Contacts of the helix formed by residues 312 - 329 (chain E) in PDB entry 1ZUM
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 GLU 312 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E VAL 3.4 0.8 + - - -
311E GLN* 1.3 72.2 - - + +
313E ASP* 1.3 77.3 + - - +
314E ILE 3.2 1.4 + - - -
315E TYR* 3.3 13.8 + - - +
316E ASP* 4.8 4.2 + - - +
409E LYS* 3.9 28.6 - - + +
410E PHE 2.8 17.1 + - - +
411E LYS* 3.3 44.4 + - - +
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Residues in contact with ASP 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E SER* 4.8 16.1 - - - -
311E GLN* 3.1 5.4 + - - +
312E GLU* 1.3 90.3 - - - +
314E ILE* 1.3 63.3 + - + +
315E TYR 3.6 0.2 - - - -
316E ASP 5.6 0.2 - - - -
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Residues in contact with ILE 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E ILE* 3.9 20.9 - - + +
278E MET 3.4 27.1 - - - +
279E SER* 3.7 30.5 - - - +
281E ALA* 5.4 2.5 - - + +
283E MET* 3.8 25.8 - - + -
310E VAL* 3.7 9.9 - - + -
311E GLN 3.2 12.8 - - - +
313E ASP* 1.3 80.9 - - + +
315E TYR* 1.3 65.3 + - - +
316E ASP 3.5 1.6 - - - -
317E GLU* 3.4 10.9 + - - +
318E PHE* 2.9 24.1 + - + +
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Residues in contact with TYR 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E VAL* 3.6 18.8 - - + -
311E GLN 3.2 8.2 + - - +
312E GLU* 3.3 20.2 + - - +
314E ILE* 1.3 78.2 - - - +
316E ASP* 1.3 81.4 + - - +
318E PHE* 3.2 0.7 + - - +
319E VAL* 2.8 45.5 + - + +
387E GLY* 3.7 5.7 - - - -
388E ASP* 2.7 47.2 + - - -
407E ILE* 3.8 19.9 + - + -
408E LEU 4.0 0.2 - - - -
409E LYS* 3.7 54.5 - - + -
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Residues in contact with ASP 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E GLU 4.8 3.7 + - - +
313E ASP 5.6 0.2 - - - -
314E ILE 3.5 0.6 - - - -
315E TYR* 1.3 92.9 - - - +
317E GLU* 1.3 57.6 + - - +
319E VAL* 3.4 4.3 + - - +
320E GLU* 3.0 29.8 + - - +
409E LYS* 5.2 3.3 + - - -
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Residues in contact with GLU 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E MET* 3.6 22.5 - - + +
314E ILE* 3.4 11.7 + - - +
315E TYR 3.3 0.6 - - - -
316E ASP* 1.3 74.9 - - - +
318E PHE* 1.3 67.8 + - - +
320E GLU* 3.1 14.1 + - - +
321E ARG* 2.9 61.5 + - + +
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Residues in contact with PHE 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E ILE* 4.0 25.1 - - + -
283E MET* 4.0 18.8 - - + +
286E ALA* 3.7 13.5 - - + -
287E VAL* 3.5 28.0 - - + -
290E ALA* 3.5 27.4 - - + -
308E THR* 3.7 15.7 - - + -
310E VAL* 3.4 32.8 - - + -
314E ILE* 2.9 18.6 + - + +
315E TYR 3.6 2.9 - - - +
317E GLU* 1.3 77.7 - - - +
319E VAL* 1.3 57.8 + - - +
321E ARG* 3.2 2.9 + - - +
322E SER* 2.9 47.8 + - - -
405E MET* 5.7 1.1 - - - -
407E ILE* 4.4 11.7 - - + -
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Residues in contact with VAL 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E TYR* 2.8 61.4 + - + +
316E ASP* 3.7 4.9 - - - +
318E PHE* 1.3 70.9 - - + +
320E GLU* 1.3 59.0 + - - +
322E SER* 3.2 6.6 + - - -
323E VAL* 2.8 38.1 + - + +
368E LEU* 3.4 33.2 - - + -
407E ILE* 4.0 20.6 - - + -
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Residues in contact with GLU 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E ASP 3.0 14.1 + - - +
317E GLU* 3.4 18.5 - - - +
319E VAL* 1.3 77.4 - - - +
321E ARG* 1.3 66.2 + - + +
323E VAL* 3.5 5.8 + - - +
324E ALA* 3.2 22.7 + - + +
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Residues in contact with ARG 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E MET* 3.4 27.6 - - - +
