Contacts of the helix formed by residues 320 - 332 (chain B) in PDB entry 2BP1
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 SER 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 3.7 15.0 - - - -
56B ALA* 6.3 0.4 - - - -
318B MET* 3.3 10.3 - - - +
319B SER* 1.3 81.8 - - - +
321B LEU* 1.3 62.8 + - - +
322B GLU* 3.8 7.3 + - - +
323B GLN* 3.3 28.7 + - - +
324B LEU 3.1 16.6 + - - -
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Residues in contact with LEU 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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52B MET* 4.1 10.2 - - + +
56B ALA* 5.0 8.0 - - + +
59B ALA* 3.7 24.5 - - + +
60B ALA* 3.5 36.1 - - - +
63B ALA* 4.3 9.4 - - + -
320B SER* 1.3 71.4 - - - +
322B GLU* 1.3 59.9 + - - +
324B LEU* 3.2 7.3 + - + +
325B GLU* 2.9 58.2 + - + +
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Residues in contact with GLU 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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320B SER* 3.3 7.8 + - - +
321B LEU* 1.3 74.3 - - - +
323B GLN* 1.3 66.6 + - + +
325B GLU* 3.4 13.9 + - + +
326B GLN* 3.0 33.0 + - + +
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Residues in contact with GLN 323 (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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237B LYS* 4.2 1.6 - - - +
318B MET* 3.4 5.1 - - + -
319B SER* 2.7 28.7 + - - -
320B SER* 3.3 22.0 + - - +
322B GLU* 1.3 81.2 - - + +
324B LEU* 1.3 56.7 + - - +
326B GLN* 3.3 3.2 + - - +
327B ASN* 2.9 36.6 + - - +
1361B NDP 3.1 79.5 + - + +
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Residues in contact with LEU 324 (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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43B LEU* 3.7 28.0 - - + -
60B ALA* 3.3 46.2 - - + +
63B ALA* 4.5 4.5 - - + -
64B PHE* 4.6 1.6 - - + +
316B LEU* 4.5 13.7 - - + -
317B GLY 5.5 0.4 - - - +
318B MET* 3.8 17.4 - - + +
320B SER 3.1 11.3 + - - +
321B LEU* 3.5 9.6 - - + +
323B GLN* 1.3 80.2 - - - +
325B GLU* 1.3 52.2 + - - +
327B ASN* 3.2 5.1 + - + +
328B LEU* 2.8 66.3 + - + +
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.6 14.9 - - + +
67B ARG* 4.4 4.8 + - - +
321B LEU* 2.9 50.8 + - + +
322B GLU* 3.9 13.3 - - + +
323B GLN 3.3 0.2 - - - -
324B LEU* 1.3 72.7 - - + +
326B GLN* 1.3 66.2 + - - +
328B LEU* 3.5 9.3 + - + +
329B ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 326 (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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291B SER* 4.5 10.9 + - - -
293B THR* 4.1 21.1 + - + -
322B GLU* 3.0 24.9 + - + +
323B GLN* 3.5 4.5 - - - +
325B GLU* 1.3 76.9 - - - +
327B ASN* 1.3 62.5 + - - +
329B ALA* 3.3 8.5 + - - +
330B ALA* 3.2 19.6 + - - +
1361B NDP 3.4 29.9 + - - +
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Residues in contact with ASN 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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229B LEU* 4.0 6.6 - - - +
293B THR* 3.8 9.6 - - - +
297B LEU* 3.8 21.2 - - + +
316B LEU* 4.6 13.8 - - + +
317B GLY 3.0 21.0 + - - +
323B GLN 2.9 14.8 + - - +
324B LEU* 3.2 6.9 + - + +
326B GLN* 1.3 75.6 - - - +
328B LEU* 1.3 61.4 + - - +
330B ALA* 3.1 13.8 + - - +
331B THR* 3.1 18.9 + - - +
1361B NDP 2.8 49.1 + - - -
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Residues in contact with LEU 328 (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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63B ALA* 4.0 31.0 - - + +
64B PHE* 4.2 10.3 - - + +
67B ARG* 4.0 24.0 - - + +
69B HIS* 4.1 27.6 - - + +
316B LEU* 4.0 19.0 - - + +
324B LEU* 2.8 45.6 + - + +
325B GLU* 3.8 8.7 - - + +
327B ASN* 1.3 73.0 - - - +
329B ALA* 1.3 60.0 + - - +
331B THR* 2.7 26.3 + - - +
332B GLU* 3.3 10.9 - - - +
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Residues in contact with ALA 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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67B ARG* 3.9 16.2 - - - +
325B GLU 3.1 12.7 + - - +
326B GLN* 3.5 11.7 - - - +
327B ASN 3.3 0.2 - - - -
328B LEU* 1.3 76.2 - - - +
330B ALA* 1.3 62.1 + - - +
332B GLU* 3.1 18.3 + - - +
333B GLU* 3.4 21.3 + - - +
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Residues in contact with ALA 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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293B THR* 5.9 0.7 - - + -
294B SER* 3.8 35.0 - - - +
297B LEU* 4.0 17.0 - - + -
298B ARG* 3.5 19.9 - - - +
302B HIS* 5.5 0.2 + - - -
326B GLN 3.2 8.0 + - - +
327B ASN* 3.1 10.8 + - - +
329B ALA* 1.3 78.6 - - - +
331B THR* 1.3 61.2 + - - +
333B GLU* 3.0 22.3 + - - +
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Residues in contact with THR 331 (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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41B SER* 4.2 5.8 - - - +
69B HIS* 4.5 9.2 + - - -
297B LEU* 5.2 1.6 - - + -
301B TYR* 3.3 53.8 - - + +
302B HIS* 4.7 5.7 + - - -
316B LEU* 4.1 20.4 - - + -
327B ASN 3.1 15.0 + - - +
328B LEU* 2.7 19.3 + - + +
330B ALA* 1.3 75.7 - - - +
332B GLU* 1.3 69.6 + - - +
333B GLU 3.6 5.7 + - - +
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Residues in contact with GLU 332 (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 ARG* 3.3 43.4 + - - +
69B HIS* 4.5 11.1 + - - -
328B LEU 3.3 14.7 - - - +
329B ALA* 3.1 7.8 + - - +
330B ALA 3.1 0.8 - - - -
331B THR* 1.3 86.2 + - - +
333B GLU* 1.3 62.9 + - - +
334B GLY 4.0 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