Contacts of the helix formed by residues 312 - 329 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310L VAL 3.4 1.0 + - - -
311L GLN* 1.3 73.5 - - + +
313L ASP* 1.3 74.9 + - - +
314L ILE 3.0 1.6 + - - -
315L TYR* 3.2 15.1 + - - +
316L ASP* 4.7 3.8 + - - +
409L LYS* 4.0 35.7 + - + +
410L PHE 2.9 16.2 + - - +
411L LYS* 3.3 46.7 - - - +
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Residues in contact with ASP 313 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L SER* 4.3 21.2 + - - -
311L GLN* 3.1 5.2 + - + +
312L GLU* 1.3 86.5 - - - +
314L ILE* 1.3 61.0 + - + +
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Residues in contact with ILE 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ILE* 4.1 13.7 - - + +
278L MET 3.4 28.0 - - - +
279L SER* 3.7 29.4 - - - +
281L ALA* 5.4 2.0 - - + +
283L MET* 3.9 26.2 - - + -
310L VAL* 3.7 16.2 - - + -
311L GLN 3.2 13.0 - - - +
313L ASP* 1.3 81.2 - - + +
315L TYR* 1.3 65.7 + - - +
316L ASP 3.5 2.2 - - - -
317L GLU* 3.3 12.5 + - - +
318L PHE* 2.9 23.4 + - + +
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Residues in contact with TYR 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310L VAL* 3.9 20.2 - - + -
311L GLN 3.2 8.7 + - - +
312L GLU* 3.2 18.6 + - - +
314L ILE* 1.3 76.5 - - - +
316L ASP* 1.3 75.8 + - - +
318L PHE* 3.2 0.7 + - - +
319L VAL* 2.8 53.6 + - + +
387L GLY* 3.7 5.4 - - - -
388L ASP* 2.7 51.0 + - - -
407L ILE* 4.0 10.1 + - + -
408L LEU 4.1 4.7 - - - -
409L LYS* 3.4 43.7 - - + -
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Residues in contact with ASP 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312L GLU 4.7 3.4 + - - +
313L ASP 5.7 0.2 - - - -
314L ILE 3.5 0.4 - - - -
315L TYR* 1.3 94.7 - - - +
317L GLU* 1.3 62.8 + - - +
319L VAL* 3.5 3.6 + - - +
320L GLU* 3.0 24.0 + - - +
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Residues in contact with GLU 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283L MET* 3.9 21.4 - - + +
314L ILE* 3.3 14.2 + - - +
315L TYR 3.3 0.4 - - - -
316L ASP* 1.3 75.5 - - - +
318L PHE* 1.3 66.2 + - - +
320L GLU* 3.3 14.8 + - - +
321L ARG* 3.0 57.2 + - + +
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Residues in contact with PHE 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ILE* 4.2 19.5 - - + -
283L MET* 4.0 19.0 - - + +
286L ALA* 3.9 6.1 - - + -
287L VAL* 3.7 37.0 - - + -
290L ALA* 3.6 25.8 - - + -
308L THR* 3.8 13.9 - - + -
310L VAL* 3.3 35.7 - - + -
314L ILE 2.9 18.6 + - - +
315L TYR 3.5 2.7 - - - +
317L GLU* 1.3 77.1 - - - +
319L VAL* 1.3 60.7 + - + +
321L ARG* 3.2 4.4 + - - +
322L SER* 2.8 47.9 + - - -
405L MET* 5.7 1.1 - - - -
407L ILE* 4.5 11.0 - - + -
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Residues in contact with VAL 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315L TYR* 2.8 59.1 + - + +
316L ASP* 3.8 4.5 - - - +
318L PHE* 1.3 71.6 - - + +
320L GLU* 1.3 63.7 + - - +
322L SER* 3.2 6.3 + - - -
323L VAL* 2.9 26.6 + - + +
368L LEU* 3.4 35.0 - - + -
407L ILE* 4.0 25.1 - - + -
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Residues in contact with GLU 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316L ASP 3.0 14.4 + - - +
317L GLU* 3.4 18.8 - - - +
319L VAL* 1.3 78.1 - - - +
321L ARG* 1.3 66.5 + - + +
323L VAL* 3.4 4.8 + - - +
324L ALA* 3.1 22.8 + - + +
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Residues in contact with ARG 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283L MET* 3.2 36.2 - - - +
284L ASP* 2.7 38.3 + - - +
287L VAL* 3.9 21.4 - - + +
317L GLU* 3.0 40.8 + - + +
