Contacts of the strand formed by residues 404 - 410 (chain H) in PDB entry 1NZX
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294H LEU* 3.6 13.4 - - - +
306H SER* 5.3 0.2 - - - -
353H ILE* 3.8 28.0 - - + -
357H ILE* 3.9 19.5 - - + -
384H THR* 3.2 7.9 - - + +
386H PHE* 3.5 30.1 - - + -
395H ILE* 5.7 0.4 - - + -
400H ILE* 3.9 27.2 - - + +
402H GLY 2.7 11.3 + - - +
403H PRO* 1.3 78.4 - - + +
405H MET* 1.3 59.4 + - - +
406H GLN* 2.9 31.8 + - - +
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Residues in contact with MET 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H ALA* 3.7 26.0 - - + +
291H HIS* 3.8 12.3 - - + +
294H LEU* 3.7 21.0 - - + +
295H PHE* 3.3 33.7 - - + -
308H THR* 4.1 16.2 - - - +
318H PHE* 5.5 2.2 - - - -
322H SER* 4.6 12.8 - - - +
384H THR 2.7 15.0 + - - +
385H VAL* 4.2 13.0 - - + -
386H PHE* 2.7 33.6 + - - +
404H VAL* 1.3 70.4 - - - +
406H GLN* 1.3 68.5 + - - +
407H ILE* 3.9 29.2 - - + -
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Residues in contact with GLN 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H LYS* 4.1 3.8 - - - +
306H SER* 3.3 29.3 + - - +
307H ARG* 4.1 1.3 - - + -
308H THR* 2.9 31.5 + - - -
386H PHE* 3.7 9.5 - - - -
389H VAL* 4.0 10.5 - - + -
395H ILE* 3.4 41.4 + - + +
396H ALA* 4.9 0.7 - - - -
400H ILE* 3.7 16.2 - - - +
404H VAL* 2.9 38.1 + - - +
405H MET* 1.3 89.6 - - - +
407H ILE* 1.3 61.9 + - - +
408H LEU* 3.7 9.4 - - + +
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Residues in contact with ILE 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H THR* 3.4 14.4 - - - +
310H VAL* 4.0 15.5 - - + -
315H TYR* 3.6 25.6 + - + +
318H PHE* 4.2 7.0 - - + -
319H VAL* 4.0 21.1 - - + -
322H SER* 4.1 16.6 - - - -
368H LEU* 5.2 0.9 - - + -
385H VAL* 3.8 22.9 - - + -
386H PHE 2.9 15.0 + - - +
387H GLY* 4.6 1.3 - - - -
388H ASP 3.4 10.2 + - - -
389H VAL* 3.2 20.7 + - - +
405H MET* 3.9 21.8 - - + -
406H GLN* 1.3 75.9 - - - +
408H LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ARG* 4.1 15.9 - - + -
308H THR 2.8 21.8 + - - +
309H PHE* 4.1 19.5 - - + -
310H VAL* 2.8 30.1 + - - +
315H TYR* 4.0 3.3 - - - -
389H VAL* 3.3 39.5 - - + +
390H GLN 4.3 1.6 - - - +
391H ASP* 3.4 30.3 - - - +
396H ALA* 4.8 4.7 - - + -
406H GLN* 3.7 19.3 - - + +
407H ILE* 1.3 78.3 - - - +
409H LYS* 1.3 60.9 + - - +
419H ARG* 3.6 10.3 - - - +
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Residues in contact with LYS 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309H PHE* 5.5 0.2 - - - -
310H VAL 3.4 4.0 - - - +
312H GLU* 3.8 34.3 - - + +
315H TYR* 3.3 48.7 - - + +
316H ASP* 4.8 5.3 + - - -
388H ASP* 4.3 18.2 + - - +
389H VAL 4.7 2.0 + - - +
408H LEU* 1.3 75.5 - - - +
410H PHE* 1.3 66.0 + - - +
419H ARG* 2.8 22.8 + - - +
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Residues in contact with PHE 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H ILE* 3.9 6.5 - - + -
277H ILE 3.7 9.9 - - - -
278H MET* 3.8 22.0 - - + -
309H PHE* 3.5 32.3 - - + -
310H VAL* 3.1 22.0 + - - -
311H GLN* 3.3 42.9 - - + -
312H GLU* 2.9 29.8 + - - +
409H LYS* 1.3 75.1 - - - +
411H LYS* 1.3 62.4 + - - +
412H THR 3.4 25.8 - - - -
415H GLU* 3.7 18.8 - - - +
416H VAL* 3.7 20.4 - - + -
419H ARG* 3.8 4.7 - - - +
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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