Contacts of the strand formed by residues 404 - 410 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294F LEU* 3.5 14.6 - - - +
306F SER* 5.4 0.2 - - - -
353F ILE* 3.9 19.3 - - + -
356F TYR 5.9 0.2 - - - +
357F ILE* 3.8 27.8 - - + -
384F THR* 3.3 9.4 - - + +
386F PHE* 3.6 30.7 - - + -
395F ILE* 5.9 0.2 - - + -
400F ILE* 4.0 25.8 - - + +
402F GLY 2.7 9.9 + - - +
403F PRO* 1.3 79.2 - - + +
405F MET* 1.3 58.7 + - - +
406F GLN* 3.3 31.4 + - - +
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Residues in contact with MET 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290F ALA* 3.3 30.5 - - + +
291F HIS* 3.8 10.3 - - + +
294F LEU* 3.7 21.7 - - + +
295F PHE* 3.6 24.7 - - + -
305F GLY 5.6 0.2 - - - +
308F THR* 4.3 11.9 - - - +
318F PHE* 5.7 0.2 - - - -
322F SER* 4.6 13.0 - - - +
384F THR 2.7 16.3 + - - +
385F VAL* 4.2 15.5 - - + -
386F PHE* 2.7 35.5 + - - +
404F VAL* 1.3 72.9 - - - +
406F GLN* 1.3 64.5 + - - +
407F ILE* 4.0 31.0 - - + -
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Residues in contact with GLN 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F LYS* 3.5 14.5 - - - +
306F SER* 2.8 36.8 + - - +
307F ARG* 5.3 0.9 - - + -
308F THR* 2.9 32.1 + - - -
386F PHE* 3.8 2.6 - - - -
389F VAL* 4.1 15.5 - - + -
395F ILE* 3.2 44.1 - - + +
396F ALA* 4.8 0.4 - - - -
400F ILE* 3.3 9.4 - - - +
404F VAL* 3.3 39.7 + - - +
405F MET* 1.3 76.6 - - - +
407F ILE* 1.3 61.1 + - - +
408F LEU* 3.7 5.9 - - + +
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Residues in contact with ILE 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F THR* 3.4 13.5 - - - +
310F VAL* 4.1 14.4 - - + -
315F TYR* 3.7 22.7 + - + -
318F PHE* 4.3 6.3 - - + -
319F VAL* 3.9 21.5 - - + -
322F SER* 4.1 19.1 - - - +
385F VAL* 4.0 13.7 - - + -
386F PHE 2.8 18.6 + - - +
387F GLY* 3.8 4.4 - - - -
388F ASP 3.4 9.0 + - - -
389F VAL* 3.2 21.8 + - - +
405F MET* 4.0 28.5 - - + -
406F GLN* 1.3 77.9 - - - +
408F LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F ARG* 4.0 17.7 - - + -
308F THR 2.8 21.8 + - - +
309F PHE* 3.5 24.1 - - + -
310F VAL* 2.8 30.0 + - - +
315F TYR* 4.1 4.3 - - - -
388F ASP 5.5 0.2 - - - +
389F VAL* 3.4 43.1 - - + +
390F GLN 4.1 3.4 - - - -
391F ASP* 3.4 27.4 - - - +
396F ALA* 4.7 4.5 - - + -
406F GLN* 3.7 18.2 - - + +
407F ILE* 1.3 79.2 - - - +
409F LYS* 1.3 59.4 + - - +
419F ARG* 4.0 4.7 - - - +
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Residues in contact with LYS 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F VAL 3.4 3.8 - - - +
312F GLU* 3.9 35.4 - - + +
315F TYR* 3.6 44.7 - - + -
316F ASP* 5.4 2.0 + - - -
388F ASP* 4.3 14.0 + - - +
389F VAL 4.8 2.4 + - - -
408F LEU* 1.3 74.9 - - - +
410F PHE* 1.3 64.3 + - - +
419F ARG* 2.8 21.9 + - - +
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Residues in contact with PHE 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F ILE* 4.0 6.7 - - + -
277F ILE 3.7 7.2 - - - -
278F MET* 3.9 22.4 - - + -
309F PHE* 3.7 23.1 - - + -
310F VAL 3.1 31.8 + - - -
311F GLN* 3.2 42.4 - - + -
312F GLU* 2.9 30.0 + - - +
409F LYS* 1.3 77.1 - - - +
411F LYS* 1.3 60.0 + - - +
412F THR 3.4 30.3 - - - -
415F GLU* 3.6 17.0 - - + +
416F VAL* 3.6 21.3 - - + -
419F ARG* 3.7 6.3 - - - +
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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