Contacts of the helix formed by residues 190 - 198 (chain E) in PDB entry 2R6C
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 190 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188E THR* 3.0 17.8 + - - -
189E GLY* 1.3 79.3 - - - +
191E THR* 1.3 67.6 + - - +
192E GLU 3.4 1.6 - - - -
193E LEU* 2.9 37.3 + - + +
194E ASP* 3.1 13.1 + - - +
219E PHE* 4.2 14.1 - + - -
222E ASN* 4.1 11.0 - - + -
223E ILE* 4.4 8.5 - - + -
226E ASN* 3.8 20.6 - - - -
429E LEU* 3.8 31.6 - - + -
438E PHE* 3.3 38.6 - - + -
439E VAL* 4.6 2.0 - - - -
440E ASN* 3.4 22.9 - - - +
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Residues in contact with THR 191 (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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189E GLY 3.6 4.8 + - - -
190E PHE* 1.3 67.9 - - - +
192E GLU* 1.3 62.6 + - + +
194E ASP* 3.1 27.5 + - - +
195E ARG* 3.3 37.8 + - - +
440E ASN* 3.1 22.4 + - - +
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Residues in contact with GLU 192 (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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190E PHE 3.0 1.6 + - - -
191E THR* 1.3 75.2 - - + +
193E LEU* 1.3 66.0 + - - +
195E ARG* 3.7 23.1 + - + +
196E MET* 3.8 8.1 + - - +
427E VAL* 3.7 35.0 - - + +
428E GLN* 4.0 16.2 + - - +
429E LEU* 5.3 5.8 - - + -
440E ASN* 5.1 0.6 + - - +
441E LEU* 5.3 15.4 - - - +
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Residues in contact with LEU 193 (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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188E THR* 3.6 30.5 - - + -
190E PHE* 2.9 28.0 + - + +
192E GLU* 1.3 77.6 - - - +
194E ASP* 1.3 57.6 + - - +
195E ARG 3.2 0.9 + - - -
196E MET* 3.3 3.6 + - - +
197E THR* 2.6 40.3 + - + +
200E PHE* 4.7 9.2 - - + -
219E PHE* 4.0 26.7 - - + -
223E ILE* 5.2 0.9 - - + -
392E ILE* 6.1 0.7 - - + -
414E ILE* 4.6 16.4 - - + -
416E ILE* 3.8 27.1 - - + -
427E VAL* 4.0 14.1 - - + +
429E LEU* 5.7 1.7 - - + +
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Residues in contact with ASP 194 (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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183E ILE* 4.2 30.2 - - + +
187E PRO* 3.3 25.1 - - - +
188E THR* 1.6 36.8 + - - -
189E GLY 4.7 1.9 + - - -
190E PHE 3.1 12.8 + - - +
191E THR* 3.1 15.1 + - - +
193E LEU* 1.3 75.3 - - - +
195E ARG* 1.3 53.8 + - + +
197E THR* 3.7 5.2 - - - -
198E SER* 2.3 39.4 + - - +
199E GLY 4.6 3.3 + - - +
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Residues in contact with ARG 195 (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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183E ILE* 5.8 4.0 - - + -
191E THR* 3.3 41.0 + - - +
192E GLU* 3.7 17.0 - - + +
193E LEU 3.2 0.4 - - - -
194E ASP* 1.3 78.4 - - + +
196E MET* 1.3 63.5 + - + +
197E THR 3.4 0.5 + - - -
198E SER* 3.8 10.7 + - - -
423E PRO* 5.5 1.7 - - - +
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Residues in contact with MET 196 (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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192E GLU 3.8 4.6 + - - +
193E LEU 3.3 8.1 + - - +
195E ARG* 1.3 80.6 - - + +
197E THR* 1.3 54.9 + - - +
198E SER* 4.9 0.6 + - - -
416E ILE* 4.1 23.1 - - + -
419E GLN* 2.5 28.5 + - - +
421E ASN* 4.8 1.7 - - - +
423E PRO* 3.4 53.0 - - + +
424E VAL* 3.9 1.3 - - - -
425E GLY* 3.6 30.3 - - - +
426E THR 4.8 2.0 - - - +
427E VAL* 3.4 29.8 - - + -
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Residues in contact with THR 197 (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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184E THR* 4.4 1.7 + - - -
188E THR* 4.9 1.7 - - - +
193E LEU* 2.6 34.4 + - + +
194E ASP* 3.3 3.3 + - - -
196E MET* 1.3 83.2 - - - +
198E SER* 1.3 69.1 + - - +
199E GLY 2.4 28.6 + - - +
200E PHE* 4.3 2.9 - - + -
201E GLN* 4.6 0.3 - - - +
392E ILE* 4.0 16.2 - - + -
416E ILE* 3.9 23.1 - - + -
419E GLN* 3.7 16.6 - - - +
421E ASN* 3.2 23.6 + - - +
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Residues in contact with SER 198 (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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183E ILE* 3.8 16.6 + - - +
184E THR* 2.4 68.8 + - - +
194E ASP 2.3 27.2 + - - -
195E ARG* 3.8 11.4 + - - -
196E MET 4.9 0.5 + - - -
197E THR* 1.3 70.4 + - - +
199E GLY* 1.3 54.5 + - - +
201E GLN* 4.7 0.2 - - - +
421E ASN* 5.9 0.5 - - - +
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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