Contacts of the helix formed by residues 325 - 342 (chain E) in PDB entry 4ZZ7
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 THR 325 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E PHE* 5.5 10.5 - - + -
176E ARG* 4.3 22.5 + - + +
323E VAL* 3.4 1.3 - - - +
324E ILE* 1.3 97.0 - - + +
326E ARG* 1.3 60.4 + - - +
327E GLN* 3.5 10.7 + - - +
328E HIS* 3.0 25.1 + - - +
329E GLN 3.0 19.9 + - - -
362E PHE* 3.4 24.3 - - + +
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Residues in contact with ARG 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E GLY* 5.7 2.0 + - - -
325E THR* 1.3 71.9 - - - +
327E GLN* 1.3 65.4 + - - +
329E GLN* 3.3 28.1 + - - +
330E GLU* 3.0 45.7 + - + +
360E ASN* 3.2 36.7 + - - +
361E GLY 3.4 10.7 + - - -
362E PHE* 3.5 35.6 - - + -
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Residues in contact with GLN 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D GLU* 5.6 6.5 + - - +
176E ARG* 5.5 4.7 + - - -
325E THR* 3.3 10.2 + - - +
326E ARG* 1.3 79.1 - - - +
328E HIS* 1.3 57.6 + - - +
330E GLU* 3.2 17.0 + - - +
331E LYS* 2.8 32.6 + - + +
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Residues in contact with HIS 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E PHE* 4.5 5.1 - + - -
176E ARG* 5.8 3.3 + - - +
278E GLU* 3.7 15.0 + - - -
323E VAL* 3.6 28.0 - - + -
324E ILE* 3.8 12.8 - - + +
325E THR* 3.0 18.2 + - - +
327E GLN* 1.3 75.7 - - - +
329E GLN* 1.3 65.4 + - - +
331E LYS* 3.2 27.8 + - + +
332E VAL* 2.9 30.6 + - + +
383E ILE 4.2 6.5 - - - -
384E PHE* 3.0 50.8 + + + -
501E NAD 6.1 0.7 - - - -
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Residues in contact with GLN 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E VAL* 3.4 12.4 - - + +
325E THR 3.0 18.0 + - - +
326E ARG* 3.3 36.3 + - - +
328E HIS* 1.3 76.3 - - - +
330E GLU* 1.3 60.1 + - + +
332E VAL* 3.2 3.3 + - - +
333E ILE* 2.9 42.6 + - + +
351E ARG 5.6 1.2 + - - -
353E PRO* 5.6 1.6 - - - +
361E GLY 3.9 5.3 + - - -
362E PHE* 3.6 13.3 - - + -
363E PHE 3.0 27.9 + - - +
364E VAL* 3.9 18.3 - - + +
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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
----------------------------------------------------------
342D GLN* 5.1 4.4 + - - +
377D THR* 3.0 43.7 + - + +
380D GLN* 5.3 3.3 - - - +
381D GLU* 4.2 5.7 - - - +
326E ARG* 3.0 39.5 + - + +
327E GLN* 3.4 16.1 - - - +
329E GLN* 1.3 77.9 - - + +
331E LYS* 1.3 58.5 + - - +
333E ILE* 3.6 9.0 + - - +
334E GLY* 2.8 25.1 + - - -
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Residues in contact with LYS 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E GLN* 2.8 17.5 + - + +
328E HIS* 3.2 32.8 + - + +
330E GLU* 1.3 75.1 - - - +
332E VAL* 1.3 63.6 - - - +
334E GLY* 3.3 2.9 + - - -
335E TYR* 3.0 58.5 + - + +
382E GLU 5.4 2.5 + - - +
383E ILE 5.2 1.1 - - - +
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Residues in contact with VAL 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E VAL* 4.6 5.2 - - + -
328E HIS* 2.9 27.2 + - + +
329E GLN* 3.6 8.5 - - - +
331E LYS* 1.3 71.5 - - - +
333E ILE* 1.3 68.3 + - - +
335E TYR* 2.9 22.0 + - - +
336E ILE* 3.1 13.6 + - + +
364E VAL* 4.0 27.6 - - + -
383E ILE* 3.7 31.9 - - + +
384E PHE 4.0 4.3 - - - +
385E GLY* 4.0 17.3 - - - -
387E VAL* 4.2 12.3 - - + -
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Residues in contact with ILE 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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341D GLN* 3.6 29.8 - - - +
329E GLN* 2.9 39.6 + - + +
330E GLU* 3.7 8.3 - - - +
332E VAL* 1.3 71.4 - - - +
334E GLY* 1.3 58.0 + - - +
336E ILE* 3.0 11.4 + - + +
337E ASN* 3.0 34.3 + - - +
351E ARG* 3.3 44.2 - - + +
363E PHE 5.5 0.2 - - - +
364E VAL* 4.5 17.3 - - + -
