Contacts of the helix formed by residues 211 - 220 (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 GLU 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C SER* 3.6 7.8 + - - +
207C GLN 4.5 1.6 + - - -
208C VAL 4.0 0.4 + - - -
210C THR* 1.3 87.8 - - + +
212C LEU* 1.3 66.8 + - - +
213C PHE 3.5 1.1 - - - -
214C PRO* 3.5 4.3 - - - +
215C CYS* 3.2 22.3 + - - +
175D ALA* 4.1 1.2 - - + +
176D SER* 2.7 30.6 + - - -
177D TRP* 3.5 15.2 + - + +
207D GLN* 5.1 3.3 - - - +
210D THR* 6.0 0.5 - - - -
211D GLU* 3.8 30.1 + - - +
358D TYR* 2.6 37.1 + - - -
359D PHE* 3.9 17.3 - - + -
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Residues in contact with LEU 212 (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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176C SER* 3.8 27.1 - - - +
179C VAL* 4.3 2.5 - - + -
197C TYR* 3.5 49.8 - - + -
208C VAL* 3.3 35.6 + - + +
211C GLU* 1.3 79.8 - - - +
213C PHE* 1.3 63.3 + - + +
215C CYS* 3.0 6.2 + - + +
216C LEU* 2.9 42.3 + - + +
223C PHE* 3.9 8.3 - - + -
358C TYR* 3.8 22.6 + - + +
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Residues in contact with PHE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C TYR* 3.9 18.4 - + - -
208C VAL* 3.0 44.6 + - + +
209C GLU* 4.0 6.7 - - + +
212C LEU* 1.3 76.9 - - + +
214C PRO* 1.3 69.2 - - + +
216C LEU* 3.3 9.7 + - + +
217C ARG* 3.0 48.7 + - - +
223C PHE* 3.8 41.5 - + + -
305C GLN* 3.2 47.1 - - + -
306C LEU* 4.2 4.0 - - + -
312C ASP* 5.5 1.6 - - - -
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Residues in contact with PRO 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLU 3.4 13.7 - - - +
210C THR 3.5 15.9 - - - +
211C GLU 3.5 11.9 - - - +
213C PHE* 1.3 95.3 - - + +
215C CYS* 1.3 60.7 + - - +
217C ARG* 3.5 22.9 + - + +
218C HIS* 3.2 22.7 + - - +
177D TRP* 4.0 18.3 - - + +
359D PHE* 5.3 7.4 - - + -
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Residues in contact with CYS 215 (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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176C SER* 3.4 28.7 - - - -
179C VAL* 4.2 11.0 - - - -
180C ALA 4.2 7.2 - - - -
211C GLU 3.2 12.6 + - - +
212C LEU* 3.0 11.3 + - + +
214C PRO* 1.3 77.1 - - - +
216C LEU* 1.3 65.6 + - - +
218C HIS* 3.3 1.9 + - - +
219C PHE* 3.1 41.2 + - - -
177D TRP* 3.7 35.3 - - + -
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C VAL* 4.2 10.3 - - + -
197C TYR* 3.8 31.9 - - + -
212C LEU* 2.9 38.7 + - + +
213C PHE* 3.8 10.3 - - + +
215C CYS* 1.3 71.9 - - - +
217C ARG* 1.3 61.5 + - + +
219C PHE 3.6 0.4 - - - +
220C GLY* 2.8 26.5 + - - -
221C LEU* 2.9 47.1 + - + +
223C PHE* 3.6 38.4 - - + -
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Residues in contact with ARG 217 (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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209C GLU 5.3 1.4 + - - -
213C PHE* 3.0 43.2 + - - +
214C PRO* 3.7 32.5 - - - +
216C LEU* 1.3 78.4 - - + +
218C HIS* 1.3 62.8 + - - +
219C PHE 3.5 0.2 + - - -
220C GLY* 3.5 8.5 + - - -
221C LEU 5.1 0.9 - - - -
305C GLN* 3.8 25.9 + - - +
307C GLN* 4.9 12.2 - - - +
310C HIS* 4.9 19.3 + - + +
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Residues in contact with HIS 218 (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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214C PRO 3.2 11.1 + - - +
215C CYS 3.6 7.6 - - - +
216C LEU 3.2 0.4 - - - -
217C ARG* 1.3 81.8 - - - +
219C PHE* 1.3 84.3 + + - +
177D TRP* 3.9 19.5 - + + -
181D GLU* 3.6 30.0 + - - -
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Residues in contact with PHE 219 (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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179C VAL* 5.2 0.2 - - + -
180C ALA* 3.9 34.5 - - + -
183C CYS* 3.4 30.1 - - + -
184C THR* 4.1 9.0 - - - -
187C LYS* 5.9 3.4 - - + -
193C LEU* 4.7 15.3 - - + +
194C PRO 5.0 1.7 - - - +
215C CYS* 3.1 29.5 + - - +
218C HIS* 1.3 100.9 - + - +
220C GLY* 1.3 62.4 + - - +
221C LEU* 3.6 24.3 - - + +
177D TRP* 4.0 11.0 - + - -
181D GLU* 3.8 22.0 - - - -
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Residues in contact with GLY 220 (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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194C PRO 5.0 0.4 - - - +
195C THR* 4.1 15.8 - - - +
216C LEU 2.8 8.6 + - - -
217C ARG* 3.5 7.0 + - - -
218C HIS 3.4 3.8 + - - -
219C PHE* 1.3 79.0 - - - +
221C LEU* 1.3 60.8 + - - -
222C ARG 4.0 1.2 + - - -
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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