Contacts of the helix formed by residues 327 - 341 (chain E) in PDB entry 1M54
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 ASN 327 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282E PRO* 5.6 2.2 - - - -
283E GLU* 4.9 15.5 - - + +
303E VAL* 5.3 0.9 - - - -
326E SER* 1.3 78.5 + - - +
328E ASP* 1.3 60.9 + - - +
329E GLU* 2.5 35.0 + - - +
330E GLU* 2.7 40.9 + - - +
331E ALA* 3.0 29.3 + - - +
352E SER* 5.2 0.4 - - - -
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Residues in contact with ASP 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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282E PRO* 6.1 0.3 - - - +
301E TYR* 3.9 12.2 - - - +
302E GLU* 3.1 38.8 + - + +
303E VAL* 2.8 34.5 + - - +
327E ASN* 1.3 77.4 + - - +
329E GLU* 1.3 56.6 + - + +
331E ALA* 3.1 2.8 + - - +
332E PHE* 2.6 41.1 + - + +
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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 ASN* 2.5 10.8 + - - +
328E ASP* 1.3 75.7 - - + +
330E GLU* 1.3 61.7 + - - +
332E PHE* 3.4 21.7 - - - +
333E THR* 2.5 56.7 + - + +
390E TRP* 6.0 1.1 - - - -
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Residues in contact with GLU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E SER* 3.1 19.1 - - - -
327E ASN* 2.7 50.9 + - - +
329E GLU* 1.3 80.1 - - - +
331E ALA* 1.3 56.1 + - - +
333E THR* 2.9 18.6 + - - -
334E PHE* 3.2 29.5 + - + +
355E ALA* 3.8 26.9 - - + +
356E VAL* 5.4 2.3 - - - +
359E LYS* 5.9 0.9 + - - +
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Residues in contact with ALA 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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303E VAL* 4.3 8.5 - - + -
327E ASN 3.0 19.8 + - - +
328E ASP 3.4 4.0 - - - +
329E GLU 3.0 0.2 - - - -
330E GLU* 1.3 77.8 - - - +
332E PHE* 1.3 62.0 + - + +
335E ALA* 3.1 26.0 + - - +
348E GLY 4.0 4.0 - - - +
351E GLY* 3.4 9.6 - - - -
352E SER* 2.8 44.9 - - - +
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Residues in contact with PHE 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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302E GLU* 3.9 26.5 - - + -
303E VAL* 4.0 19.1 - - + -
328E ASP* 2.6 24.5 + - + +
329E GLU* 2.8 19.9 + - - +
331E ALA* 1.3 78.5 - - - +
333E THR* 1.3 60.9 + - - +
335E ALA* 3.5 4.2 - - - +
336E ARG* 3.2 27.0 + - - +
348E GLY* 3.8 21.1 - - - -
381E TYR* 4.6 11.2 - + - -
384E LYS* 5.0 3.8 - - + -
385E PHE* 3.6 28.0 - + + +
390E TRP* 3.1 44.9 - + - -
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Residues in contact with THR 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* 2.5 37.3 + - + +
330E GLU* 2.9 17.4 + - - -
332E PHE* 1.3 70.8 - - - +
334E PHE* 1.3 78.7 + - - +
335E ALA 2.9 2.0 + - - -
336E ARG* 3.0 10.0 + - - +
337E MET* 2.9 20.4 + - - +
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Residues in contact with PHE 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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95E ILE* 4.4 0.2 - - + -
99E PHE* 3.4 33.9 - + - -
330E GLU* 3.2 30.7 + - + +
333E THR* 1.3 88.4 + - - +
335E ALA* 1.3 52.2 + - - +
337E MET* 3.2 37.3 - - + +
338E LEU* 2.6 45.2 + - + +
351E GLY* 4.1 14.1 - - - +
354E VAL* 4.2 9.6 - - + -
355E ALA* 3.7 22.4 - - + -
358E VAL* 3.9 30.7 - - + -
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Residues in contact with ALA 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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331E ALA 3.1 20.8 + - - +
