Contacts of the helix formed by residues 327 - 338 (chain E) in PDB entry 1XSK
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 ASP 327 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283E GLU* 4.2 8.5 + - - +
325E PHE* 3.3 2.0 - - - -
326E PRO* 1.3 83.5 - - + +
328E PRO* 1.3 65.5 - - - +
329E GLU* 3.9 6.2 + - - +
330E GLY* 3.0 29.5 + - - -
331E MET* 3.0 24.3 + - - +
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Residues in contact with PRO 328 (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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320E TRP* 3.2 60.8 - - + +
325E PHE 3.6 8.5 - - - +
326E PRO 3.7 4.5 - - - +
327E ASP* 1.3 89.7 - - - +
329E GLU* 1.3 58.8 + - - +
331E MET* 3.7 12.4 - - + +
332E ILE* 2.9 37.8 + - - +
408E MET* 3.9 8.1 - - + -
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Residues in contact with GLU 329 (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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327E ASP* 3.5 6.1 + - - +
328E PRO* 1.3 77.4 - - - +
330E GLY* 1.3 60.9 + - - +
332E ILE* 3.8 0.4 - - - +
333E ARG* 2.8 62.0 + - + +
407E ALA 4.4 2.5 - - - +
408E MET* 3.4 48.7 - - + +
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Residues in contact with GLY 330 (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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327E ASP* 3.0 26.2 + - - -
328E PRO 3.3 0.2 - - - -
329E GLU* 1.3 78.0 - - - +
331E MET* 1.3 62.6 + - - +
333E ARG* 3.4 5.6 + - - +
334E ARG* 3.1 26.4 + - - +
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Residues in contact with MET 331 (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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283E GLU* 3.1 30.0 + - - +
286E VAL* 4.8 4.5 - - + -
305E PHE* 3.4 34.8 - - + -
320E TRP* 3.8 20.9 - - + -
325E PHE* 3.4 42.4 - - + -
327E ASP* 3.0 13.4 + - - +
328E PRO* 3.7 9.0 - - + +
330E GLY* 1.3 76.2 - - - +
332E ILE* 1.3 63.3 + - + +
334E ARG* 3.3 25.4 + - - +
335E LEU* 3.2 27.7 + - + +
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Residues in contact with ILE 332 (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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305E PHE* 4.8 8.3 - - + -
320E TRP* 3.9 25.4 - - + -
328E PRO 2.9 28.5 + - - +
329E GLU 3.8 3.1 - - - +
331E MET* 1.3 84.9 - - + +
333E ARG* 1.3 61.8 + - - +
334E ARG 3.3 0.2 + - - -
335E LEU* 3.4 7.3 + - - +
336E LYS* 2.9 29.8 + - - +
342E ILE* 4.2 17.7 - - + +
408E MET* 3.7 29.8 - - - +
409E GLY* 3.8 20.6 - - - +
410E VAL* 4.1 19.1 - - + -
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Residues in contact with ARG 333 (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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329E GLU* 2.8 48.4 + - + +
330E GLY* 3.9 5.8 - - - +
332E ILE* 1.3 76.1 - - - +
334E ARG* 1.3 56.7 + - - +
336E LYS* 3.3 38.0 + - - +
337E ALA* 2.9 27.0 + - - +
407E ALA 3.3 25.7 + - - -
408E MET 3.7 16.3 + - - -
409E GLY* 4.3 2.2 - - - -
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Residues in contact with ARG 334 (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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283E GLU* 3.2 32.9 + - - +
286E VAL* 5.8 0.2 - - - +
287E ASN* 2.6 47.7 + - - +
330E GLY 3.1 15.7 + - - +
331E MET* 3.3 32.3 + - - +
332E ILE 3.1 0.2 - - - -
333E ARG* 1.3 73.5 - - - +
335E LEU* 1.3 60.1 + - + +
337E ALA* 2.7 34.9 + - + +
338E LYS* 3.2 21.2 + - + +
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Residues in contact with LEU 335 (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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286E VAL* 4.0 16.8 - - + -
287E ASN* 4.0 20.0 - - - +
290E ILE* 3.2 39.0 - - + -
303E PHE* 4.3 4.5 - - + -
305E PHE* 4.2 13.7 - - + -
331E MET* 3.2 15.8 + - + +
332E ILE* 3.8 5.6 - - - +
334E ARG* 1.3 84.9 - - + +
336E LYS* 1.3 63.9 + - - +
338E LYS* 3.0 23.0 + - + +
340E LEU* 3.3 20.7 + - + +
342E ILE* 3.7 28.3 - - + -
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Residues in contact with LYS 336 (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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332E ILE* 2.9 16.6 + - + +
333E ARG* 3.3 45.2 - - - +
335E LEU* 1.3 76.4 - - - +
337E ALA* 1.3 59.4 + - - +
339E GLY* 2.9 21.5 + - - -
340E LEU 3.7 15.8 + - - +
342E ILE* 5.1 3.7 - - + +
409E GLY* 3.2 31.8 + - - -
411E ASP* 4.3 10.7 + - - +
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Residues in contact with ALA 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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333E ARG 2.9 13.7 + - - +
334E ARG* 2.7 18.0 + - + +
336E LYS* 1.3 77.8 - - - +
338E LYS* 1.3 55.9 + - + +
339E GLY* 3.0 5.2 + - - -
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Residues in contact with LYS 338 (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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287E ASN* 5.0 8.3 + - - +
290E ILE* 4.2 21.0 - - + +
291E ASP* 2.7 31.7 + - - -
334E ARG* 3.9 23.0 - - + +
335E LEU* 3.0 17.2 + - + +
337E ALA* 1.3 76.0 - - + +
339E GLY* 1.3 59.5 + - - +
340E LEU* 3.3 12.0 + - + +
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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