Contacts of the helix formed by residues 219 - 223 (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 GLY 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B CYS* 4.4 11.1 - - - +
194B PRO 3.9 12.5 - - - +
195B VAL* 4.1 8.8 - - - +
218B VAL* 1.3 74.8 - - - +
220B LEU* 1.3 62.1 + - - +
221B ASP* 2.9 9.6 + - - +
222B GLY* 3.2 12.5 + - - -
223B VAL* 5.0 0.2 - - - +
160C SER* 4.3 9.2 + - - -
164C SER* 3.9 9.6 - - - -
324C ASN* 4.1 16.4 - - - +
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Residues in contact with LEU 220 (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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114B LEU* 5.2 8.3 - - + -
195B VAL* 3.8 31.6 - - + -
217B LEU* 3.4 37.9 + - + +
218B VAL 3.5 2.4 - - - -
219B GLY* 1.3 79.1 - - - +
221B ASP* 1.3 59.8 + - - +
222B GLY 3.0 3.2 + - - -
223B VAL* 3.1 29.8 + - + +
224B LEU* 4.4 0.5 - - - +
274B GLN* 4.3 16.2 - - + +
275B PRO* 3.4 25.7 - - + +
276B PHE* 3.7 21.8 - - + +
278B LEU* 4.3 12.8 - - + -
291B TRP* 5.1 4.5 - - + -
296B THR* 5.6 1.8 - - + -
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Residues in contact with ASP 221 (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 2.9 1.7 + - - -
220B LEU* 1.3 77.9 - - - +
222B GLY* 1.3 57.2 + - - +
223B VAL 3.1 3.9 + - - -
224B LEU* 3.4 36.3 + - - +
273B GLY 4.1 0.2 - - - +
275B PRO* 3.5 17.8 - - - +
364B CA 2.3 31.2 - - - -
160C SER 4.5 3.4 - - - +
161C ASP* 3.0 36.2 - - - +
324C ASN* 4.4 4.7 - - - +
326C ASN* 3.1 20.2 + - - +
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Residues in contact with GLY 222 (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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191B TRP* 2.7 31.7 + - - -
193B CYS* 3.2 11.9 - - - -
219B GLY 3.2 9.0 + - - -
220B LEU 3.0 2.2 - - - -
221B ASP* 1.3 75.8 - - - +
223B VAL* 1.3 54.8 + - - +
224B LEU 3.3 0.9 - - - -
225B ALA 3.4 7.0 - - - +
324C ASN* 4.7 1.5 - - - +
325C PRO* 3.7 18.0 - - - +
326C ASN* 3.1 17.5 + - - -
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Residues in contact with VAL 223 (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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112B PHE* 4.1 11.4 - - + -
114B LEU* 4.2 16.2 - - + -
133B PHE* 3.1 18.6 - - - -
134B PRO* 4.4 7.4 - - + -
140B PHE* 4.8 0.9 - - + -
191B TRP* 3.1 19.5 - - - +
193B CYS* 4.8 5.2 - - + -
195B VAL* 5.8 0.2 - - + -
219B GLY 5.0 0.7 - - - +
220B LEU* 3.3 29.8 - - + +
221B ASP 3.1 1.0 - - - -
222B GLY* 1.3 82.2 - - - +
224B LEU* 1.3 57.9 + - - +
225B ALA 3.1 2.6 + - - -
276B PHE* 3.8 24.9 - - + -
296B THR* 5.3 2.7 - - + -
298B VAL* 4.1 31.4 - - + -
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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