Contacts of the helix formed by residues 202 - 206 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201H THR* 1.3 30.1 - - - +
203H THR 1.3 20.9 - - - -
204H ALA 2.7 0.2 + - - -
205H GLU* 3.1 2.0 - - - +
285J CYS 2.6 2.6 + - - +
286J ASP 1.6 47.6 - - - +
287J VAL* 0.7 371.9 - - - +
288J ASP 2.0 0.5 + - - -
290J ARG* 1.5 84.5 + - + +
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Residues in contact with THR 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H GLN 3.4 12.1 - - - +
62H ARG* 4.2 16.8 - - + -
63H GLY* 5.7 0.2 - - - -
201H THR 3.8 0.4 + - - -
202H THR* 1.3 57.1 - - - +
204H ALA* 1.4 55.3 - - - +
205H GLU 3.2 0.2 - - - -
206H ARG* 2.9 21.7 + - - +
207H GLU* 3.7 1.0 + - - +
270I GLU* 4.1 3.6 + - - +
286J ASP* 0.6 146.8 + - - +
287J VAL* 1.5 17.1 - - - +
288J ASP* 1.9 48.6 - - - +
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Residues in contact with ALA 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H SER* 3.6 1.3 - - - +
203H THR 1.4 57.8 - - - -
205H GLU* 1.3 53.1 + - - +
206H ARG 2.7 0.2 + - - -
207H GLU* 2.6 34.4 + - - +
208H ILE* 3.5 6.4 + - + +
288J ASP* 1.4 101.6 - - + +
291J LYS* 3.0 27.6 - - + -
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Residues in contact with GLU 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H SER 2.8 26.7 - - - +
200H PHE* 3.2 24.3 - - - +
201H THR 3.6 3.1 - - - -
202H THR* 2.8 10.2 + - - +
204H ALA* 1.3 72.5 - - - +
206H ARG* 1.3 54.9 + - - -
207H GLU 3.2 0.2 - - - -
208H ILE* 3.1 41.9 + - + +
209H VAL* 3.9 1.7 + - - +
242H LEU* 4.4 13.3 - - + +
243H PRO* 5.3 4.1 - - + +
244H ASP* 5.4 8.7 - - - +
287J VAL* 2.0 44.7 - - + +
290J ARG* 3.4 27.7 + - - +
291J LYS* 4.7 4.6 + - - +
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Residues in contact with ARG 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H GLU* 4.0 22.9 + - - +
183H ARG* 5.0 8.3 - - - +
186H THR* 3.7 23.4 - - - +
187H ASP* 3.1 25.2 + - - -
190H MET* 3.7 32.0 - - - +
200H PHE 4.8 6.3 - - - +
203H THR* 2.9 18.6 + - - +
204H ALA 2.7 3.2 + - - -
205H GLU* 1.3 71.8 - - - +
207H GLU* 1.3 70.0 + - - +
208H ILE 3.2 0.9 - - - -
209H VAL* 2.9 19.2 - - - +
210H ARG 4.5 0.3 + - - -
287J VAL* 3.3 4.9 - - + +
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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