Contacts of the strand formed by residues 404 - 410 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LEU* 3.6 13.7 - - - +
306B SER* 5.3 0.2 - - - -
353B ILE* 3.9 19.1 - - + -
357B ILE* 3.7 29.6 - - + +
384B THR* 3.4 7.2 - - + +
386B PHE* 3.7 27.4 - - + -
395B ILE* 5.4 1.3 - - + -
400B ILE* 4.0 24.7 - - + +
402B GLY 2.8 10.1 + - - +
403B PRO* 1.3 77.7 - - + +
405B MET* 1.3 59.5 + - - +
406B GLN* 3.1 33.9 + - - +
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Residues in contact with MET 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA* 3.6 39.5 - - + +
291B HIS* 4.3 4.3 - - - +
294B LEU* 3.7 23.0 - - + +
295B PHE* 3.9 18.2 - - + -
308B THR* 3.7 24.0 - - + +
322B SER* 4.5 17.9 - - - +
384B THR 2.7 16.2 + - - +
385B VAL* 4.1 13.5 - - + -
386B PHE* 2.7 32.8 + - - -
404B VAL* 1.3 72.5 - - - +
406B GLN* 1.3 65.0 + - - +
407B ILE* 4.1 23.1 - - + -
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS* 3.7 3.4 - - - +
294B LEU* 5.1 0.2 - - - +
306B SER* 3.1 31.6 + - - +
307B ARG* 5.4 0.9 - - + -
308B THR* 2.9 32.1 + - - -
386B PHE* 3.7 3.3 - - - -
389B VAL* 4.1 10.1 - - + -
395B ILE* 3.3 51.3 + - + +
396B ALA* 4.9 0.7 - - - -
400B ILE* 3.6 12.9 - - - +
404B VAL* 3.1 45.8 + - - +
405B MET* 1.3 77.7 - - - +
407B ILE* 1.3 62.6 + - - +
408B LEU* 3.7 8.4 - - + +
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B THR* 3.4 7.2 - - - +
310B VAL* 3.8 22.9 - - + -
315B TYR* 3.7 22.1 + - + -
318B PHE* 4.7 3.4 - - + -
319B VAL* 3.9 22.9 - - + -
322B SER* 4.2 23.1 - - - +
385B VAL* 3.8 21.1 - - + -
386B PHE 2.9 18.5 + - - +
387B GLY* 4.4 4.7 - - - -
388B ASP 3.4 9.9 + - - -
389B VAL* 3.2 22.3 + - - +
405B MET* 4.1 16.6 - - + -
406B GLN* 1.3 77.7 - - - +
408B LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ARG* 4.0 18.2 - - + -
308B THR 2.8 20.8 + - - +
309B PHE* 3.4 23.9 - - + +
310B VAL* 2.8 29.3 + - - +
315B TYR* 4.2 3.6 - - - -
389B VAL* 3.5 38.1 - - + +
390B GLN 4.2 0.4 - - - -
391B ASP* 3.4 30.3 - - - +
396B ALA* 4.6 4.9 - - + -
406B GLN* 3.7 25.1 - - + +
407B ILE* 1.3 76.0 - - - +
409B LYS* 1.3 60.8 + - - +
419B ARG* 3.9 4.5 - - - +
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Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL 3.3 5.4 - - - +
312B GLU* 3.9 35.2 - - + +
315B TYR* 3.4 46.5 - - + -
316B ASP* 5.1 2.8 + - - -
388B ASP* 4.3 12.5 + - - +
389B VAL 4.8 2.4 + - - -
408B LEU* 1.3 76.1 - - - +
410B PHE* 1.3 64.8 + - - +
415B GLU* 4.6 0.2 - - - +
419B ARG* 2.9 22.1 + - - +
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Residues in contact with PHE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ILE* 3.9 16.2 - - + -
277B ILE 3.6 12.1 - - - -
278B MET* 3.9 14.6 - - + -
309B PHE* 3.7 21.3 - - + -
310B VAL 3.1 27.6 + - - -
311B GLN* 3.1 43.7 - - + -
312B GLU* 2.9 30.5 + - - +
409B LYS* 1.3 76.5 - - - +
411B LYS* 1.3 62.7 + - - +
412B THR 3.4 27.4 - - - -
415B GLU* 3.8 11.4 - - + +
416B VAL* 3.6 21.3 - - + -
419B ARG* 3.9 11.4 - - - +
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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