284E ASP* 2.7 30.1 + - - +
287E VAL* 3.7 22.8 - - + +
317E GLU* 2.9 48.5 + - + +
320E GLU* 1.3 80.6 - - + +
322E SER* 1.3 57.6 + - - +
324E ALA* 3.5 6.0 + - - +
325E ARG* 3.0 27.9 + - - +
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Residues in contact with SER 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E VAL* 4.0 13.7 + - - +
290E ALA* 5.5 0.2 - - - +
291E HIS* 5.0 3.2 + - - -
295E PHE* 6.0 0.2 - - - -
318E PHE* 2.9 45.8 + - - -
319E VAL 3.5 3.8 - - - -
321E ARG* 1.3 75.2 - - - +
323E VAL* 1.3 59.8 + - - +
325E ARG* 3.3 3.9 + - - +
326E ALA* 2.9 30.1 + - - +
385E VAL* 4.6 4.1 - - - +
405E MET* 4.4 14.4 - - - +
407E ILE* 4.1 18.2 - - - -
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Residues in contact with VAL 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E VAL* 2.8 25.4 + - + +
320E GLU* 3.8 6.7 - - - +
322E SER* 1.3 75.4 - - - +
324E ALA* 1.3 64.3 + - - +
326E ALA* 3.3 6.9 + - - +
327E LYS* 3.0 52.2 + - + +
368E LEU* 3.7 45.3 - - + +
369E CYS* 4.2 5.4 - - + -
385E VAL* 4.6 8.7 - - + -
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E GLU* 3.2 15.1 + - + +
321E ARG* 3.7 7.6 - - - +
323E VAL* 1.3 82.6 - - - +
325E ARG* 1.3 60.4 + - - +
327E LYS* 3.5 8.9 + - - +
328E SER* 3.2 24.1 + - - -
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Residues in contact with ARG 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E VAL* 4.6 9.0 - - + -
288E GLU* 2.8 46.8 + - - +
291E HIS* 3.3 53.7 + - + +
321E ARG 3.0 17.3 + - - +
322E SER* 3.6 7.9 - - - +
323E VAL 3.3 0.2 - - - -
324E ALA* 1.3 77.0 - - - +
326E ALA* 1.3 60.0 + - - +
328E SER* 2.7 27.3 + - - -
329E ARG* 3.2 17.7 + - - +
340E GLU* 2.6 38.4 + - - -
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Residues in contact with ALA 326 (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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291E HIS* 4.0 10.3 - - + -
295E PHE* 4.4 8.5 - - + -
322E SER 2.9 17.0 + - - +
323E VAL 3.6 3.8 - - - +
325E ARG* 1.3 77.6 - - - +
327E LYS* 1.3 61.1 + - - +
329E ARG* 3.2 17.5 + - - +
369E CYS* 3.8 8.1 - - - -
383E PRO* 3.5 26.2 - - + +
385E VAL* 3.6 26.5 - - + -
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Residues in contact with LYS 327 (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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323E VAL* 3.0 34.3 + - + +
324E ALA* 3.9 6.7 - - - +
325E ARG 3.3 0.2 - - - -
326E ALA* 1.3 75.7 - - - +
328E SER* 1.3 60.0 + - - +
329E ARG 3.3 4.0 + - - +
368E LEU 4.2 5.0 + - - -
369E CYS* 3.7 30.5 - - + +
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Residues in contact with SER 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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324E ALA 3.2 14.1 + - - -
325E ARG* 2.7 34.1 + - - -
327E LYS* 1.3 76.0 - - - +
329E ARG* 1.3 63.1 + - - +
330E VAL* 3.2 12.8 + - - +
340E GLU* 3.7 6.0 - - - +
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Residues in contact with ARG 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E HIS* 3.0 36.1 + - + -
292E PHE* 5.8 1.4 - - - +
295E PHE* 3.1 39.2 + - - +
296E PHE* 4.3 4.0 - - - +
297E ASN 4.9 1.8 - - - +
298E GLN 5.1 1.0 - - - +
325E ARG* 3.2 16.0 + - - +
326E ALA 3.2 18.0 + - - +
327E LYS 4.4 3.6 - - - +
328E SER* 1.3 74.5 - - - +
330E VAL* 1.3 63.3 + - - +
331E VAL* 3.5 10.2 + - - +
340E GLU* 3.5 47.7 + - + +
341E GLN* 3.0 34.4 + - + +
383E PRO* 4.0 10.6 - - + +
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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