 + - - +
383B GLU 3.6 0.3 + - - -
384B THR* 4.2 3.8 + - - -
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Residues in contact with LEU 382 (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* 4.1 6.5 - - + -
338B LEU* 3.7 36.8 - - + -
378B LEU* 3.0 22.4 + - + +
381B GLN* 1.3 73.4 - - - +
383B GLU* 1.3 65.2 + - - +
384B THR 3.1 3.1 - - - -
385B VAL* 3.0 16.1 + - + +
390B VAL* 4.0 21.1 - - + +
391B GLN* 2.9 17.5 + - - -
393B LEU 5.6 0.2 - - - -
394B ARG* 4.0 33.9 - - + -
397B MET* 4.6 9.4 - - + -
552B LEU* 4.0 31.0 - - + -
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ARG 3.2 14.6 + - - +
380B ALA* 3.2 19.4 + - - +
382B LEU* 1.3 76.3 - - - +
384B THR* 1.3 69.6 + - - +
385B VAL 4.1 0.3 - - - +
391B GLN* 3.1 19.8 + - - +
394B ARG* 3.8 25.1 + - - +
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 3.8 26.9 - - + -
380B ALA 5.3 2.2 - - - -
381B GLN 4.2 3.3 + - - -
382B LEU 3.1 1.0 + - - -
383B GLU* 1.3 87.3 + - - +
385B VAL* 1.3 64.3 + - - +
386B ASP* 3.3 4.5 + - - +
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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