Contacts of the helix formed by residues 206 - 210 (chain D) 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 ARG 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D TYR* 4.1 9.6 - - + -
202D ASN 3.7 9.4 - - - +
203D ALA 2.9 24.4 + - - -
205D THR* 1.3 77.3 - - - +
207D GLN* 1.3 66.5 + - - +
208D VAL 3.1 2.7 - - - -
209D GLU* 3.0 49.1 + - - +
210D THR* 4.4 2.1 + - - -
299D TRP* 3.3 29.7 - - - +
344D PHE* 3.1 22.2 + - - +
345D ASN* 3.1 31.7 + - - +
348D TRP* 3.4 52.9 - - + +
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Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C THR* 3.6 19.5 + - + +
211C GLU* 5.1 2.6 - - - +
200D MET 5.9 0.2 + - - -
205D THR* 3.7 2.4 - - + +
206D ARG* 1.3 77.0 - - - +
208D VAL* 1.3 62.6 + - - +
209D GLU 3.1 1.0 + - - -
210D THR* 3.4 19.0 + - - -
211D GLU 4.6 1.0 + - - -
348D TRP* 3.9 7.5 - - + -
355D CYS* 3.8 26.3 + - + +
356D PRO 4.0 5.0 + - - +
357D ASN* 3.1 27.5 + - - +
358D TYR* 2.9 52.7 + - + +
359D PHE* 3.9 2.3 - - - -
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D GLY* 5.2 0.4 - - - -
200D MET 3.6 17.2 + - - +
201D TYR* 3.5 31.0 - - + -
206D ARG 4.4 0.9 - - - -
207D GLN* 1.3 76.3 - - - +
209D GLU* 1.3 61.6 + - - +
210D THR 3.3 0.2 - - - -
212D LEU* 3.2 26.0 + - + -
213D PHE* 3.0 52.0 + - + -
223D PHE* 4.3 5.6 - - + -
358D TYR* 3.5 38.6 - - + -
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Residues in contact with GLU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TYR* 2.4 37.4 + - + +
206D ARG* 3.0 40.9 + - - +
208D VAL* 1.3 77.4 - - - +
210D THR* 1.3 65.3 + - - +
213D PHE* 4.2 10.8 - - + +
214D PRO* 3.6 14.2 - - - +
217D ARG* 5.4 0.5 + - - -
299D TRP* 4.2 3.6 - - - -
304D SER* 5.2 0.2 - - - -
305D GLN* 3.3 34.7 + - + +
348D TRP* 5.4 1.6 + - - -
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Residues in contact with THR 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C GLN* 3.7 24.0 + - + +
211C GLU* 6.0 0.4 - - - -
357C ASN* 4.0 4.7 - - - +
359C PHE* 3.5 35.9 - - + -
206D ARG 4.9 2.1 + - - -
207D GLN* 3.4 12.8 + - - -
208D VAL 3.3 1.2 - - - -
209D GLU* 1.3 81.2 - - - +
211D GLU* 1.3 64.4 + - + +
214D PRO* 3.5 11.7 - - - +
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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