Contacts of the helix formed by residues 203 - 208 (chain I) in PDB entry 4XLN
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 ASP 203 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I ARG* 5.9 2.2 - - - +
201I GLY 4.2 0.8 - - - -
202I TYR* 1.3 72.5 - - - +
204I GLN* 1.3 80.3 + - - +
205I GLU* 3.1 7.5 + - + +
206I THR* 3.2 12.9 + - - +
207I LEU* 3.1 28.5 + - - +
227I LEU* 3.6 15.8 - - - +
228I ALA 4.7 2.9 - - - +
229I MET 4.5 6.0 - - - +
230I ARG* 3.9 26.3 - - - +
231I PRO* 5.0 4.9 - - - +
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Residues in contact with GLN 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I ASP* 1.3 84.3 + - - +
205I GLU* 1.3 68.0 + - + +
207I LEU* 3.9 3.5 + - - +
208I VAL* 3.2 23.4 + - - +
222I LEU* 3.4 24.5 - - - +
224I GLU* 3.5 18.4 + - - +
227I LEU* 3.2 56.4 - - + +
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Residues in contact with GLU 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I ASP* 3.2 4.4 - - + +
204I GLN* 1.3 84.3 - - + +
206I THR* 1.3 64.2 + - - +
207I LEU 3.1 5.9 + - - -
208I VAL* 3.3 21.1 + - - +
209I ARG* 3.6 12.3 + - - +
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Residues in contact with THR 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201I GLY 4.1 5.6 + - - +
202I TYR* 3.7 28.7 - - + +
203I ASP* 3.2 27.1 + - - +
205I GLU* 1.3 77.9 - - - +
207I LEU* 1.3 58.6 + - - +
209I ARG* 3.1 56.7 + - - +
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Residues in contact with LEU 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I VAL* 4.9 4.0 - - - +
197I LEU* 3.6 35.2 - - + -
202I TYR* 3.6 30.1 - - + +
203I ASP 3.1 12.3 + - - +
204I GLN 4.0 5.4 - - - +
205I GLU 3.1 0.8 - - - -
206I THR* 1.3 81.0 - - - +
208I VAL* 1.3 60.5 + - + +
209I ARG* 3.3 6.3 + - - +
210I GLU* 6.0 0.2 - - - +
211I LEU* 3.2 25.3 + - - +
221I LEU* 3.6 31.9 - - + +
227I LEU* 3.8 29.4 - - + -
304I LEU* 5.8 3.6 - - + -
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Residues in contact with VAL 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204I GLN* 3.2 24.9 - - - +
205I GLU* 3.4 13.5 - - - +
207I LEU* 1.3 76.8 - - + +
209I ARG* 1.3 65.1 + - - +
210I GLU 3.9 0.2 - - - -
211I LEU* 4.1 12.7 + - + +
212I SER* 4.6 6.2 + - - -
218I VAL* 4.1 13.0 - - + +
221I LEU 4.6 3.8 - - - +
222I LEU* 3.9 40.8 - - + -
227I LEU* 5.9 0.2 - - + -
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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