Contacts of the strand formed by residues 404 - 410 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294J LEU* 3.2 13.9 - - - +
306J SER* 5.2 0.2 - - - -
353J ILE* 4.0 19.5 - - + -
356J TYR* 3.5 18.4 - - + -
357J ILE* 3.9 25.8 - - + -
384J THR* 3.3 9.6 - - - +
386J PHE* 3.6 24.7 - - + -
400J ILE* 4.0 11.9 - - + +
402J GLY 2.8 10.1 + - - +
403J PRO* 1.3 79.0 - - + +
405J MET* 1.3 58.3 + - - +
406J GLN* 3.1 34.8 + - - +
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Residues in contact with MET 405 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J ALA* 4.7 17.9 - - - +
291J HIS* 5.1 3.1 - - - +
294J LEU* 3.6 21.9 - - + +
295J PHE* 4.1 16.8 - - + -
308J THR* 4.1 17.5 - - - +
318J PHE* 5.3 0.7 - - + -
322J SER* 3.4 23.8 - - - +
384J THR 2.7 16.8 + - - +
385J VAL* 3.4 24.2 - - + -
386J PHE* 2.8 28.5 + - - +
404J VAL* 1.3 73.5 - - - +
406J GLN* 1.3 70.1 + - - +
407J ILE* 3.4 35.0 - - + -
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Residues in contact with GLN 406 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J LYS* 3.8 4.2 - - - +
294J LEU* 4.6 1.4 - - - +
306J SER* 3.0 29.2 + - - +
307J ARG* 5.2 1.3 - - + -
308J THR* 2.8 32.1 + - - -
356J TYR* 2.9 29.1 + - - -
386J PHE* 3.8 8.5 - - - -
389J VAL* 4.1 10.5 - - + -
395J ILE* 3.4 33.9 + - + +
396J ALA* 5.0 0.4 - - - -
400J ILE* 6.0 0.2 - - - +
404J VAL* 3.1 39.1 + - - +
405J MET* 1.3 77.4 - - - +
407J ILE* 1.3 60.4 + - - +
408J LEU* 4.1 9.4 - - + -
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Residues in contact with ILE 407 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J THR* 3.4 6.1 - - - +
310J VAL* 3.6 28.7 - - + -
315J TYR* 3.9 19.3 + - + +
318J PHE* 4.3 7.4 - - + -
319J VAL* 3.9 25.6 - - + -
322J SER* 4.2 10.8 - - - -
368J LEU* 5.2 0.4 - - + -
385J VAL* 4.0 8.7 - - + -
386J PHE 3.0 15.8 + - - +
387J GLY* 4.6 0.4 - - - -
388J ASP 3.4 9.4 + - - -
389J VAL* 3.2 21.4 + - - +
405J MET* 3.4 36.8 - - + -
406J GLN* 1.3 76.9 - - - +
408J LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307J ARG* 4.0 20.2 - - + -
308J THR 2.8 21.0 + - - +
309J PHE* 3.5 26.5 - - + -
310J VAL* 2.8 29.3 + - - +
315J TYR* 4.1 3.3 - - - -
388J ASP 5.4 0.2 - - - -
389J VAL* 3.6 34.1 - - + +
390J GLN 4.3 4.7 - - - -
391J ASP* 3.3 27.1 - - - +
396J ALA* 4.6 7.2 - - + -
406J GLN* 3.8 19.3 - - + +
407J ILE* 1.3 79.9 - - - +
409J LYS* 1.3 59.5 + - - +
419J ARG* 4.0 3.8 - - - +
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Residues in contact with LYS 409 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J PHE* 5.3 0.2 - - - -
310J VAL 3.4 3.8 - - - +
312J GLU* 4.0 34.1 - - + +
315J TYR* 3.6 45.3 - - + -
316J ASP* 5.5 2.2 + - - -
388J ASP* 4.2 15.8 + - - +
389J VAL 4.7 3.0 + - - -
408J LEU* 1.3 73.6 - - - +
410J PHE* 1.3 63.0 + - - +
419J ARG* 2.8 24.0 + - - +
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Residues in contact with PHE 410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J ILE* 3.9 7.2 - - + -
277J ILE 3.6 7.0 - - - -
278J MET* 3.8 18.6 - - - -
309J PHE* 3.6 28.3 - - + -
310J VAL 3.1 29.1 + - - -
311J GLN* 3.1 50.5 - - + -
312J GLU* 2.8 28.0 + - - +
409J LYS* 1.3 77.4 - - - +
411J LYS* 1.3 59.5 + - - +
412J THR 3.3 29.4 - - - -
415J GLU* 3.8 11.2 - - - +
416J VAL* 3.5 21.3 - - + -
419J ARG* 3.7 13.0 - - - +
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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