Contacts of the helix formed by residues 211 - 219 (chain L) in PDB entry 5XVO
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 PHE 211 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78K LEU* 4.3 20.0 - - + -
79K PRO 3.6 19.1 - - - -
80K PHE* 3.1 35.4 - + + -
82K GLY 5.7 0.9 - - - -
184L LEU* 3.7 35.7 - - + -
188L ALA* 5.4 3.4 - - + -
198L THR* 3.3 10.8 - - - +
209L ASN* 3.3 35.2 - - + -
210L ASP* 1.3 83.0 - - + +
212L ASN* 1.3 66.9 + - - +
213L LEU 3.2 3.1 - - - -
214L ALA* 2.9 17.3 + - + -
215L SER* 3.0 14.0 + - - -
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Residues in contact with ASN 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L THR 3.2 2.8 + - - -
199L GLN 3.9 3.8 - - - +
201L GLY* 3.9 8.7 - - - -
204L HIS* 4.4 18.4 - - - +
205L ALA 2.8 30.4 + - - +
206L ASN* 3.9 2.6 - - - +
207L GLN 4.0 4.4 - - - +
208L PHE* 4.0 8.2 - - - +
209L ASN* 3.7 42.5 + - - +
210L ASP 3.7 0.8 - - - -
211L PHE* 1.3 76.3 - - - +
213L LEU* 1.3 62.5 + - - +
215L SER* 2.9 24.5 + - - -
216L ASP* 3.0 16.4 + - - +
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Residues in contact with LEU 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L GLN* 3.8 14.6 - - - +
96L TRP* 4.2 13.0 - - + -
191L LEU* 3.7 30.0 - - + +
196L CYS* 4.4 1.8 - - + -
197L PHE 3.5 19.1 - - - +
198L THR* 3.0 19.4 + - - +
200L LEU 3.7 16.8 - - - +
201L GLY* 3.8 5.1 - - - -
202L LEU* 3.8 35.7 - - + +
212L ASN* 1.3 78.3 - - - +
214L ALA* 1.3 61.8 + - - +
216L ASP* 3.4 3.9 + - - +
217L LEU* 3.1 28.7 + - + +
276L LEU* 5.4 1.1 - - + -
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Residues in contact with ALA 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L LEU* 3.6 18.2 - - + +
187L PHE* 4.2 4.9 - - - +
188L ALA* 3.8 35.4 - - + +
191L LEU* 3.6 11.5 - - + +
198L THR* 4.3 3.4 + - - -
211L PHE* 2.9 12.8 + - + +
213L LEU* 1.3 76.6 - - - +
215L SER* 1.3 64.8 + - - +
217L LEU* 3.2 3.3 + - - +
218L MET* 3.0 25.3 + - - +
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Residues in contact with SER 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L LEU* 3.6 12.0 - - - +
209L ASN* 4.7 4.4 + - - -
211L PHE* 3.0 15.7 + - - -
212L ASN* 2.9 31.4 + - - -
214L ALA* 1.3 74.3 - - - +
216L ASP* 1.3 64.9 + - - +
218L MET* 3.1 27.4 - - - +
219L GLU* 3.2 21.1 - - - +
222L ARG* 5.2 4.5 - - - -
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Residues in contact with ASP 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L TRP* 3.5 30.9 + - + +
108L ILE* 3.5 12.8 - - + +
201L GLY* 3.5 7.6 - - - -
202L LEU* 2.8 43.8 + - + +
203L LYS* 3.8 5.5 + - - +
204L HIS 5.2 0.5 + - - -
212L ASN* 3.0 15.6 + - - +
213L LEU* 3.5 9.9 - - + +
215L SER* 1.3 80.1 + - - +
217L LEU* 1.3 63.6 + - - +
219L GLU* 3.2 25.6 + - - +
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Residues in contact with LEU 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ILE* 4.1 12.3 - - + -
187L PHE* 4.1 13.7 - - + -
191L LEU* 3.8 19.3 - - + -
202L LEU* 4.9 3.6 - - + -
213L LEU* 3.1 27.4 + - + +
214L ALA* 3.2 4.4 + - - +
216L ASP* 1.3 83.4 - - + +
218L MET* 1.3 59.0 + - - +
219L GLU 3.2 1.4 + - - -
220L PRO* 3.4 12.1 - - - +
221L PHE* 4.0 3.8 - - - -
268L TYR* 3.7 17.9 - - + -
269L THR* 3.6 43.1 - - + +
272L VAL* 3.8 33.2 - - + -
273L VAL* 5.5 0.9 - - + -
276L LEU* 5.6 0.7 - - + -
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Residues in contact with MET 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L TYR* 3.5 26.0 - - + +
183L LEU* 3.9 14.8 - - + +
184L LEU* 3.8 35.4 - - - -
187L PHE* 3.8 29.8 - - + -
214L ALA 3.0 11.3 + - - +
215L SER* 3.1 20.6 - - - +
217L LEU* 1.3 76.4 - - - +
219L GLU* 1.3 65.5 + - - +
220L PRO* 3.4 1.6 - - - -
221L PHE* 2.9 19.3 + - - +
222L ARG* 3.5 47.9 + - + +
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Residues in contact with GLU 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L TRP* 5.9 1.1 - - - +
108L ILE* 4.1 7.6 - - + -
109L ILE* 3.7 12.9 - - + +
112L LYS* 3.0 48.5 + - + +
148L GLU* 3.4 17.5 - - - +
215L SER* 3.2 17.4 - - - +
216L ASP* 3.2 22.1 - - - +
217L LEU 3.2 0.4 - - - -
218L MET* 1.3 77.4 - - - +
220L PRO* 1.3 70.7 - - + +
221L PHE 3.0 1.2 + - - -
222L ARG* 3.2 41.7 + - - +
223L PRO* 4.0 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