Contacts of the helix formed by residues 318 - 331 (chain B) in PDB entry 2BAP
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 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B ALA* 3.5 1.2 - - - +
317B GLU* 1.3 81.6 - - + +
319B LEU* 1.3 58.3 + - - +
320B ASP* 3.1 22.1 - - + +
321B PHE* 2.7 48.9 + - + +
322B ARG* 3.5 5.6 + - - +
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Residues in contact with LEU 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 GLU 3.3 6.5 + - - -
318B GLU* 1.3 70.4 - - - +
320B ASP* 1.3 60.5 + - - +
322B ARG* 3.3 19.5 + - - +
323B VAL* 3.1 25.4 + - + +
363B ASP* 3.7 43.7 - - + +
366B ASP* 3.7 29.8 - - + +
367B LEU* 4.1 23.6 - - + -
370B ARG* 3.5 28.5 - - - +
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 2.9 18.3 + - + +
319B LEU* 1.3 74.8 - - - +
321B PHE* 1.3 64.4 + - - +
323B VAL* 3.7 11.9 - - - +
324B HIS* 3.1 25.5 + - - +
367B LEU* 5.2 0.5 - - - +
370B ARG* 3.1 31.3 + - - +
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Residues in contact with PHE 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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267B ASN* 3.7 20.0 - - - -
268B GLU* 3.4 37.0 - - + -
271B LEU* 4.3 14.1 - - + -
312B LEU 4.2 7.6 - - - -
313B ILE* 5.7 1.6 - - - -
316B ALA* 3.7 26.9 - - + -
318B GLU* 2.7 36.5 + - + +
320B ASP* 1.3 73.4 - - - +
322B ARG* 1.3 63.1 + - - +
324B HIS* 3.2 18.7 - - - +
325B ILE* 3.2 31.9 + - + +
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Residues in contact with ARG 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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313B ILE* 3.8 29.8 + - + +
314B THR 5.7 2.0 + - - -
316B ALA* 3.0 23.2 + - + +
317B GLU* 2.9 35.6 + - - +
318B GLU 3.9 2.7 - - - +
319B LEU* 3.3 25.5 + - - +
321B PHE* 1.3 78.9 - - + +
323B VAL* 1.3 58.1 + - - +
324B HIS 3.3 0.2 + - - -
325B ILE* 3.4 5.4 + - - +
326B ARG* 2.8 34.0 + - - +
359B GLN* 4.2 18.4 + - - -
363B ASP* 3.3 38.9 + - - +
366B ASP* 5.3 5.9 + - - -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.1 21.7 + - + +
320B ASP* 3.7 18.8 - - - +
322B ARG* 1.3 76.1 - - - +
324B HIS* 1.3 62.7 + - - +
326B ARG* 4.1 19.2 - - + +
327B SER* 2.7 36.6 + - - +
363B ASP* 5.5 2.9 - - + -
367B LEU* 4.0 23.8 - - + -
433B VAL* 3.6 23.8 - - + +
434B LEU 5.2 4.3 - - - +
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Residues in contact with HIS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 4.3 11.8 + - - -
320B ASP 3.1 22.1 + - - +
321B PHE* 3.2 9.3 - - - +
323B VAL* 1.3 76.9 - - - +
325B ILE* 1.3 67.7 + - + +
327B SER* 3.1 7.7 + - - -
328B GLU* 2.7 43.3 + - + -
331B ARG* 5.3 4.9 + - - -
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Residues in contact with ILE 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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271B LEU* 3.9 21.3 - - + -
285B ARG* 3.9 23.1 - - - +
286B PHE* 4.4 11.9 - - + -
309B ILE* 5.9 0.2 - - + -
312B LEU* 5.3 8.1 - - + +
313B ILE* 3.8 28.9 - - + -
321B PHE* 3.2 38.7 + - + +
322B ARG 3.9 1.6 - - - +
324B HIS* 1.3 87.3 - - + +
326B ARG* 1.3 68.6 + - - +
328B GLU* 3.1 8.5 + - - +
329B LEU* 3.0 33.1 + - + +
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Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.3 21.7 - - + +
322B ARG 2.8 31.5 + - - +
323B VAL* 4.0 14.6 - - + +
325B ILE* 1.3 74.7 - - - +
327B SER* 1.3 65.5 + - - +
329B LEU* 3.3 13.3 + - - +
330B MET* 3.2 32.8 + - + +
334B LEU* 4.9 0.2 - - - +
356B PHE* 4.5 24.2 + - + -
359B GLN* 3.4 27.3 + - - +
360B GLY* 3.6 19.1 + - - +
363B ASP* 2.4 39.2 + - - +
434B LEU 5.5 5.8 - - - -
435B HIS 5.5 7.2 - - - +
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Residues in contact with SER 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 VAL* 2.7 28.9 + - - +
324B HIS* 3.1 5.2 + - - -
326B ARG* 1.3 77.1 - - - +
328B GLU* 1.3 68.0 + - - +
330B MET* 3.0 18.8 + - - +
331B ARG* 3.3 30.0 + - - +
432B ILE* 3.5 25.6 + - - -
433B VAL 5.4 0.2 - - - -
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 4.0 25.0 - - - +
285B ARG* 3.6 36.2 + - - +
286B PHE* 3.3 31.5 - - + +
324B HIS* 2.7 28.5 + - + +
325B ILE* 3.1 12.8 + - - +
327B SER* 1.3 72.8 - - - +
329B LEU* 1.3 61.5 + - - +
331B ARG* 3.4 35.3 + - - +
332B LEU* 4.2 7.8 - - - +
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Residues in contact with LEU 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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286B PHE* 3.5 35.0 - - + -
289B LEU* 4.9 3.4 - - + -
290B LEU* 4.2 14.3 - - + +
309B ILE* 3.9 40.2 - - + -
312B LEU* 6.5 0.2 - - + -
313B ILE* 4.9 1.3 - - + -
325B ILE* 3.0 31.6 + - + +
326B ARG* 3.6 9.9 - - - +
328B GLU* 1.3 74.3 - - - +
330B MET* 1.3 53.6 + - - +
331B ARG 2.7 16.7 + - - -
332B LEU* 3.0 23.2 + - - +
333B GLY 3.5 4.7 + - - -
334B LEU* 3.8 30.9 + - + +
356B PHE* 5.5 0.7 - - + -
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Residues in contact with MET 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 ARG* 3.2 21.9 + - + +
327B SER* 3.0 10.1 + - - +
329B LEU* 1.3 75.6 - - - +
331B ARG* 1.3 60.6 + - - +
332B LEU 3.5 0.2 - - - -
333B GLY* 3.6 11.7 + - - -
334B LEU* 3.6 35.0 - - + +
335B HIS* 3.4 46.2 + - + +
336B GLN 5.7 0.2 + - - -
338B LEU* 4.9 9.6 - - + -
356B PHE* 5.0 7.2 - - + -
435B HIS 4.4 17.7 - - - +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B HIS* 5.3 4.6 + - - -
327B SER* 3.3 30.2 + - - +
328B GLU* 3.4 34.2 + - - +
329B LEU 2.7 5.7 + - - -
330B MET* 1.3 73.9 - - - +
332B LEU* 1.3 62.0 + - + +
333B GLY* 3.0 5.7 + - - -
432B ILE* 5.6 11.1 - - + +
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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