Contacts of the helix formed by residues 389 - 394 (chain E) in PDB entry 2WTK
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 ALA 389 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E LEU* 6.4 0.7 - - + -
174E TYR* 3.4 32.5 - - + +
384E ARG* 3.7 24.5 - - + +
385E ARG 3.6 1.7 + - - +
387E SER 3.6 0.8 - - - -
388E GLU* 1.3 81.1 - - - +
390E LEU* 1.3 60.6 + - - +
391E PRO* 3.5 2.7 - - - +
392E GLU* 3.2 11.0 - - - +
393E LEU* 3.0 30.7 + - + +
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E ALA* 4.0 33.7 - - + +
174E TYR* 4.1 15.7 - - + -
175E ILE* 5.0 4.0 - - + -
203E ILE* 3.6 29.6 - - + -
207E GLY* 3.5 26.2 - - - +
209E VAL* 3.8 13.7 - - + -
386E ALA* 4.3 8.4 - - + +
387E SER 4.3 2.2 - - - +
389E ALA* 1.3 73.7 - - - +
391E PRO* 1.4 73.4 - - + +
392E GLU 3.1 1.8 - - - -
393E LEU* 2.9 7.9 + - + +
394E LEU* 2.9 46.3 + - + +
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Residues in contact with PRO 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E TYR* 3.5 26.6 + - + +
206E ASP* 4.2 9.2 - - + -
207E GLY* 4.0 24.8 - - - +
387E SER 4.3 12.1 - - - +
388E GLU 4.8 0.9 - - - -
389E ALA 3.7 9.9 - - - +
390E LEU* 1.4 93.2 - - + +
392E GLU* 1.3 59.5 + - - +
394E LEU 3.5 17.7 - - - +
395E ARG* 3.8 3.3 + - - +
397E VAL 4.8 0.5 - - - +
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Residues in contact with GLU 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E ARG* 2.6 40.2 + - - -
388E GLU 4.0 1.7 - - - +
389E ALA* 3.2 11.9 - - - +
391E PRO* 1.3 81.0 - - - +
393E LEU* 1.3 60.2 + - + +
395E ARG* 2.8 73.2 + - - +
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Residues in contact with LEU 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E PHE* 4.6 2.1 - - - -
168E ASN* 3.3 33.2 + - + +
170E LEU* 3.6 32.3 - - + -
171E ALA* 3.5 36.1 - - + +
174E TYR* 3.7 27.4 - - + -
389E ALA* 3.0 17.8 + - + +
390E LEU* 2.9 10.3 + - + +
392E GLU* 1.3 74.9 - - + +
394E LEU* 1.3 58.3 + - - +
395E ARG* 2.9 10.9 + - - +
396E PRO* 4.8 0.7 - - - +
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Residues in contact with LEU 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E TYR* 3.7 38.4 - - + -
158E LEU* 3.6 16.6 - - + -
163E PHE* 4.1 16.2 - - + -
167E MET* 3.3 34.5 - - + -
168E ASN* 5.5 0.2 - - - +
171E ALA* 4.7 2.7 - - + -
203E ILE* 4.0 22.0 - - + -
390E LEU* 2.9 34.1 + - + +
391E PRO 3.5 5.0 - - - +
393E LEU* 1.3 74.8 - - - +
395E ARG* 1.3 58.1 + - - +
396E PRO* 3.6 4.9 - - - -
397E VAL* 2.9 29.2 + - + +
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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