Contacts of the strand formed by residues 211 - 216 (chain E) in PDB entry 6VMS
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 ALA 211 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159E CYS 3.7 2.0 - - - -
160E ARG* 3.6 25.1 - - - +
207E GLY* 3.4 3.8 - - - -
208E SER 3.0 27.5 + - - +
209E GLY 3.6 0.4 - - - -
210E THR* 1.3 80.2 - - - +
212E PHE* 1.3 61.1 + - - +
213E THR* 5.5 2.0 - - + -
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Residues in contact with PHE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E SER* 3.2 4.5 - - - -
159E CYS* 2.6 47.8 + - + +
160E ARG* 4.9 0.6 - - - +
161E SER* 4.8 3.8 - - - -
165E LEU* 3.4 37.0 - - + -
172E THR* 4.6 2.7 - - + -
174E LEU* 3.2 29.2 - - + -
176E TRP* 5.0 0.4 - - - +
192E MET* 3.2 44.6 - - + -
206E SER 3.4 5.4 - - - +
207E GLY* 4.2 0.2 - - - -
208E SER* 3.7 16.6 - - - -
209E GLY 2.9 36.1 - - - -
210E THR* 4.0 3.8 - - - -
211E ALA* 1.3 79.9 - - - +
213E THR* 1.3 62.8 + - - +
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Residues in contact with THR 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E SER* 4.4 13.7 - - - +
157E ILE 3.3 5.8 - - - -
158E SER* 3.7 18.2 - - - +
176E TRP* 4.2 6.5 + - - -
205E GLY* 3.0 23.9 - - - -
206E SER* 2.8 30.1 + - - +
211E ALA 5.5 0.9 - - - -
212E PHE* 1.3 83.5 - - - +
214E LEU* 1.3 59.2 + - - +
215E THR* 4.6 8.7 - - - +
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Residues in contact with LEU 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E VAL 3.8 0.5 - - - +
156E SER* 3.3 4.0 + - - -
157E ILE* 2.5 54.8 + - + +
176E TRP* 3.5 41.8 - - + -
188E LEU* 4.1 10.5 - - + -
189E ILE* 3.5 23.3 - - + -
203E PHE* 4.6 1.1 - - + -
204E SER 3.2 19.3 - - - +
205E GLY* 4.3 0.4 - - - -
213E THR* 1.3 71.6 - - - +
215E THR* 1.3 64.4 + - - +
216E ILE* 4.0 21.7 - - + +
227E TYR* 3.6 27.6 - - + -
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Residues in contact with THR 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E VAL 3.7 3.4 - - - +
156E SER* 4.6 13.2 - - - +
202E ARG 3.7 1.1 - - - +
203E PHE* 3.5 4.0 - - - -
204E SER* 2.2 71.2 + - - +
205E GLY* 3.6 2.6 + - - -
206E SER* 5.7 1.8 - - - +
213E THR* 4.0 13.7 + - - +
214E LEU* 1.3 75.5 - - - +
216E ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E SER* 3.0 7.7 - - - -
155E VAL* 2.7 52.5 + - + +
157E ILE* 3.9 27.8 - - + -
202E ARG* 3.6 4.9 - - + +
203E PHE* 3.7 30.5 - - + -
214E LEU* 4.0 11.9 - - + +
215E THR* 1.3 77.5 - - - +
217E SER* 1.3 74.1 + - - +
218E ARG 4.9 2.0 - - - +
219E LEU* 3.7 14.8 - - + -
223E ASP* 5.1 3.1 - - - +
227E TYR* 3.9 25.6 - - + +
245E LEU* 4.6 4.9 - - + -
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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