Contacts of the helix formed by residues 354 - 374 (chain G) in PDB entry 4D1Q
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 LYS 354 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330G LEU* 5.7 5.8 - - + -
333G TRP* 3.3 63.7 - - + +
334G GLU* 4.0 13.5 + - - -
352G ILE 3.4 6.2 + - - -
353G ASN* 1.3 74.6 + - - +
355G SER* 1.3 58.1 + - - +
357G ILE* 3.1 11.5 + - + +
358G GLN* 2.9 51.2 + - + +
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Residues in contact with SER 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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353G ASN* 2.9 26.8 + - - -
354G LYS* 1.3 73.7 - - - +
356G ILE* 1.3 56.4 + - - +
357G ILE 2.9 9.0 + - - -
358G GLN* 4.2 7.5 - - - +
359G THR* 3.0 29.9 + - - -
403G VAL* 5.6 5.9 - - - +
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Residues in contact with ILE 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G LEU* 3.5 30.3 - - + -
287G PRO* 4.9 12.1 - - + -
353G ASN* 3.0 45.4 + - + +
355G SER* 1.3 73.4 - - - +
357G ILE* 1.3 61.0 + - + +
359G THR* 4.5 1.8 - - - -
360G MET* 2.9 25.5 - - - +
403G VAL* 5.1 15.9 - - + -
405G ASP* 5.0 13.7 - - + +
406G ILE* 4.2 20.3 - - + +
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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
----------------------------------------------------------
287G PRO* 4.2 18.2 - - + +
291G CYS* 4.6 12.1 - - - -
326G LEU* 4.2 23.6 - - + -
330G LEU* 3.3 31.0 - - + -
333G TRP* 5.6 5.6 - - + -
352G ILE* 4.2 22.4 - - + -
353G ASN 3.2 18.6 - - - +
354G LYS* 3.3 10.1 - - + +
355G SER 2.9 0.2 - - - -
356G ILE* 1.3 86.6 - - + +
358G GLN* 1.3 59.9 + - - +
359G THR 2.9 1.8 - - - -
360G MET* 2.6 34.6 + - - +
361G VAL* 3.1 11.5 + - + +
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Residues in contact with GLN 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G LEU* 3.1 33.3 - - + +
354G LYS* 2.9 43.0 + - + +
355G SER* 4.2 7.2 - - - +
357G ILE* 1.3 75.0 - - - +
359G THR* 1.3 61.4 + - - +
361G VAL* 3.3 20.0 - - - +
362G ASN* 3.2 22.2 + - - +
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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
----------------------------------------------------------
355G SER* 3.0 18.1 + - - -
356G ILE 4.6 0.2 - - - -
357G ILE 2.9 0.4 - - - -
358G GLN* 1.3 77.6 - - - +
360G MET* 1.3 65.7 + - - +
362G ASN* 3.1 20.0 + - + +
363G ILE* 3.2 21.9 + - + +
402G ASP* 5.9 0.7 - - - +
406G ILE* 3.3 45.2 - - + +
410G LYS* 6.0 0.4 - - - +
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Residues in contact with MET 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G PHE* 3.4 38.8 - - + -
284G LEU* 3.4 33.4 - - + -
287G PRO* 5.6 1.1 - - - -
288G ILE* 4.6 9.6 - - + -
326G LEU* 4.1 28.7 - - + -
356G ILE* 2.9 27.8 - - + +
357G ILE* 2.6 23.1 + - - +
359G THR* 1.3 72.3 - - - +
361G VAL* 1.3 60.7 + - - +
363G ILE* 3.5 7.4 + - - +
364G LEU* 2.8 34.4 + - + +
406G ILE* 5.0 6.3 - - + -
409G LEU* 4.7 7.2 - - + -
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Residues in contact with VAL 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G TYR* 4.2 21.3 - - + -
326G LEU* 4.5 11.4 - - + +
327G ARG* 4.4 23.3 - - + +
330G LEU* 3.5 32.3 - - + -
357G ILE 3.1 7.0 + - - +
358G GLN* 3.3 15.7 - - - +
360G MET* 1.3 74.8 - - + +
362G ASN* 1.3 67.4 + - - +
364G LEU* 2.8 3.8 + - - -
365G ASP* 2.4 41.6 + - + +
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Residues in contact with ASN 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 GLN* 3.2 18.2 + - - +
359G THR* 3.1 12.8 + - + +
361G VAL* 1.3 90.1 - - - +
363G ILE* 1.3 62.0 + - + +
365G ASP* 3.7 22.6 + - - +
366G GLY* 3.8 5.0 + - - -
395G ILE* 4.4 9.0 - - - +
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Residues in contact with ILE 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* 3.2 19.2 + - + +
360G MET* 3.9 8.1 - - - +
361G VAL 3.1 1.0 - - - -
362G ASN* 1.3 79.0 - - + +
364G LEU* 1.3 59.1 + - + +
366G GLY* 3.8 2.8 + - - -
367G PHE* 2.7 48.7 + - + -
395G ILE* 4.1 24.5 - - + +
396G CYS* 4.6 5.8 - - - -
