Contacts of the helix formed by residues 202 - 208 (chain A) in PDB entry 3RIE
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 GLY 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR 5.6 0.4 - - - -
89A ASP* 4.4 7.6 - - - -
200A PRO 3.5 1.6 + - - -
201A ILE* 1.3 77.5 - - - +
203A PRO* 1.4 75.0 - - - +
204A ALA 3.1 4.0 + - - -
205A GLU* 3.1 30.4 + - - +
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Residues in contact with PRO 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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71A TYR* 4.1 23.3 - - + +
72A GLN* 3.9 36.1 - - + +
89A ASP* 4.5 2.2 - - - +
148A ILE* 4.1 24.7 - - + +
178A ASP* 4.9 1.7 - - - +
198A SER* 4.9 3.1 - - - +
201A ILE 4.8 0.7 - - - +
202A GLY* 1.4 81.9 - - - +
204A ALA* 1.3 58.7 + - - +
205A GLU* 3.1 10.1 + - + +
206A THR* 3.8 7.6 + - - +
401A MTA 3.2 37.4 + - + +
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Residues in contact with ALA 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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197A SER* 4.2 7.0 - - - -
198A SER* 3.3 37.7 - - - +
199A ASP 3.3 13.9 - - - +
202A GLY 3.1 2.0 + - - -
203A PRO* 1.3 74.8 - - - +
205A GLU* 1.3 63.9 + - - +
206A THR 3.1 3.4 - - - -
207A LEU* 2.9 18.4 + - + +
208A PHE* 3.2 15.7 - - + -
401A MTA 3.2 16.3 + - + +
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Residues in contact with GLU 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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200A PRO* 3.1 27.5 + - - +
202A GLY* 3.1 18.5 + - - +
203A PRO* 3.1 4.1 - - - +
204A ALA* 1.3 78.0 - - - +
206A THR* 1.3 72.4 + - + +
207A LEU 3.4 0.9 + - - -
208A PHE* 3.9 11.6 + - - +
209A ASN* 4.1 5.9 + - - -
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Residues in contact with THR 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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178A ASP* 3.3 30.3 + - - +
180A SER* 3.6 19.1 + - - +
203A PRO 3.8 2.8 + - - +
205A GLU* 1.3 89.1 - - + +
207A LEU* 1.3 60.1 + - - +
208A PHE 3.4 2.5 - - - -
209A ASN* 3.2 20.2 + - - +
212A PHE* 3.9 10.2 - - - +
401A MTA 3.6 10.9 + - - -
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Residues in contact with LEU 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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123A VAL* 3.9 19.3 - - + -
179A ALA* 4.1 4.0 - - + -
180A SER 4.1 13.0 - - - +
195A VAL* 4.6 4.6 - - + +
197A SER* 3.6 27.8 - - - -
204A ALA* 2.9 14.4 + - + +
206A THR* 1.3 89.5 - - - +
208A PHE* 1.3 70.1 + - + +
209A ASN 3.7 2.4 + - - -
212A PHE* 3.2 55.0 - - + -
213A TYR* 4.3 6.2 + - - -
401A MTA 3.8 32.8 - - + +
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Residues in contact with PHE 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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197A SER* 3.7 10.3 - - - -
198A SER 3.6 15.7 - - - -
199A ASP* 5.5 0.2 - - - -
200A PRO* 3.9 39.9 - - + -
204A ALA* 3.2 27.4 - - + -
205A GLU 3.9 7.5 + - - +
206A THR 3.4 3.0 - - - -
207A LEU* 1.3 85.1 - - + +
209A ASN* 1.3 60.0 + - - +
229A GLN* 3.5 39.3 - - - -
230A CYS* 5.5 3.4 - - - -
231A GLU 6.1 0.7 - - - -
239A THR* 5.6 6.1 - - + -
243A MET* 3.4 44.1 - - + +
246A TYR* 3.9 2.1 + - - -
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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