Contacts of the helix formed by residues 341 - 353 (chain B) in PDB entry 2BBV
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 GLU 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B CYS* 3.7 12.7 - - - -
340B ASP* 1.3 74.2 + - - +
342B VAL* 1.3 63.2 + - + +
344B LEU* 3.7 4.2 + - - +
345B GLN* 3.2 24.0 + - - +
87C ARG* 2.5 42.9 + - - -
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Residues in contact with VAL 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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58B ARG* 4.2 46.9 - - + +
59B LEU* 3.9 21.1 - - + -
340B ASP* 3.0 5.3 + - - +
341B GLU* 1.3 80.8 - - + +
343B ALA* 1.3 55.5 + - - +
345B GLN* 3.2 4.2 + - - +
346B GLU* 2.8 46.6 + - + +
378E LEU* 4.6 11.7 - - + -
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Residues in contact with ALA 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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59B LEU* 3.3 13.6 - - + +
63B GLY* 3.5 24.9 - - - +
66B PHE* 4.4 3.1 - - + -
67B LEU* 4.0 4.3 - - + +
85B PRO* 4.2 8.1 - - + -
340B ASP* 2.7 38.8 + - + +
342B VAL* 1.3 73.2 - - - +
344B LEU* 1.3 57.4 + - - +
346B GLU* 3.7 2.2 - - - +
347B TYR* 2.8 33.9 + - - +
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Residues in contact with LEU 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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66B PHE* 4.2 20.0 - - + -
84B ILE* 5.1 0.7 - - + -
85B PRO* 3.6 29.2 - - + +
86B ASP* 3.8 20.6 - - + +
250B PHE* 4.5 18.6 - - + -
339B CYS* 4.1 16.2 - - - -
340B ASP 2.9 15.8 + - - +
341B GLU* 3.8 9.0 - - - +
343B ALA* 1.3 79.6 - - - +
345B GLN* 1.3 60.3 + - - +
347B TYR* 3.6 12.4 - - + +
348B ARG* 3.8 15.6 + - - +
87C ARG* 4.4 29.6 + - - +
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Residues in contact with GLN 345 (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 GLU* 3.2 17.2 + - - +
342B VAL* 3.8 4.5 - - - +
343B ALA 3.2 0.4 - - - -
344B LEU* 1.3 72.9 + - - +
346B GLU* 1.3 63.6 + - - +
347B TYR 2.9 9.5 + - - -
348B ARG* 3.0 21.0 + - - +
349B THR* 3.2 22.7 + - + +
87C ARG* 3.6 27.1 + - - +
89C GLU* 3.5 22.4 + - - -
338C PRO* 5.6 1.4 - - - +
339C CYS* 4.0 20.6 - - - +
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.8 1.6 - - + -
67B LEU* 3.9 16.8 - - + +
342B VAL* 2.8 33.9 + - + +
343B ALA 3.8 3.6 - - - +
345B GLN* 1.3 77.0 - - - +
347B TYR* 1.3 56.4 + - - +
348B ARG 3.4 0.2 - - - -
349B THR* 4.0 12.5 + - - +
350B VAL* 3.0 34.5 + - - +
374E ILE* 3.3 47.0 - - + +
377E SER* 3.9 22.1 + - - +
378E LEU* 4.5 13.2 - - + +
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Residues in contact with TYR 347 (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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66B PHE* 3.4 31.2 - + + -
67B LEU* 3.7 11.9 - - + -
70B ALA* 4.2 11.4 - - + -
71B PHE* 3.4 30.0 - + - -
169B ALA 4.9 6.0 + - - -
244B VAL* 3.6 20.3 - - + +
245B CYS* 3.0 29.3 + - + +
250B PHE* 3.7 23.7 - + - -
294B MET* 4.6 2.1 - - - +
343B ALA 2.8 17.8 + - - +
344B LEU* 3.6 7.0 - - - +
345B GLN 2.9 0.2 - - - -
346B GLU* 1.3 78.3 - - - +
348B ARG* 1.3 91.4 + - - +
351B ALA* 3.0 30.1 + - - +
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Residues in contact with ARG 348 (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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244B VAL* 5.2 2.8 - - - +
245B CYS* 3.1 26.8 + - - +
247B GLU 2.2 37.9 + - - +
248B PRO* 3.4 16.8 + - - +
250B PHE* 3.8 24.7 - - - -
344B LEU 4.0 7.9 + - - +
345B GLN* 3.0 22.6 + - - +
347B TYR* 1.3 101.3 - - - +
349B THR* 1.3 58.3 + - - +
351B ALA* 3.5 4.8 + - - +
352B ARG* 3.2 26.9 + - - +
87C ARG* 3.0 32.9 + - + +
88C PHE* 4.4 8.5 - - - +
89C GLU* 3.8 20.1 - - + +
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Residues in contact with THR 349 (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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345B GLN* 3.2 31.4 + - + +
346B GLU* 4.1 15.3 + - - +
348B ARG* 1.3 74.3 - - - +
350B VAL* 1.3 64.8 + - - +
351B ALA 3.1 0.2 - - - -
352B ARG* 3.3 34.8 - - - +
353B SER* 2.8 34.7 + - - -
89C GLU* 4.1 1.8 - - - +
338C PRO* 6.1 1.1 - - + -
373E ILE* 4.8 4.3 - - - +
377E SER* 4.0 18.1 + - - +
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Residues in contact with VAL 350 (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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67B LEU* 5.8 0.7 - - + -
71B PHE* 3.6 35.7 - - + -
346B GLU* 3.0 25.6 + - - +
347B TYR 4.1 1.8 - - - +
349B THR* 1.3 77.6 + - - +
351B ALA* 1.3 63.4 + - - +
353B SER* 3.1 9.5 + - - -
354B LEU* 3.2 28.9 + - + +
370E VAL* 4.1 15.9 - - + +
373E ILE* 3.8 28.7 - - + +
374E ILE* 3.8 27.4 - - + -
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.1 8.5 - - + -
244B VAL* 3.7 37.9 - - + -
347B TYR* 3.0 21.7 + - + +
348B ARG* 3.6 7.9 - - + +
349B THR 3.1 0.2 - - - -
350B VAL* 1.3 80.9 - - - +
352B ARG* 1.3 60.2 + - - +
353B SER 3.4 0.3 + - - -
354B LEU* 3.6 16.2 + - - +
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Residues in contact with ARG 352 (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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348B ARG 3.2 15.7 + - - +
349B THR* 3.3 35.6 + - - +
351B ALA* 1.3 75.0 - - - +
353B SER* 1.3 65.1 + - - +
354B LEU 3.5 4.2 - - - +
89C GLU* 2.5 55.8 + - - +
335C ASP* 4.4 23.5 - - - +
338C PRO* 4.7 11.7 - - - +
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Residues in contact with SER 353 (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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349B THR* 2.8 21.2 + - - -
350B VAL 3.1 1.7 + - - -
352B ARG* 1.3 87.4 + - - +
354B LEU* 1.3 60.9 + - - +
355B PRO* 4.4 1.6 - - - +
373E ILE* 3.3 37.4 - - - +
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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