332E PHE 3.5 2.2 - - - +
334E PHE* 1.3 84.0 - - - +
336E ARG* 1.3 54.4 + - - +
338E LEU* 2.9 23.6 + - - +
339E ILE* 3.0 17.7 + - - +
346E CYS* 4.8 1.3 - - - -
347E GLY 4.1 4.3 - - - +
348E GLY* 4.0 10.1 - - - -
351E GLY* 4.0 2.9 - - - -
385E PHE* 2.8 36.3 - - + -
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Residues in contact with ARG 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 PHE 3.2 19.1 + - - +
333E THR* 3.0 5.0 + - - +
335E ALA* 1.3 70.7 - - - +
337E MET* 1.3 59.8 + - - +
338E LEU 3.2 0.2 - - - -
339E ILE* 3.2 19.4 + - + +
340E ALA* 3.0 28.1 + - - +
385E PHE* 2.7 35.7 + - + +
386E LEU* 3.0 31.2 + - - +
388E ASP* 2.7 41.5 + - - +
183F ALA* 4.3 12.3 - - + +
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Residues in contact with MET 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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95E ILE* 2.6 47.5 - - + +
98E LYS* 6.3 0.7 - - - -
99E PHE* 4.1 13.2 - - + -
333E THR* 2.9 13.1 + - - +
334E PHE* 3.2 45.3 - - + +
336E ARG* 1.3 77.8 - - - +
338E LEU* 1.3 58.8 + - - +
339E ILE 3.1 0.7 - - - -
340E ALA* 4.2 4.7 - - - +
341E GLN* 2.8 58.4 + - - +
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Residues in contact with LEU 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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92E ILE* 4.4 8.7 - - + -
95E ILE* 3.7 17.0 - - + -
334E PHE* 2.6 34.4 + - + +
335E ALA* 3.2 13.7 - - - +
337E MET* 1.3 72.7 - - - +
339E ILE* 1.3 57.5 + - - +
340E ALA 3.4 0.2 - - - -
342E GLU* 3.2 17.0 - - + +
343E GLY 3.3 1.0 + - - -
344E LEU* 2.9 41.9 + - + +
346E CYS* 4.2 14.4 - - - -
350E ALA 4.2 2.2 - - - +
351E GLY* 4.0 12.1 - - - +
354E VAL* 3.4 47.8 - - + -
374E LEU* 4.9 3.4 - - + -
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Residues in contact with ILE 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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335E ALA 3.0 12.3 - - - +
336E ARG* 3.2 31.9 - - + +
337E MET 3.1 0.2 - - - -
338E LEU* 1.3 80.7 - - - +
340E ALA* 1.3 56.4 + - - +
343E GLY* 3.7 10.9 + - - -
344E LEU 3.5 16.6 - - - +
345E LEU* 3.8 28.5 - - + -
346E CYS* 4.0 17.9 - - - +
378E VAL* 4.3 6.7 - - + -
385E PHE* 4.1 11.4 - - + -
386E LEU* 4.9 11.2 - - + -
156F LEU* 4.3 0.9 - - - +
180F VAL 5.6 0.4 - - - +
183F ALA* 4.3 15.3 - - + -
184F LEU* 3.4 25.2 - - + +
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Residues in contact with ALA 340 (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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336E ARG 3.0 14.6 + - - +
337E MET* 3.4 4.5 + - - +
339E ILE* 1.3 78.0 - - - +
341E GLN* 1.3 66.6 + - + +
342E GLU 3.4 1.6 - - - -
159F ALA* 2.9 27.1 - - - +
183F ALA 3.2 22.9 - - - +
184F LEU 4.4 6.8 - - - +
185F GLY* 5.6 1.6 - - - -
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Residues in contact with GLN 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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94E LYS* 3.4 41.9 - - + +
95E ILE* 4.2 23.2 + - + -
98E LYS* 5.4 5.5 - - - +
337E MET* 2.8 43.2 + - - +
340E ALA* 1.3 80.1 - - + +
342E GLU* 1.3 70.2 + - - +
159F ALA 4.2 5.5 - - - +
160F VAL* 5.1 0.9 - - - -
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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