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Residues in contact with GLY 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D GLY* 6.1 2.7 - - - -
337D ASN* 5.4 0.9 + - - -
330E GLU 2.8 17.9 + - - -
331E LYS* 3.6 3.8 - - - -
332E VAL 3.1 0.4 - - - -
333E ILE* 1.3 76.9 - - - +
335E TYR* 1.3 56.7 + - - +
337E ASN* 3.2 14.1 + - - +
338E SER* 2.9 29.2 + - - -
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Residues in contact with TYR 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 LYS* 3.0 53.7 + - + +
332E VAL* 2.9 7.3 + - - +
334E GLY* 1.3 71.5 - - - +
336E ILE* 1.3 65.1 + - - +
338E SER* 3.4 6.4 + - - -
339E ALA* 3.1 24.8 + - - +
377E THR* 4.6 4.3 - - + -
378E SER* 3.5 26.8 - - - -
381E GLU* 3.0 40.0 + - + +
382E GLU 3.6 22.9 + - - -
383E ILE* 3.7 41.5 - - + -
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Residues in contact with ILE 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E VAL* 3.5 21.1 - - + +
333E ILE* 3.0 9.5 + - - +
335E TYR* 1.3 77.2 - - + +
337E ASN* 1.3 61.2 + - - +
339E ALA* 3.6 6.2 + - - +
340E GLU* 3.3 22.0 + - - +
346E ILE* 3.9 20.9 - - + +
349E ASP* 4.3 5.4 - - - +
351E ARG* 3.9 35.1 + - + +
364E VAL* 4.5 6.5 - - + -
367E THR* 3.7 37.5 - - + +
369E ILE* 4.5 9.9 - - + -
387E VAL* 4.2 16.4 - - + -
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Residues in contact with ASN 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D ASN* 4.0 29.3 + - + +
338D SER* 4.5 5.3 - - - +
341D GLN* 3.7 24.3 + - - +
333E ILE* 3.0 31.1 + - - +
334E GLY* 3.2 11.0 + - - +
336E ILE* 1.3 75.9 - - - +
338E SER* 1.3 60.2 + - - +
340E GLU* 3.3 4.1 + - - +
341E GLN* 2.9 31.3 + - - +
351E ARG* 2.9 36.1 + - - +
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Residues in contact with SER 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D ASN* 4.4 11.1 - - - +
334E GLY 2.9 16.3 + - - -
335E TYR* 3.7 11.2 - - - -
337E ASN* 1.3 74.4 - - - +
339E ALA* 1.3 58.5 + - - +
341E GLN* 3.5 7.1 + - - +
342E GLN* 2.8 56.2 + - - +
377E THR* 4.2 12.0 - - - -
378E SER* 4.2 4.5 + - - -
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Residues in contact with ALA 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 TYR 3.1 13.7 + - - +
336E ILE 3.8 5.8 - - - +
338E SER* 1.3 73.3 + - - +
340E GLU* 1.3 65.2 + - - +
342E GLN* 3.3 5.2 + - - +
343E GLY 3.3 5.7 + - - -
344E ALA* 2.9 29.9 + - + +
346E ILE* 4.8 0.4 - - + -
369E ILE* 4.2 30.7 - - + -
372E VAL* 5.8 0.2 - - + -
376E MET* 4.3 4.2 - - - +
378E SER* 3.4 23.3 + - - +
389E GLN* 4.8 1.8 - - - +
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Residues in contact with GLU 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 ILE 3.3 10.4 + - - +
337E ASN* 3.6 6.9 - - - +
339E ALA* 1.3 77.0 - - - +
341E GLN* 1.3 59.5 + - - +
343E GLY* 3.0 21.8 + - - -
344E ALA 3.7 13.4 + - - +
346E ILE* 3.8 18.8 - - + +
351E ARG* 2.7 37.1 + - - -
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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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333D ILE* 3.6 10.8 - - - +
337D ASN* 3.1 32.3 + - - +
351D ARG* 3.8 30.5 - - - +
352D GLN* 3.8 25.3 + - - -
337E ASN 2.9 18.1 + - - +
338E SER* 3.8 7.0 - - - +
340E GLU* 1.3 77.7 - - - +
342E GLN* 1.3 63.9 + - - +
343E GLY 3.4 0.2 - - - -
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Residues in contact with GLN 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 SER* 2.8 37.8 + - - +
339E ALA 3.3 4.9 + - - +
340E GLU 3.2 0.2 - - - -
341E GLN* 1.3 84.5 - - + +
343E GLY* 1.3 56.4 + - - +
344E ALA 3.8 0.7 - - - -
375E GLU 4.9 2.4 + - - -
376E MET* 3.8 32.4 - - + +
377E THR* 3.4 38.0 + - - +
378E SER* 4.2 1.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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