Contacts of the helix formed by residues 202 - 206 (chain B) in PDB entry 3LUE
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 THR 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B THR* 1.3 30.4 - - - +
203B THR 1.3 20.6 - - - -
204B ALA 2.7 0.3 + - - -
205B GLU* 3.1 2.6 - - - +
285D CYS 2.6 2.4 + - - +
286D ASP 1.6 47.6 - - - +
287D VAL* 0.7 372.7 - - - +
288D ASP 2.0 0.3 + - - -
290D ARG* 1.5 83.7 + - + +
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Residues in contact with THR 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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59B GLN 3.4 11.7 - - - +
62B ARG* 4.2 16.8 - - + -
202B THR* 1.3 57.2 - - - +
204B ALA* 1.4 55.7 - - - +
205B GLU 3.2 0.2 - - - -
206B ARG* 2.9 22.5 + - - +
207B GLU* 3.7 1.2 + - - +
270C GLU* 4.1 3.4 + - - -
286D ASP* 0.6 146.3 + - - +
287D VAL* 1.5 18.3 - - - +
288D ASP* 1.9 49.8 - - - +
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Residues in contact with ALA 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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60B SER* 3.6 1.6 - - - +
203B THR 1.4 58.0 - - - -
205B GLU* 1.3 52.3 + - - +
207B GLU* 2.6 34.6 + - - +
208B ILE* 3.5 6.5 + - + -
288D ASP* 1.4 101.9 - - + +
291D LYS* 3.0 27.8 - - + -
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Residues in contact with GLU 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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199B SER 2.8 26.7 - - - +
200B PHE* 3.2 23.4 - - - +
201B THR 3.6 3.1 - - - -
202B THR 2.8 10.0 + - - +
204B ALA* 1.3 70.9 - - - +
206B ARG* 1.3 54.8 + - - -
207B GLU 3.2 0.4 - - - -
208B ILE* 3.1 41.0 + - + +
209B VAL* 3.9 1.9 + - - +
242B LEU* 4.4 13.5 - - + +
243B PRO* 5.3 4.7 - - + +
244B ASP* 5.4 8.5 - - - +
287D VAL* 2.0 46.7 - - + +
290D ARG* 3.4 27.4 + - - +
291D LYS* 4.0 4.9 + - - +
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Residues in contact with ARG 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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72B GLU* 4.0 23.3 + - - +
183B ARG* 5.0 8.1 - - - +
186B THR* 3.7 22.6 - - - +
187B ASP* 3.1 26.1 + - - -
190B MET* 3.7 31.3 - - + +
200B PHE 4.8 6.5 - - - +
203B THR* 2.9 18.1 + - - +
204B ALA 2.7 3.4 + - - -
205B GLU* 1.3 71.1 - - - +
207B GLU* 1.3 69.3 + - - +
208B ILE 3.2 0.9 - - - -
209B VAL* 2.9 19.8 - - - +
210B ARG 4.5 0.2 + - - -
287D VAL* 3.3 4.7 - - + +
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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