Contacts of the helix formed by residues 403 - 414 (chain B) in PDB entry 1BO1
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 TYR 403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B LYS* 2.7 42.8 + - - +
219B GLY 4.6 0.7 - - - -
220B SER* 4.2 3.2 - - - -
278B ASP* 3.3 26.7 + - + +
279B TYR* 2.8 60.6 + + - +
398B VAL* 5.4 3.3 - - + +
399B ASN 4.3 0.4 + - - -
400B PRO* 2.9 33.4 + - + +
402B GLN* 1.3 76.5 - - - +
404B SER* 1.3 57.9 + - - +
406B ARG* 3.4 38.6 - - - +
407B PHE* 2.8 37.3 + + + +
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Residues in contact with SER 404 (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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268B VAL* 3.1 37.7 + - - +
269B GLU* 5.4 1.1 - - - -
272B ALA* 3.1 30.0 - - - +
279B TYR* 3.5 3.6 + - - -
400B PRO 4.0 3.5 + - - -
401B GLU* 3.3 13.7 + - - -
402B GLN 3.1 0.2 - - - -
403B TYR* 1.3 80.4 - - - +
405B LYS* 1.3 65.0 + - - +
408B ASN* 3.0 22.7 + - - +
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Residues in contact with LYS 405 (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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401B GLU 4.7 0.4 + - - +
402B GLN* 3.8 9.4 + - - +
404B SER* 1.3 79.8 - - - +
406B ARG* 1.3 57.7 + - - +
408B ASN* 4.1 4.7 - - - +
409B GLU* 3.0 30.8 + - - +
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Residues in contact with ARG 406 (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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219B GLY 3.1 18.1 + - - +
220B SER* 3.1 32.3 - - - +
221B THR* 2.8 47.8 + - - +
278B ASP* 5.9 0.4 + - - -
398B VAL* 4.4 29.8 + - - +
402B GLN 3.5 11.2 + - - +
403B TYR* 3.4 31.1 + - - +
404B SER 3.1 0.2 - - - -
405B LYS* 1.3 77.3 - - - +
407B PHE* 1.3 60.5 + - - +
409B GLU* 3.2 5.3 + - - +
410B PHE* 2.8 31.0 + - + +
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Residues in contact with PHE 407 (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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217B LEU 3.6 7.9 - - - -
218B LYS 3.6 17.9 - - - +
219B GLY* 4.8 4.7 - - - -
264B LEU* 3.4 25.6 - - + -
268B VAL* 3.6 20.4 - - + -
279B TYR* 3.6 29.2 - + + +
280B SER* 3.5 12.6 - - - -
281B LEU* 3.3 45.3 - - + -
367B ILE* 4.2 7.0 - - + -
403B TYR* 2.8 24.1 + + + +
404B SER 3.5 3.8 - - - +
406B ARG* 1.3 72.0 - - - +
408B ASN* 1.3 60.8 + - - +
410B PHE* 3.6 1.5 + - - -
411B MET* 2.9 48.1 + - + +
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Residues in contact with ASN 408 (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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261B LEU* 4.1 7.2 + - - +
264B LEU* 3.4 24.8 + - + +
265B LYS* 3.4 40.6 - - - +
268B VAL* 5.0 4.0 - - + +
404B SER 3.0 16.1 + - - +
405B LYS* 4.1 4.7 - - - +
407B PHE* 1.3 77.4 - - - +
409B GLU* 1.3 54.7 + - - +
411B MET* 3.6 1.0 - - - +
412B SER* 2.6 39.2 + - - -
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Residues in contact with GLU 409 (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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405B LYS 3.0 21.0 + - - +
406B ARG* 3.7 6.3 - - - +
408B ASN* 1.3 73.6 - - - +
410B PHE* 1.3 65.1 + - - +
412B SER* 3.5 10.5 + - - -
413B ASN* 3.1 33.1 + - - +
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Residues in contact with PHE 410 (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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217B LEU* 4.0 16.6 - - + -
219B GLY* 3.8 22.9 - - - +
220B SER 5.5 2.0 - - - -
240B ASP* 3.1 47.1 - - + -
241B ASN* 5.4 0.7 - - - -
243B PHE* 4.4 5.6 - + - -
244B LEU* 4.2 31.6 - - + -
406B ARG* 2.8 16.3 + - + +
407B PHE 3.9 4.3 - - - +
409B GLU* 1.3 78.3 - - - +
411B MET* 1.3 79.6 + - + +
413B ASN* 3.2 15.0 + - - +
414B ILE* 3.6 18.4 + - + +
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Residues in contact with MET 411 (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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217B LEU* 3.4 33.7 - - + +
219B GLY* 4.0 4.7 - - - -
260B PHE* 5.3 5.1 - - + -
261B LEU* 3.9 9.4 - - + +
264B LEU* 3.7 17.3 - - + -
281B LEU* 4.0 18.4 - - + -
407B PHE* 2.9 55.3 + - + +
410B PHE* 1.3 95.7 - - + +
412B SER* 1.3 63.6 + - - +
413B ASN 3.1 1.2 + - - -
414B ILE* 3.2 42.5 + - + +
415B LEU* 4.0 6.6 + - - +
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Residues in contact with SER 412 (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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257B LYS* 4.3 11.6 + - - -
261B LEU* 3.8 28.9 - - - +
408B ASN* 2.6 32.3 + - - -
409B GLU* 3.6 15.7 - - - -
410B PHE 3.1 0.4 - - - -
411B MET* 1.3 74.9 - - - +
413B ASN* 1.3 64.1 + - - +
415B LEU 4.5 0.9 + - - +
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Residues in contact with ASN 413 (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 LEU* 6.6 0.2 - - + -
409B GLU* 3.1 28.3 + - - +
410B PHE* 3.2 8.3 + - - +
411B MET 3.1 0.8 - - - -
412B SER* 1.3 82.2 + - - +
414B ILE* 1.3 65.5 + - - +
415B LEU 3.4 7.6 + - - +
416B THR* 4.9 3.3 - - - +
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Residues in contact with ILE 414 (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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217B LEU* 3.7 20.0 - - + -
243B PHE* 3.2 35.7 - - + -
248B GLN 4.4 8.0 - - - +
250B LEU* 3.6 30.8 + - + +
260B PHE* 6.4 1.6 - - + -
281B LEU* 4.4 6.7 - - + -
283B VAL* 5.5 1.3 - - + -
365B MET* 5.8 3.4 - - - -
410B PHE* 3.7 9.2 - - + +
411B MET* 3.2 49.5 + - + +
413B ASN* 1.3 81.3 - - - +
415B LEU* 1.3 68.3 + - + +
416B THR* 4.3 5.2 + - - +
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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