Contacts of the helix formed by residues 394 - 402 (chain E) in PDB entry 2W3S
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 394 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382E ILE* 2.8 36.6 + - + +
384E PHE* 4.4 1.3 - - + -
393E ARG* 1.3 70.1 - - - +
395E ALA* 1.3 65.0 + - - +
397E PHE* 2.8 20.0 + - + -
398E GLU* 2.8 10.5 + - - +
418E LEU* 4.0 13.7 - - + -
421E ASP* 2.8 25.8 - - - +
422E PHE* 4.1 7.4 - - + -
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Residues in contact with ALA 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393E ARG* 3.4 9.8 + - + +
394E ALA* 1.3 71.1 - - - +
396E ALA* 1.3 65.2 + - - +
398E GLU* 3.4 10.6 + - - +
399E ALA* 3.0 26.1 + - - +
421E ASP* 3.7 6.3 + - - +
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Residues in contact with ALA 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E ALA* 1.3 73.8 - - - +
397E PHE* 1.3 56.6 + - - +
399E ALA* 3.8 4.6 - - - +
400E ALA* 2.9 32.0 + - - +
417E LEU* 4.0 28.7 - - + +
420E GLN* 4.6 11.2 - - + +
421E ASP* 2.8 21.6 + - - +
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Residues in contact with PHE 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E LEU* 5.3 3.6 - - + -
382E ILE* 3.6 37.0 - - + -
394E ALA* 2.8 17.8 + - + +
396E ALA* 1.3 67.7 - - - +
398E GLU* 1.3 67.2 + - - +
400E ALA* 3.1 13.9 + - - +
401E LEU* 3.4 22.7 + - + +
411E ILE* 3.8 13.7 - - + -
414E ALA* 3.4 46.9 - - + -
415E LEU* 3.8 11.0 - - + -
417E LEU* 4.4 4.8 - - - +
418E LEU* 3.8 27.1 - - + +
421E ASP* 3.0 12.0 + - - +
443E ALA* 3.8 29.2 - - + -
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Residues in contact with GLU 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E ALA* 3.0 23.1 - - - +
381E ARG* 3.1 3.5 - - - -
382E ILE* 2.6 48.8 + - + +
393E ARG* 2.9 47.4 + - - +
394E ALA 2.8 16.2 + - - +
395E ALA* 3.6 12.7 - - - +
397E PHE* 1.3 75.1 - - - +
399E ALA* 1.3 61.5 + - - +
401E LEU* 3.3 16.7 + - - +
402E ILE* 3.5 16.7 - - + +
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Residues in contact with ALA 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E ALA 3.0 15.4 + - - +
396E ALA* 3.8 4.9 - - - +
398E GLU* 1.3 74.3 - - - +
400E ALA* 1.3 62.2 + - - +
401E LEU 3.0 6.4 + - - -
402E ILE* 3.5 28.0 + - + +
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Residues in contact with ALA 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E ALA 2.9 17.9 + - - +
397E PHE* 3.1 5.6 + - - +
399E ALA* 1.3 76.2 - - - +
401E LEU* 1.3 63.3 + - - +
402E ILE 4.9 0.4 - - - +
404E GLN* 3.6 19.6 + - - +
414E ALA* 4.9 7.8 - - + +
417E LEU* 3.5 29.8 - - + -
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Residues in contact with LEU 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LEU* 4.5 10.1 - - + -
377E ILE* 4.0 19.7 - - + +
380E ALA* 4.3 12.3 - - + -
382E ILE* 3.7 30.1 - - + -
397E PHE* 3.4 21.6 + - + +
398E GLU 3.3 7.4 + - - +
399E ALA 3.0 0.2 - - - -
400E ALA* 1.3 80.1 - - - +
402E ILE* 1.3 69.7 + - - +
403E GLY 3.2 0.2 + - - -
404E GLN* 2.8 29.4 + - - +
410E THR* 4.8 6.1 - - + -
411E ILE* 4.1 21.8 - - + -
414E ALA* 3.7 29.2 - - + -
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Residues in contact with ILE 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E ILE* 3.6 7.4 - - - +
378E GLU* 3.1 26.0 - - - +
379E THR* 5.4 2.5 - - + -
380E ALA* 4.3 16.8 - - + +
398E GLU* 3.5 20.2 - - + +
399E ALA* 3.5 20.8 + - + +
400E ALA 4.9 0.7 - - - +
401E LEU* 1.3 75.7 - - - +
403E GLY* 1.3 61.3 + - - +
404E GLN* 3.6 2.9 + - - +
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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