Contacts of the helix formed by residues 320 - 332 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C MET* 4.2 8.5 - - - -
56C ALA* 6.4 0.2 - - - -
318C MET* 3.3 15.5 - - - +
319C SER* 1.3 81.5 + - - +
321C LEU* 1.3 60.1 + - - +
322C GLU* 3.5 7.7 + - - +
323C GLN* 3.2 30.9 + - - +
324C LEU 3.1 20.6 + - - -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C MET* 4.4 7.3 - - + +
56C ALA* 5.0 9.4 - - + +
59C ALA* 3.7 22.9 - - + +
60C ALA* 3.6 34.5 - - - +
63C ALA* 4.3 12.8 - - + -
320C SER* 1.3 72.0 - - - +
322C GLU* 1.3 60.4 + - - +
324C LEU* 3.3 7.7 + - + +
325C GLU* 2.9 30.9 + - + +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C SER* 3.3 8.6 + - - +
321C LEU* 1.3 75.3 - - - +
323C GLN* 1.3 60.2 + - + +
325C GLU* 3.3 5.9 + - - +
326C GLN* 2.9 31.0 + - - +
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Residues in contact with GLN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LYS* 4.0 3.0 - - - +
318C MET* 3.5 3.5 - - + -
319C SER* 2.7 36.8 + - - -
320C SER* 3.2 20.3 + - - +
322C GLU* 1.3 81.0 - - + +
324C LEU* 1.3 62.4 + - - +
326C GLN* 3.4 2.6 + - - +
327C ASN* 2.9 30.5 + - - +
1361C NDP 2.8 81.4 + - + +
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.6 28.5 - - + -
60C ALA* 3.5 43.7 - - + +
63C ALA* 4.5 4.5 - - + -
64C PHE* 4.7 1.1 - - + -
316C LEU* 4.4 18.2 - - + -
317C GLY 5.3 0.2 - - - +
318C MET* 3.8 19.4 - - + +
320C SER 3.1 11.2 + - - +
321C LEU* 3.6 9.4 - - + +
322C GLU 3.3 0.2 - - - -
323C GLN* 1.3 80.7 - - - +
325C GLU* 1.3 57.2 + - - +
327C ASN* 3.1 6.1 + - + +
328C LEU* 2.8 52.8 + - + +
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Residues in contact with GLU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ALA* 6.0 0.2 - - - -
67C ARG* 4.1 7.9 + - - +
321C LEU* 2.9 20.9 + - + +
322C GLU* 3.3 6.3 + - - +
324C LEU* 1.3 73.4 - - - +
326C GLN* 1.3 67.2 + - - +
328C LEU* 3.5 11.9 + - - +
329C ALA* 3.1 23.0 + - - +
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C SER* 3.7 25.3 + - - -
293C THR* 3.9 17.4 + - + +
294C SER* 5.1 1.4 - - - +
322C GLU 2.9 17.5 + - - +
323C GLN* 3.6 4.7 - - - +
325C GLU* 1.3 76.5 - - - +
327C ASN* 1.3 61.7 + - - +
329C ALA* 3.3 9.8 + - + +
330C ALA* 3.2 19.4 + - - +
1361C NDP 3.0 26.6 + - - +
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Residues in contact with ASN 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C LEU* 4.2 5.2 - - - +
293C THR* 3.7 13.0 - - - +
297C LEU* 3.8 20.4 - - + +
316C LEU* 4.6 13.7 - - + +
317C GLY 2.9 29.1 + - - +
323C GLN 2.9 17.7 + - - +
324C LEU* 3.6 6.0 - - + +
326C GLN* 1.3 74.5 - - - +
328C LEU* 1.3 64.4 + - - +
330C ALA* 3.2 13.7 + - - +
331C THR* 3.2 20.0 + - - +
1361C NDP 3.0 40.5 + - - -
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ALA* 4.0 31.9 - - + +
64C PHE* 4.2 9.4 - - + +
67C ARG* 4.0 25.4 - - + +
69C HIS* 4.1 28.9 - - + +
316C LEU* 3.9 19.3 - - + -
324C LEU* 2.8 45.1 + - + +
325C GLU* 3.8 7.6 - - - +
327C ASN* 1.3 72.3 - - - +
329C ALA* 1.3 63.3 + - - +
331C THR* 2.7 25.6 + - - +
332C GLU* 3.5 11.3 + - - +
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ARG* 3.9 15.3 - - - +
325C GLU 3.1 13.2 + - - +
326C GLN* 3.4 13.0 - - + +
327C ASN 3.3 0.2 - - - -
328C LEU* 1.3 76.5 - - - +
330C ALA* 1.3 61.1 + - - +
332C GLU* 3.2 14.9 + - - +
333C GLU* 3.4 19.4 + - - +
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Residues in contact with ALA 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C THR* 5.8 1.1 - - + -
294C SER* 3.8 32.5 - - - +
297C LEU* 4.0 17.3 - - + -
298C ARG* 3.5 12.6 - - - +
326C GLN 3.2 7.8 + - - +
327C ASN* 3.2 11.2 + - - +
329C ALA* 1.3 78.2 - - - +
331C THR* 1.3 58.3 + - - +
333C GLU* 3.0 36.3 + - - +
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Residues in contact with THR 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C SER* 4.1 8.3 + - - +
69C HIS* 4.6 10.0 + - - -
297C LEU* 5.2 2.0 - - + -
301C TYR* 3.5 56.1 - - + +
302C HIS* 5.0 3.1 + - - -
316C LEU* 3.9 15.7 - - + -
327C ASN 3.2 17.2 + - - +
328C LEU* 2.7 22.2 + - - +
330C ALA* 1.3 76.7 - - - +
332C GLU* 1.3 67.0 + - - +
333C GLU 3.8 5.2 + - - +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 2.8 56.6 + - - +
69C HIS* 4.8 4.5 + - + +
328C LEU* 3.7 4.0 - - - +
329C ALA* 3.2 9.7 + - - +
330C ALA 3.1 0.8 - - - -
331C THR* 1.3 87.9 + - - +
333C GLU* 1.3 63.0 + - - +
334C GLY 4.1 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