Contacts of the helix formed by residues 336 - 346 (chain E) in PDB entry 4P0S
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 ARG 336 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334E ARG* 3.8 21.0 - - - +
335E LYS* 1.3 77.0 - - - +
337E LEU* 1.3 60.6 + - - +
338E ASP* 3.5 29.6 + - - +
339E ASP* 3.2 15.9 + - + +
340E LEU* 2.9 25.5 + - - +
369E GLU* 3.1 38.7 + - + +
370E GLU* 3.0 29.0 + - + -
405E ILE* 5.2 3.2 - - - +
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Residues in contact with LEU 337 (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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335E LYS 5.4 0.2 - - - +
336E ARG* 1.3 71.1 - - - +
338E ASP* 1.3 64.4 + - - +
340E LEU* 3.3 12.8 + - + +
341E CYS* 3.2 26.9 + - - -
368E VAL* 4.4 14.8 - - + -
369E GLU 3.4 21.1 + - - +
370E GLU* 3.1 34.9 + - + +
371E HIS* 5.5 2.9 - - + +
373E SER* 4.8 11.2 - - - +
374E VAL 5.5 0.2 - - - +
375E HIS* 5.3 4.5 - - + +
377E LEU* 3.5 28.5 - - + -
384E LEU* 4.8 10.0 - - + +
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Residues in contact with ASP 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E ARG* 3.8 34.8 + - - +
337E LEU* 1.3 75.5 - - - +
339E ASP* 1.3 85.2 + - - +
340E LEU 3.4 0.2 + - - -
341E CYS* 3.5 4.9 + - - +
342E SER* 3.4 26.5 + - - -
370E GLU* 4.5 6.4 - - - +
376E ASN 5.8 0.7 - - - +
377E LEU* 3.8 20.9 - - + +
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Residues in contact with ASP 339 (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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334E ARG* 5.9 1.2 + - - -
335E LYS* 4.1 14.7 + - - +
336E ARG* 3.2 27.7 + - + +
338E ASP* 1.3 88.2 + - - +
340E LEU* 1.3 53.6 + - - +
342E SER* 4.1 3.5 - - - -
343E SER* 2.4 34.5 + - - -
348E ARG* 3.5 23.8 + - - -
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Residues in contact with LEU 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E LYS* 4.1 18.1 - - + +
336E ARG 2.9 13.7 + - - +
337E LEU* 3.4 16.6 - - + +
338E ASP 3.2 0.2 - - - -
339E ASP* 1.3 74.8 - - - +
341E CYS* 1.3 59.8 + - - +
343E SER* 3.1 6.7 + - - -
344E ILE* 2.9 48.8 + - + +
349E PHE* 3.5 36.1 - - + -
366E TYR* 5.4 2.0 - - + +
384E LEU* 4.4 18.4 - - + -
387E ALA* 5.1 6.5 - - + -
388E VAL* 5.3 9.9 - - + -
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Residues in contact with CYS 341 (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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337E LEU 3.2 15.6 + - - -
338E ASP* 3.5 7.8 + - - +
340E LEU* 1.3 77.6 - - - +
342E SER* 1.3 67.7 + - - +
344E ILE* 3.3 4.1 + - - +
345E ILE* 3.2 28.5 + - - +
377E LEU* 3.6 25.8 - - + -
378E SER* 3.4 19.3 - - - +
379E LEU* 4.0 21.4 - - + +
384E LEU* 3.5 26.2 - - - -
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Residues in contact with SER 342 (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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338E ASP 3.4 15.3 + - - -
339E ASP* 4.1 5.2 - - - -
340E LEU 3.4 0.4 - - - -
341E CYS* 1.3 77.2 - - - +
343E SER* 1.3 62.9 - - - +
345E ILE* 3.4 9.7 + - - +
346E ASP* 3.1 32.9 + - - +
348E ARG* 4.3 11.9 - - - -
378E SER* 4.6 2.0 + - - -
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Residues in contact with SER 343 (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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335E LYS* 3.3 12.6 - - - -
339E ASP 2.4 25.2 + - - -
340E LEU* 3.1 12.1 + - - -
342E SER* 1.3 77.2 - - - +
344E ILE* 1.3 58.3 + - - +
346E ASP* 3.0 8.7 - - - +
348E ARG* 2.7 57.0 + - - +
349E PHE* 2.9 20.9 + - - -
352E GLN* 5.0 0.9 - - - -
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Residues in contact with ILE 344 (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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340E LEU* 2.9 52.2 + - + +
341E CYS* 3.9 5.2 - - - +
343E SER* 1.3 72.4 - - - +
345E ILE* 1.3 64.1 + - - +
347E GLY* 3.2 11.8 + - - -
349E PHE* 3.7 20.4 - - + -
379E LEU* 4.6 11.0 - - + -
383E THR* 6.1 1.1 - - + -
384E LEU* 4.3 20.0 - - + -
387E ALA* 4.5 14.8 - - + -
1Q G 3.4 51.3 - - + +
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Residues in contact with ILE 345 (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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341E CYS 3.2 16.5 + - - +
342E SER* 3.7 7.2 - - - +
344E ILE* 1.3 82.2 - - - +
346E ASP* 1.3 63.4 + - + +
347E GLY* 3.3 1.4 + - - -
378E SER* 3.6 28.7 - - - +
379E LEU* 4.0 25.1 - - + -
1Q G 4.4 8.2 - - - +
33R T 4.9 36.6 - - + +
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Residues in contact with ASP 346 (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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342E SER* 3.1 17.2 - - - +
343E SER 3.0 15.9 - - - +
345E ILE* 1.3 80.0 - - + +
347E GLY* 1.3 58.5 + - - +
348E ARG* 3.2 34.9 + - - +
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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