Contacts of the helix formed by residues 346 - 363 (chain G) 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 ASP 346 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40G VAL* 6.3 2.5 - - + -
196G GLN* 3.3 31.8 - - + +
344G GLN* 3.3 1.5 + - - +
345G VAL* 1.3 91.8 - - + +
347G GLU* 1.3 59.4 + - - +
348G THR* 3.7 12.7 + - - -
349G GLN* 3.0 28.7 + - - +
350G PHE* 2.9 28.1 + - - +
379G TYR* 3.5 20.0 - - + +
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Residues in contact with GLU 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346G ASP* 1.3 73.7 - - - +
348G THR* 1.3 60.2 + - - +
350G PHE* 3.0 7.8 + - + +
351G LYS* 2.8 54.8 + - + +
379G TYR* 3.5 34.8 + - + +
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Residues in contact with THR 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G ASP* 3.4 13.7 + - - -
347G GLU* 1.3 78.2 - - - +
349G GLN* 1.3 68.6 + - - +
351G LYS* 3.4 7.0 + - - +
352G LYS* 3.0 29.8 + - + +
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Residues in contact with GLN 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G TRP* 3.7 34.5 - - + +
196G GLN* 5.8 0.7 - - - +
300G GLN* 4.8 1.8 - - - +
344G GLN* 4.6 8.5 - - + -
345G VAL* 3.7 9.2 - - + -
346G ASP* 3.0 22.4 + - - +
348G THR* 1.3 84.4 + - - +
350G PHE* 1.3 66.1 + - - +
352G LYS* 3.3 12.8 + - - +
353G ILE* 3.0 34.5 + - + +
400G ILE 4.8 3.1 - - - +
401G PHE* 4.0 24.8 - - - +
7502G NAD 4.8 7.6 + - - -
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Residues in contact with PHE 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344G GLN* 4.6 3.7 - - - +
346G ASP 2.9 15.5 + - - +
347G GLU* 3.1 15.9 - - + +
349G GLN* 1.3 79.6 - - - +
351G LYS* 1.3 69.0 + - + +
353G ILE* 3.4 3.5 + - - +
354G LEU* 3.2 38.0 + - + +
373G ILE* 3.7 35.4 - - + -
378G GLY 4.6 4.3 - - - -
379G TYR* 3.6 44.6 - + + -
380G PHE 3.4 22.9 - - - -
381G ILE* 3.5 23.3 - - + +
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Residues in contact with LYS 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347G GLU* 2.8 44.9 + - + +
348G THR* 3.8 6.1 - - - +
350G PHE* 1.3 76.5 - - + +
352G LYS* 1.3 60.3 + - - +
354G LEU* 3.2 11.9 + - + +
355G GLY* 2.9 27.0 + - - -
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Residues in contact with LYS 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348G THR* 3.0 20.2 + - + +
349G GLN* 3.3 17.9 + - - +
351G LYS* 1.3 75.5 - - - +
353G ILE* 1.3 58.4 + - + +
355G GLY* 3.3 3.7 + - - -
356G TYR* 3.0 69.0 + - + -
398G GLU* 5.5 1.0 + - - -
400G ILE 5.3 3.1 - - - +
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Residues in contact with ILE 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344G GLN* 3.5 42.2 - - + +
349G GLN* 3.0 24.5 + - + +
352G LYS* 1.3 74.6 - - + +
354G LEU* 1.3 64.6 + - - +
356G TYR* 3.0 11.0 + - - +
357G ILE* 2.9 31.2 + - + +
381G ILE* 3.6 17.7 - - + -
400G ILE* 4.0 19.3 - - + +
401G PHE 3.7 5.6 - - - +
402G GLY* 3.6 15.9 - - - -
403G PRO* 4.4 3.1 - - + -
404G VAL* 3.9 24.9 - - + -
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Residues in contact with LEU 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350G PHE* 3.2 42.7 + - + +
351G LYS* 3.2 10.3 + - + +
353G ILE* 1.3 78.6 - - - +
355G GLY* 1.3 57.6 + - - +
357G ILE* 3.2 19.1 + - + +
358G ASN* 2.9 29.9 + - - +
371G GLY 4.8 2.2 - - - +
372G GLY* 4.5 8.1 - - - -
373G ILE* 4.3 30.3 - - + +
381G ILE* 4.4 11.9 - - + -
