Contacts of the strand formed by residues 404 - 410 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294K LEU* 3.2 12.9 - - - +
306K SER* 5.1 0.2 - - - -
353K ILE* 4.0 9.9 - - + -
356K TYR 6.2 0.4 - - - -
357K ILE* 3.9 26.2 - - + -
384K THR* 3.3 9.2 - - + -
386K PHE* 3.7 27.4 - - + -
395K ILE* 5.5 2.7 - - + -
400K ILE* 3.4 32.1 - - + +
402K GLY 2.8 9.9 + - - +
403K PRO* 1.3 78.1 - - + +
405K MET* 1.3 58.8 + - - +
406K GLN* 3.0 34.6 + - - +
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Residues in contact with MET 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290K ALA* 4.7 17.0 - - - +
291K HIS* 5.2 3.1 - - + +
294K LEU* 3.5 22.4 - - + +
295K PHE* 4.1 14.8 - - + -
308K THR* 4.1 17.5 - - - +
318K PHE* 5.6 0.4 - - - -
322K SER* 3.6 31.9 - - - +
384K THR 2.7 15.4 + - - +
385K VAL* 3.4 33.8 - - + -
386K PHE* 2.8 31.4 + - - +
404K VAL* 1.3 73.8 - - - +
406K GLN* 1.3 65.8 + - - +
407K ILE* 3.6 17.9 - - + -
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Residues in contact with GLN 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K LYS* 3.9 9.7 - - - +
294K LEU* 4.7 0.2 - - - +
306K SER* 3.0 35.0 + - - +
307K ARG* 3.9 1.3 - - + -
308K THR* 2.9 31.9 + - - -
386K PHE* 3.8 3.3 - - - -
389K VAL* 4.2 9.6 - - + -
395K ILE* 3.2 54.7 + - + +
396K ALA* 5.5 0.2 - - - -
400K ILE* 6.0 1.4 - - - +
404K VAL* 3.0 47.3 + - - +
405K MET* 1.3 78.5 - - - +
407K ILE* 1.3 61.6 + - - +
408K LEU* 3.8 9.5 - - + +
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Residues in contact with ILE 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308K THR* 3.4 11.7 - - - +
310K VAL* 3.8 21.5 - - + -
315K TYR* 4.0 6.3 + - + +
318K PHE* 4.5 4.3 - - + -
319K VAL* 3.9 35.4 - - + -
322K SER* 4.2 12.1 - - - +
368K LEU* 5.0 0.9 - - + -
385K VAL* 3.7 12.3 - - + -
386K PHE 3.0 14.3 + - - +
387K GLY* 4.6 2.2 - - - -
388K ASP 3.4 8.8 + - - -
389K VAL* 3.1 22.2 + - - +
405K MET* 3.6 37.2 - - + -
406K GLN* 1.3 76.5 - - - +
408K LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K ARG* 4.0 19.1 - - + -
308K THR 2.8 19.8 + - - +
309K PHE* 3.4 26.1 - - + -
310K VAL* 2.8 29.5 + - - +
315K TYR* 4.0 3.8 - - - -
389K VAL* 3.6 34.3 - - + +
390K GLN 4.3 1.8 - - - -
391K ASP* 3.4 29.6 - - - +
396K ALA* 4.6 7.0 - - + -
406K GLN* 3.8 22.2 - - + +
407K ILE* 1.3 78.6 - - - +
409K LYS* 1.3 60.9 + - - +
419K ARG* 3.9 4.3 - - - +
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Residues in contact with LYS 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309K PHE* 5.3 0.2 - - - -
310K VAL 3.4 4.0 - - - +
312K GLU* 3.9 35.9 - - + +
315K TYR* 3.5 44.7 - - + -
316K ASP* 5.3 2.6 + - - -
388K ASP* 4.2 16.1 + - - +
389K VAL 4.8 2.6 + - - +
408K LEU* 1.3 73.4 - - - +
410K PHE* 1.3 64.7 + - - +
419K ARG* 2.8 23.8 + - - -
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Residues in contact with PHE 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K ILE* 4.0 7.0 - - + -
277K ILE 3.7 8.3 - - - -
278K MET* 3.9 17.7 - - - -
309K PHE* 3.6 22.0 - - + -
310K VAL* 3.1 27.9 + - - -
311K GLN* 3.1 41.2 - - + -
312K GLU* 2.9 29.3 + - - +
409K LYS* 1.3 77.3 - - - +
411K LYS* 1.3 58.7 + - - +
412K THR 3.2 32.5 - - - -
415K GLU* 3.8 7.9 - - - +
416K VAL* 3.4 24.5 - - + -
419K ARG* 3.6 15.5 - - - +
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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