Contacts of the helix formed by residues 207 - 219 (chain C) in PDB entry 4BVH
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 ASN 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C ILE 2.9 23.8 + - - -
151C PRO* 3.6 27.4 - - + +
152C SER* 2.9 24.4 + - - +
206C PRO* 1.3 73.8 - - - +
208C VAL* 1.3 67.6 + - + +
209C THR* 2.8 38.8 + - - -
210C HIS* 2.9 21.4 + - - +
211C TYR* 3.0 19.1 + - - -
367C VAL* 3.9 7.0 - - + +
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Residues in contact with VAL 208 (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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207C ASN* 1.3 75.0 - - - +
209C THR* 1.3 62.7 + - - +
211C TYR* 3.7 7.4 - - - +
212C PHE* 2.9 23.4 + - - +
367C VAL* 4.3 16.8 - - + +
370C VAL* 4.0 15.5 - - + -
371C GLU* 4.0 36.1 - - + +
374C VAL* 6.0 0.4 - - + -
383C MET* 4.2 15.1 - - + +
387C VAL* 4.4 21.5 - - + -
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Residues in contact with THR 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ILE* 3.7 39.3 + - + -
207C ASN* 2.8 21.5 + - - -
208C VAL* 1.3 79.1 - - - +
210C HIS* 1.3 64.1 + - - +
212C PHE* 3.3 9.5 + - - +
213C LEU* 3.3 18.7 + - + +
318C LEU* 3.8 23.6 - - + -
366C VAL* 4.0 15.8 - - + +
367C VAL* 4.0 12.6 - - - +
370C VAL* 4.3 13.8 - - + +
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Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ILE* 3.4 36.9 - - + +
149C SER* 3.5 16.7 + - - -
206C PRO* 3.5 18.6 - - + +
207C ASN* 2.9 43.2 + - - +
209C THR* 1.3 79.7 - - - +
211C TYR* 1.3 63.7 + - - +
213C LEU* 3.1 12.8 + - + +
214C ARG 3.0 16.8 + - - -
231C ASP* 4.7 0.2 + - - -
233C LEU* 3.6 37.0 - - + +
234C GLU* 4.1 13.6 + - + -
237C SER* 3.8 16.4 + - - +
239C ILE* 4.6 0.8 - - - +
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Residues in contact with TYR 211 (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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205C LYS* 5.7 0.3 - - - +
206C PRO* 3.8 39.7 + - + +
207C ASN* 3.0 25.6 + - - +
208C VAL 4.0 1.1 - - - +
210C HIS* 1.3 76.8 - - - +
212C PHE* 1.3 57.8 + - - +
214C ARG* 3.2 6.2 + - + +
215C LEU* 2.9 23.7 + - - +
236C VAL 5.4 0.6 + - - -
237C SER* 4.0 30.0 - - - -
383C MET* 3.9 19.3 - - - -
386C LEU* 3.5 19.1 - - + +
387C VAL* 3.8 22.9 - - + -
390C GLU* 3.7 41.9 + - + +
391C THR* 4.3 17.5 - - + +
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Residues in contact with PHE 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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132C ILE* 5.2 2.2 - - + -
208C VAL 2.9 18.0 + - - +
209C THR 3.6 3.6 - - - +
210C HIS 3.2 0.2 - - - -
211C TYR* 1.3 75.5 - - - +
213C LEU* 1.3 70.5 + - + +
215C LEU* 3.1 2.0 + - + +
216C LEU* 2.9 44.1 + - + +
316C LEU* 3.9 25.4 - - + -
318C LEU* 5.4 3.1 - - + -
343C ILE* 6.0 0.4 - - + -
370C VAL* 3.6 28.0 - - + -
373C LEU* 3.7 26.0 - - + -
374C VAL* 3.5 19.3 - - + -
377C LEU* 3.7 24.9 - - + -
379C TRP* 3.9 16.8 - + - -
383C MET* 3.7 14.5 - - + +
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Residues in contact with LEU 213 (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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142C VAL* 4.0 38.4 - - + -
