Contacts of the strand formed by residues 404 - 410 (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 VAL 404 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294L LEU* 3.3 11.9 - - - +
306L SER* 5.0 1.0 - - - -
353L ILE* 3.8 28.0 - - + -
356L TYR* 3.5 20.6 - - + -
357L ILE* 3.9 15.9 - - + -
381L ILE* 5.6 0.4 - - + -
384L THR* 3.3 13.0 - - + +
386L PHE* 3.8 22.9 - - + -
400L ILE* 4.2 9.1 - - + +
402L GLY 2.8 11.4 + - - +
403L PRO* 1.3 75.8 - - + +
405L MET* 1.3 60.0 + - - +
406L GLN* 2.8 37.3 + - - +
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Residues in contact with MET 405 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290L ALA* 3.5 33.7 - - + +
291L HIS* 3.8 9.0 - - + +
294L LEU* 3.4 21.4 - - + +
295L PHE* 3.5 31.0 - - + -
308L THR* 4.2 14.4 - - - +
318L PHE* 5.7 0.4 - - - -
322L SER* 4.5 14.4 - - - +
384L THR 2.7 16.3 + - - +
385L VAL* 4.2 12.6 - - - -
386L PHE* 2.8 34.5 + - - +
404L VAL* 1.3 70.2 - - - +
406L GLN* 1.3 66.3 + - - +
407L ILE* 4.2 27.1 - - + -
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Residues in contact with GLN 406 (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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272L LYS* 4.2 2.6 - - - +
294L LEU* 4.2 1.6 - - - +
306L SER* 3.0 26.2 + - - +
307L ARG* 4.4 1.3 + - + -
308L THR* 2.8 31.2 + - - -
356L TYR* 2.9 26.4 + - - -
386L PHE* 3.7 3.5 - - - -
389L VAL* 3.9 10.3 - - + -
395L ILE* 3.3 39.2 - - + +
404L VAL* 2.8 38.7 + - - +
405L MET* 1.3 76.3 - - - +
407L ILE* 1.3 63.4 + - - +
408L LEU* 3.9 10.3 - - + +
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Residues in contact with ILE 407 (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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308L THR* 3.3 6.7 - - - +
310L VAL* 3.7 28.3 - - + -
315L TYR* 4.0 8.1 + - + +
318L PHE* 4.5 3.8 - - + -
319L VAL* 4.0 35.0 - - + -
322L SER* 4.2 15.9 - - - +
368L LEU* 5.1 0.4 - - + -
385L VAL* 3.9 21.1 - - + -
386L PHE 2.9 15.5 + - - +
387L GLY* 4.6 3.6 - - - -
388L ASP 3.4 9.0 + - - -
389L VAL* 3.2 21.4 + - - +
405L MET* 4.2 22.0 - - + -
406L GLN* 1.3 75.8 - - - +
408L LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 408 (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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307L ARG* 4.3 20.0 - - + +
308L THR 2.8 9.2 + - - +
309L PHE* 3.3 29.7 - - + -
310L VAL* 2.8 33.6 + - - +
315L TYR* 4.1 2.9 - - - -
389L VAL* 3.4 43.3 - - + +
390L GLN 4.4 0.2 - - - -
391L ASP* 3.3 33.2 - - - +
396L ALA* 4.8 4.3 - - + -
406L GLN* 3.9 17.7 - - + +
407L ILE* 1.3 78.1 - - - +
409L LYS* 1.3 55.5 + - - +
419L ARG* 3.8 6.1 - - - +
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Residues in contact with LYS 409 (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 3.4 7.4 - - - +
312L GLU* 4.0 35.5 + - + +
315L TYR* 3.4 32.6 - - + -
388L ASP* 5.6 5.7 - - - +
389L VAL 4.7 3.0 + - - +
408L LEU* 1.3 73.4 - - - +
410L PHE* 1.3 63.3 + - - +
411L LYS* 5.9 0.2 - - + -
415L GLU* 4.4 0.2 - - - +
419L ARG* 2.7 29.9 + - - +
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Residues in contact with PHE 410 (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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276L ILE* 3.9 7.0 - - + -
277L ILE 3.6 10.5 - - - -
278L MET* 3.8 16.4 - - - -
309L PHE* 3.4 30.7 - - + -
310L VAL 3.1 29.5 + - - -
311L GLN* 3.1 50.9 - - + -
312L GLU* 2.9 27.4 + - - +
409L LYS* 1.3 81.1 - - - +
411L LYS* 1.3 61.0 + - - +
412L THR 3.4 22.0 - - - -
415L GLU* 3.7 7.6 - - + +
416L VAL* 3.6 22.4 - - + -
419L ARG* 3.4 17.7 - - - +
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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
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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