Contacts of the helix formed by residues 202 - 208 (chain B) in PDB entry 5EJC
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 PRO 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B LYS 3.7 2.8 - - - +
201B LEU* 1.3 88.8 - - + +
203B TYR* 1.3 61.5 + - - +
204B ASP* 3.3 3.1 - - + +
205B LEU* 3.3 22.8 + - + +
206B TRP* 3.3 41.3 + - + +
260B THR* 4.9 6.5 - - + -
263B LEU* 4.2 15.7 - - + +
264B GLU* 4.0 34.1 - - + +
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Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B PRO* 3.9 35.1 + - + -
177B PHE* 3.9 23.1 - + - -
178B GLU* 4.1 13.0 + - - +
198B ALA* 2.9 28.5 + - - -
199B PRO* 4.1 12.6 - - + -
201B LEU* 2.7 42.9 + - + +
202B PRO* 1.3 71.9 - - - +
204B ASP* 1.3 58.9 + - - +
206B TRP* 3.2 10.3 + + - +
207B PHE* 2.7 65.2 + + + +
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Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 6.3 1.3 - - + -
202B PRO* 3.3 0.6 - - + -
203B TYR* 1.3 82.1 - - - +
205B LEU* 1.3 60.3 + - - +
208B LYS* 3.1 45.0 + - + +
209B ARG* 3.1 29.2 + - + +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PRO* 3.3 24.2 + - + +
203B TYR 3.3 0.4 - - - -
204B ASP* 1.3 78.3 - - - +
206B TRP* 1.3 64.8 + - + +
209B ARG* 3.6 25.2 - - - +
211B PHE 3.0 21.3 + - - -
212B ALA 3.6 24.2 - - - +
213B GLY* 4.8 2.7 - - - +
214B CYS* 4.0 32.8 - - + +
263B LEU 4.6 2.5 - - - +
264B GLU* 4.5 27.8 - - + +
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Residues in contact with TRP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B PHE* 3.8 20.9 - + - -
201B LEU* 4.3 13.0 - - + -
202B PRO* 3.3 41.2 + - + +
203B TYR* 3.2 16.8 + + - +
205B LEU* 1.3 92.4 - - + +
207B PHE* 1.3 84.0 + + + +
208B LYS 3.7 0.4 - - - -
210B CYS* 3.2 20.2 - - - -
211B PHE* 3.2 44.5 - + + +
214B CYS* 4.8 4.0 - - - -
235B LEU* 3.8 2.8 - - - +
239B ALA* 3.5 23.1 - - + -
242B ILE* 4.5 10.6 - - + +
243B LEU* 4.1 24.2 - - + -
263B LEU* 4.4 19.7 + - + -
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 3.5 36.3 - - - +
173B LEU* 3.6 35.9 - - + -
174B PRO* 3.7 27.8 - - + -
177B PHE* 4.3 8.7 - - + -
203B TYR* 2.7 45.7 + + + +
206B TRP* 1.3 98.2 - + + +
208B LYS* 1.3 62.8 + - + +
210B CYS* 4.4 2.9 - - - -
235B LEU* 3.7 36.1 - - + -
236B VAL* 3.9 13.7 - - + -
239B ALA* 4.3 2.5 - - + -
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Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP* 5.5 6.8 + - - +
133B VAL* 3.4 34.4 - - + +
137B ILE* 4.0 0.3 - - - +
162B LEU* 3.7 20.4 - - - +
170B LEU* 5.2 5.4 - - + -
204B ASP* 3.1 49.2 + - + +
207B PHE* 1.3 80.9 - - + +
209B ARG* 1.3 62.8 + - - +
210B CYS* 3.4 2.2 - - - -
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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