144C VAL* 4.1 13.5 - - + -
148C ILE* 4.8 6.7 - - + -
209C THR* 3.4 18.8 - - + +
210C HIS* 3.1 13.1 + - - +
212C PHE* 1.3 96.1 - - + +
214C ARG* 1.3 60.2 + - - +
216C LEU* 3.4 12.5 + - + +
217C HIS* 3.0 22.0 + - - +
222C LEU* 4.2 8.0 - - + +
225C LEU* 3.8 31.6 - - + -
234C GLU* 5.6 1.1 - - + -
239C ILE* 4.3 4.5 - - + -
316C LEU* 4.7 2.2 - - + -
318C LEU* 4.9 6.3 - - + -
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Residues in contact with ARG 214 (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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210C HIS 3.0 11.9 + - - +
211C TYR* 3.3 13.0 - - + +
213C LEU* 1.3 74.7 - - - +
215C LEU* 1.3 61.1 + - - +
217C HIS* 3.2 7.5 + - - +
218C ASP* 2.8 55.4 + - - +
237C SER* 2.9 35.2 + - - +
238C GLY* 3.6 26.5 + - - -
239C ILE* 4.3 9.5 - - + +
386C LEU* 4.0 22.2 - - + +
390C GLU* 3.4 28.5 + - - -
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Residues in contact with LEU 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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211C TYR 2.9 12.4 + - - +
212C PHE 3.1 8.7 + - - +
214C ARG* 1.3 77.8 - - - +
216C LEU* 1.3 62.9 + - - +
218C ASP* 3.1 13.4 + - + +
219C LYS* 2.9 40.7 + - + +
379C TRP* 3.6 39.0 - - + -
382C GLU* 3.5 38.4 - - + +
383C MET* 3.7 26.9 - - + +
386C LEU* 4.4 12.1 - - + -
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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
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132C ILE* 4.4 13.0 - - + -
140C VAL* 4.2 19.7 - - + -
142C VAL* 4.3 4.9 - - + -
212C PHE* 2.9 25.9 + - + +
213C LEU* 3.5 23.8 - - + +
214C ARG 3.3 0.2 - - - -
215C LEU* 1.3 75.2 - - - +
217C HIS* 1.3 64.2 + - - +
219C LYS* 3.4 7.8 + - - +
221C LEU* 3.0 43.5 + - + +
222C LEU* 4.1 10.8 - - + -
316C LEU* 4.0 26.5 - - + -
379C TRP* 3.9 25.5 - - + -
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Residues in contact with HIS 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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213C LEU 3.0 14.4 + - - +
214C ARG* 3.4 11.4 - - - +
216C LEU* 1.3 77.9 - - - +
218C ASP* 1.3 87.2 + - - +
220C GLY* 3.0 14.9 + - - -
222C LEU* 3.7 21.7 - - + +
238C GLY 4.9 5.2 - - - -
239C ILE* 5.1 2.2 - - + -
240C PRO* 3.4 40.0 - - + +
243C LYS* 3.1 38.9 + - - +
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Residues in contact with ASP 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 ARG* 2.8 53.1 + - - +
215C LEU* 3.1 16.0 + - + +
217C HIS* 1.3 94.0 + - - +
219C LYS* 1.3 61.8 + - + +
220C GLY 3.2 1.1 + - - -
386C LEU* 5.2 3.8 - - - +
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Residues in contact with LYS 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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135C ARG* 4.0 22.4 + - - +
215C LEU* 2.9 28.2 + - + +
216C LEU 3.8 4.9 - - - +
217C HIS 3.1 0.6 - - - -
218C ASP* 1.3 78.0 - - - +
220C GLY* 1.3 60.2 + - - +
221C LEU* 3.6 21.2 + - + +
379C TRP* 3.4 44.4 - - + +
382C GLU* 2.8 41.9 + - - +
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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