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Residues in contact with GLY 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351G LYS 2.9 14.9 + - - -
352G LYS* 3.3 5.4 + - - -
353G ILE 3.1 0.2 - - - -
354G LEU* 1.3 77.2 - - - +
356G TYR* 1.3 55.5 + - - +
358G ASN* 3.3 8.5 + - - +
359G THR* 2.9 33.3 + - - -
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Residues in contact with TYR 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G LYS* 3.0 58.6 + - + -
353G ILE 3.0 7.9 + - - +
355G GLY* 1.3 72.6 - - - +
357G ILE* 1.3 60.1 + - + +
359G THR* 3.2 8.6 + - - -
360G GLY 2.9 24.6 + - - -
394G THR* 4.2 18.4 - - + -
395G ILE* 3.5 13.0 - - + +
398G GLU* 2.8 42.8 + - + +
399G GLU 3.8 21.1 + - - -
400G ILE* 3.9 44.0 - - + -
404G VAL* 5.9 0.2 - - - -
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Residues in contact with ILE 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G ILE* 2.9 20.2 + - + +
354G LEU* 3.4 15.9 - - + +
356G TYR* 1.3 74.6 - - - +
358G ASN* 1.3 62.6 + - - +
360G GLY 3.2 1.2 + - - -
361G LYS* 3.1 33.2 + - + +
367G LEU* 5.1 0.4 - - + -
371G GLY* 3.4 35.7 - - - +
381G ILE* 4.1 20.4 - - + -
384G THR* 3.9 18.8 - - + +
386G PHE* 3.5 20.8 - - + -
404G VAL* 3.7 26.7 - - + -
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Residues in contact with ASN 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G LEU 2.9 12.7 + - - +
355G GLY* 3.3 13.5 - - - +
357G ILE* 1.3 78.4 - - - +
359G THR* 1.3 57.3 + - - +
361G LYS* 3.2 25.4 + - - +
362G GLN* 3.0 47.7 + - - +
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Residues in contact with THR 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355G GLY 2.9 16.0 + - - -
356G TYR* 3.2 14.6 + - - -
358G ASN* 1.3 74.8 + - - +
360G GLY* 1.3 64.8 + - - +
362G GLN* 3.3 7.5 + - + +
363G GLU* 2.9 48.6 + - + +
394G THR* 3.7 25.8 - - + +
395G ILE* 4.8 2.0 - - + -
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Residues in contact with GLY 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356G TYR 2.9 11.3 + - - -
357G ILE 3.2 4.4 + - - -
359G THR* 1.3 78.8 - - - +
361G LYS* 1.3 58.6 - - - +
363G GLU* 3.5 7.2 + - - +
365G ALA* 3.1 28.1 + - - +
386G PHE* 3.8 14.1 - - - -
395G ILE* 3.6 27.5 - - - +
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Residues in contact with LYS 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G ILE* 3.1 23.8 + - + +
358G ASN* 3.5 27.6 - - - +
359G THR 3.2 0.2 - - - -
360G GLY* 1.3 74.8 - - - +
362G GLN* 1.3 66.6 + - + +
364G GLY* 3.4 12.1 + - - -
365G ALA 4.4 5.8 + - - +
367G LEU* 4.3 24.1 - - + +
371G GLY 4.6 10.7 + - - -
386G PHE* 4.1 15.5 - - + -
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Residues in contact with GLN 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358G ASN* 3.0 41.0 + - - +
359G THR* 3.5 9.2 - - + +
361G LYS* 1.3 80.9 - - + +
363G GLU* 1.3 60.9 + - + +
364G GLY 3.3 3.6 + - - -
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Residues in contact with GLU 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359G THR* 2.9 32.1 + - + +
360G GLY* 3.5 4.3 + - - +
361G LYS 3.3 0.4 - - - -
362G GLN* 1.3 77.9 - - + +
364G GLY* 1.3 56.9 + - - +
365G ALA 3.5 1.8 - - - -
392G GLY 4.9 0.5 - - - +
393G MET* 3.4 33.6 - - + +
394G THR* 2.8 46.7 + - - -
395G ILE* 4.6 0.7 + - - +
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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