Contacts of the helix formed by residues 202 - 208 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LYS 3.7 2.2 - - - +
201A LEU* 1.4 87.2 - - + +
203A TYR* 1.3 63.4 + - - +
204A ASP* 3.3 3.4 - - + +
205A LEU* 3.3 22.5 + - + +
206A TRP* 3.3 42.0 + - + +
260A THR* 4.4 8.3 - - + -
263A LEU* 4.2 16.8 - - + +
264A GLU* 4.0 33.9 - - + +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PRO* 3.8 37.0 + - + -
177A PHE* 3.9 22.7 - + - -
178A GLU* 4.1 10.9 + - - +
198A ALA* 2.9 30.5 + - - +
199A PRO* 4.0 13.0 - - + -
201A LEU* 2.7 43.1 + - + +
202A PRO* 1.3 72.5 - - - +
204A ASP* 1.3 58.5 + - - +
206A TRP* 3.2 9.8 + + - -
207A PHE* 2.7 66.2 + + + +
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PRO* 3.3 0.8 - - + -
203A TYR* 1.3 81.7 - - - +
205A LEU* 1.3 63.6 + - - +
208A LYS* 3.1 47.1 + - + +
209A ARG* 3.1 27.6 + - + +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PRO* 3.3 22.4 + - + +
203A TYR 3.3 0.6 - - - -
204A ASP* 1.3 78.8 - - - +
206A TRP* 1.3 65.2 + - + +
209A ARG* 3.6 25.2 - - - +
211A PHE* 3.0 21.3 + - - -
212A ALA 3.6 24.2 - - - +
213A GLY* 4.8 2.9 - - - +
214A CYS* 4.0 33.4 - - + +
263A LEU 4.6 3.6 - - - +
264A GLU* 4.5 26.9 - - + +
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Residues in contact with TRP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.8 20.2 - + - -
201A LEU* 4.3 14.1 - - + -
202A PRO* 3.3 41.1 + - + +
203A TYR* 3.2 16.0 + + - +
205A LEU* 1.3 93.6 - - + +
207A PHE* 1.3 83.6 + + + +
208A LYS 3.7 0.4 - - - -
210A CYS* 3.2 21.1 - - - -
211A PHE* 3.2 42.0 - + + +
214A CYS* 4.8 3.4 - - - -
235A LEU* 3.8 2.6 - - - +
239A ALA* 3.5 25.1 - - + -
242A ILE* 4.5 10.7 - - + +
243A LEU* 4.1 23.8 - - + -
263A LEU* 4.4 19.1 + - + -
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 3.5 37.0 - - - +
173A LEU* 3.6 36.8 - - + -
174A PRO* 3.7 28.3 - - + -
177A PHE* 4.3 9.0 - - + -
203A TYR* 2.7 45.7 + + + +
206A TRP* 1.3 98.6 - + + +
208A LYS* 1.3 63.5 + - + +
210A CYS* 4.5 2.5 - - - -
235A LEU* 3.7 36.1 - - + +
236A VAL* 3.9 14.6 - - + -
239A ALA* 4.3 2.0 - - + -
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 5.3 9.4 + - - +
133A VAL* 3.4 35.0 - - + +
137A ILE* 4.0 0.5 - - - +
162A LEU* 3.7 20.1 - - - +
170A LEU* 5.2 5.6 - - + -
204A ASP* 3.1 48.5 + - + +
207A PHE* 1.3 80.0 - - + +
209A ARG* 1.3 62.6 + - - +
210A CYS* 3.4 2.5 - - - -
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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