318L PHE 3.7 3.4 - - - +
320L GLU* 1.3 80.7 - - + +
322L SER* 1.3 57.4 + - - +
324L ALA* 3.4 7.4 + - - +
325L ARG* 3.0 29.1 + - - +
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Residues in contact with SER 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287L VAL* 4.0 13.3 + - - +
290L ALA* 5.4 0.3 - - - +
291L HIS* 5.1 2.6 + - - -
295L PHE* 5.8 0.3 - - - -
318L PHE* 2.8 47.0 + - - -
319L VAL 3.6 4.3 - - - -
321L ARG* 1.3 74.1 - - - +
323L VAL* 1.3 61.4 + - - +
325L ARG* 3.3 4.2 + - - +
326L ALA* 2.9 29.5 + - - +
385L VAL* 4.6 2.5 - - - +
405L MET* 4.5 14.9 - - - +
407L ILE* 4.2 18.4 - - - -
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Residues in contact with VAL 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L VAL* 2.9 23.7 + - + +
320L GLU* 3.9 4.7 - - - +
322L SER* 1.3 74.2 - - - +
324L ALA* 1.3 63.4 + - - +
326L ALA* 3.2 6.6 + - - +
327L LYS* 3.0 37.6 + - + +
368L LEU* 3.6 54.1 - - + +
369L CYS* 3.9 11.0 - - + -
385L VAL* 4.1 11.4 - - + -
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Residues in contact with ALA 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320L GLU* 3.1 17.3 + - + +
321L ARG* 3.6 8.5 - - - +
323L VAL* 1.3 77.5 - - - +
325L ARG* 1.3 61.2 + - - +
327L LYS* 3.4 9.1 + - - +
328L SER* 3.2 23.3 + - - -
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Residues in contact with ARG 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287L VAL* 4.7 9.2 - - + +
288L GLU* 5.0 18.9 + - - +
291L HIS* 3.3 55.9 + - + +
321L ARG 3.0 18.3 + - - +
322L SER* 3.6 8.1 - - - +
323L VAL 3.3 0.2 - - - -
324L ALA* 1.3 75.9 - - - +
326L ALA* 1.3 61.1 + - - +
328L SER* 2.9 26.9 + - - -
329L ARG* 3.3 11.1 + - - +
340L GLU* 3.4 33.3 + - - -
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Residues in contact with ALA 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291L HIS* 4.1 10.9 - - - -
295L PHE* 4.3 8.7 - - + -
322L SER 2.9 16.4 + - - +
323L VAL 3.2 6.0 + - - +
325L ARG* 1.3 77.6 - - - +
327L LYS* 1.3 60.7 + - - +
329L ARG* 3.3 10.4 + - - +
369L CYS* 3.7 9.4 - - - -
383L PRO* 3.4 31.3 - - + +
385L VAL* 3.6 25.4 - - + -
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Residues in contact with LYS 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323L VAL* 3.0 30.9 + - + +
324L ALA* 3.8 8.3 - - - +
325L ARG 3.3 0.2 - - - -
326L ALA* 1.3 76.0 - - - +
328L SER* 1.3 60.7 + - - +
329L ARG 3.5 4.0 + - - +
368L LEU 4.4 4.6 + - - -
369L CYS* 3.9 29.6 - - + +
383L PRO* 6.2 0.4 - - - -
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Residues in contact with SER 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324L ALA 3.2 13.2 + - - -
325L ARG* 2.9 31.8 + - - -
327L LYS* 1.3 76.0 - - - +
329L ARG* 1.3 62.8 + - - +
330L VAL* 3.2 14.4 + - - +
340L GLU* 4.3 5.0 - - - +
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Residues in contact with ARG 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291L HIS* 3.3 35.9 + - + +
292L PHE* 6.1 0.8 - - - +
295L PHE* 3.2 39.2 + - - +
296L PHE* 4.3 4.6 - - - +
297L ASN 4.9 2.2 - - - +
298L GLN* 4.9 0.8 + - - +
325L ARG* 3.3 12.0 + - - +
326L ALA 3.4 13.3 - - - +
327L LYS 3.3 4.9 - - - +
328L SER* 1.3 75.4 - - - +
330L VAL* 1.3 63.4 + - - +
331L VAL* 3.4 9.9 + - - +
340L GLU* 3.3 52.6 + - + +
341L GLN* 3.3 33.7 + - + +
383L PRO* 4.0 14.7 - - + +
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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
------------------------------------------------------------
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