Contacts of the strand formed by residues 404 - 410 (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 VAL 404 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E LEU* 3.2 14.3 - - - +
306E SER* 5.1 0.3 - - - -
353E ILE* 4.0 17.5 - - + -
356E TYR* 3.6 19.2 + - + -
357E ILE* 3.8 28.3 - - + -
384E THR* 3.3 9.0 - - + -
386E PHE* 3.7 27.6 - - + -
400E ILE* 4.1 12.9 - - + +
402E GLY 2.8 9.7 + - - +
403E PRO* 1.3 78.0 - - + +
405E MET* 1.3 58.8 + - - +
406E GLN* 3.2 32.5 + - - +
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Residues in contact with MET 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E ALA* 3.4 33.0 - - + +
291E HIS* 3.8 16.4 - - + +
294E LEU* 3.5 21.3 - - + +
295E PHE* 3.9 14.6 - - + -
308E THR* 4.0 19.1 - - - +
318E PHE* 5.7 0.2 - - - -
322E SER* 4.4 14.8 - - - +
384E THR 2.7 15.4 + - - +
385E VAL* 3.5 14.5 - - + -
386E PHE* 2.8 35.0 + - - +
404E VAL* 1.3 73.3 - - - +
406E GLN* 1.3 62.0 + - - +
407E ILE* 3.9 28.0 - - + -
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Residues in contact with GLN 406 (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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272E LYS* 3.9 3.2 - - - +
306E SER* 2.8 38.1 + - - +
307E ARG* 5.3 1.1 - - + -
308E THR* 2.8 31.7 + - - -
356E TYR* 2.9 27.1 + - - -
386E PHE* 3.8 3.9 - - - -
389E VAL* 4.0 11.9 - - + -
395E ILE* 3.1 39.8 + - + +
404E VAL* 3.2 36.2 + - - +
405E MET* 1.3 73.7 - - - +
407E ILE* 1.3 62.0 + - - +
408E LEU* 3.7 9.7 - - + +
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Residues in contact with ILE 407 (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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308E THR* 3.4 13.2 - - - +
310E VAL* 3.8 22.4 - - + -
315E TYR* 3.8 18.4 + - + +
318E PHE* 4.4 3.6 - - + -
319E VAL* 4.0 24.2 - - + -
322E SER* 4.1 18.2 - - - +
368E LEU* 5.4 0.7 - - + -
385E VAL* 3.9 21.1 - - + -
386E PHE 3.0 13.3 + - - +
387E GLY* 4.7 1.3 - - - -
388E ASP 3.4 10.2 + - - -
389E VAL* 3.2 21.4 + - - +
405E MET* 3.9 22.7 - - + -
406E GLN* 1.3 76.8 - - - +
408E LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 408 (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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307E ARG* 4.0 26.0 - - + -
308E THR 2.8 11.2 + - - +
309E PHE* 3.5 25.3 - - + -
310E VAL* 2.9 30.0 + - - +
315E TYR* 4.0 3.1 - - - -
389E VAL* 3.5 40.4 - - + +
390E GLN 4.2 3.6 - - - +
391E ASP* 3.4 25.6 - - - +
396E ALA* 4.5 7.2 - - + -
406E GLN* 3.7 23.1 - - + +
407E ILE* 1.3 76.8 - - - +
409E LYS* 1.3 59.3 + - - +
419E ARG* 3.9 4.9 - - - +
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Residues in contact with LYS 409 (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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309E PHE* 5.3 0.2 - - - -
310E VAL 3.4 2.9 - - - +
312E GLU* 3.9 35.0 - - + +
315E TYR* 3.7 44.9 - - + +
316E ASP* 5.2 3.8 + - - -
388E ASP* 4.3 13.8 + - - +
389E VAL 4.7 3.0 + - - -
408E LEU* 1.3 75.2 - - - +
410E PHE* 1.3 64.7 + - - +
415E GLU* 4.4 0.2 - - - +
419E ARG* 2.8 22.6 + - - +
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Residues in contact with PHE 410 (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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276E ILE* 3.8 16.2 - - + -
277E ILE 3.6 7.6 - - - -
278E MET* 3.8 9.0 - - - -
309E PHE* 3.5 24.7 - - + -
310E VAL 3.1 36.3 + - - -
311E GLN* 3.1 52.3 - - + -
312E GLU* 2.8 32.3 + - - +
409E LYS* 1.3 76.5 - - - +
411E LYS* 1.3 60.6 + - - +
412E THR 3.5 20.2 - - - -
415E GLU* 3.8 11.7 - - + +
416E VAL* 3.6 24.0 - - + -
419E ARG* 3.8 11.9 - - - +
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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