406G ILE* 4.0 15.9 - - + -
409G LEU* 5.0 14.8 - - + -
410G LYS* 3.7 33.4 - - + +
413G ILE* 4.3 15.5 - - + -
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Residues in contact with LEU 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G LEU* 3.9 29.2 - - + -
278G PHE* 4.3 21.8 - - + -
320G ASN* 3.2 25.3 + - - +
322G THR* 5.1 3.6 - - - -
323G TYR* 3.7 34.1 - - + +
326G LEU* 5.1 6.3 - - + -
360G MET* 2.8 32.0 + - + +
361G VAL* 2.8 4.1 + - - +
363G ILE* 1.3 78.4 - - + +
365G ASP* 1.3 58.2 + - - +
366G GLY 3.2 2.0 - - - -
367G PHE* 2.9 12.7 + - + +
368G GLU* 2.8 26.5 + - - +
409G LEU* 6.5 0.2 - - + -
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Residues in contact with ASP 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B HIS* 3.4 36.1 + - + +
495B SER* 3.5 16.1 + - - -
323G TYR* 3.8 24.1 + - + -
361G VAL* 2.4 33.6 + - - +
362G ASN* 3.7 20.8 + - - +
363G ILE 3.3 0.2 - - - -
364G LEU* 1.3 68.2 - - - +
366G GLY* 1.3 63.1 + - - +
368G GLU* 3.2 16.1 + - - +
369G ARG* 3.5 4.9 + - - +
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Residues in contact with GLY 366 (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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494B HIS* 5.2 4.4 + - - -
503B PHE* 4.0 14.3 - - - -
362G ASN 3.8 3.8 + - - -
363G ILE 3.8 3.0 + - - -
364G LEU 3.2 0.4 - - - -
365G ASP* 1.3 80.3 - - - +
367G PHE* 1.3 61.9 + - - +
368G GLU 3.1 0.3 + - - -
369G ARG* 3.4 4.4 + - - +
370G ILE* 3.1 31.2 + - - +
395G ILE* 4.1 22.2 - - - -
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Residues in contact with PHE 367 (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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270G LEU* 3.2 45.0 - - + +
273G VAL* 5.2 0.4 - - + -
274G LEU* 3.8 24.9 - - + -
320G ASN* 4.0 11.9 - - - +
363G ILE* 2.7 41.1 - - + -
364G LEU* 2.9 20.8 + - + +
366G GLY* 1.3 77.5 - - - +
368G GLU* 1.3 54.3 + - - +
370G ILE* 3.6 9.0 + - + +
371G PHE* 3.0 33.6 + - - -
392G VAL* 4.4 20.4 - - + -
395G ILE* 5.6 4.5 - - + -
396G CYS* 4.7 4.9 - - - -
413G ILE* 3.8 34.5 - - + -
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Residues in contact with GLU 368 (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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495B SER* 3.8 11.0 - - - +
319G TRP 4.7 2.6 - - - +
320G ASN* 3.2 25.4 + - - +
323G TYR* 3.0 41.4 - - + +
324G THR* 5.4 5.2 - - - +
364G LEU 2.8 6.4 + - - +
365G ASP 3.4 9.6 - - - +
366G GLY 3.1 0.4 - - - -
367G PHE* 1.3 73.6 - - - +
369G ARG* 1.3 59.2 + - - +
371G PHE* 2.5 33.8 + - - +
372G LYS* 2.8 28.8 + - + +
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Residues in contact with ARG 369 (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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494B HIS* 5.6 2.0 - - - +
495B SER* 3.0 26.1 + - - +
496B LYS* 3.5 27.8 + - - +
498B ILE* 3.0 39.6 + - - +
499B SER* 4.5 1.1 - - - +
500B THR* 3.4 32.0 + - - +
503B PHE* 3.8 34.7 - - + +
365G ASP 3.5 2.6 + - - +
366G GLY 3.4 6.9 + - - +
368G GLU* 1.3 78.8 - - - +
370G ILE* 1.3 63.2 + - - +
372G LYS* 3.1 9.9 + - - +
373G GLU* 2.8 49.3 + - + +
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Residues in contact with ILE 370 (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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503B PHE* 3.8 16.8 - - + -
504B PHE* 4.6 2.0 - - + -
270G LEU* 4.0 16.8 - - + -
366G GLY 3.1 21.1 + - - +
367G PHE* 3.7 9.2 - - + +
368G GLU 3.0 0.8 - - - -
369G ARG* 1.3 75.5 - - - +
371G PHE* 1.3 61.6 + - - +
373G GLU* 3.9 6.0 - - - +
374G LEU* 3.1 49.5 + - + +
388G SER* 3.7 37.5 - - - +
391G LYS* 3.8 17.0 - - + -
392G VAL* 4.0 15.3 - - + +
395G ILE* 5.5 2.2 - - + -
421G TRP* 4.4 3.8 - - + -
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Residues in contact with PHE 371 (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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267G SER* 3.3 37.2 - - - -
270G LEU* 3.4 36.3 - - + -
271G SER* 3.8 10.8 - - - -
274G LEU* 4.2 12.6 - - + -
319G TRP* 3.7 36.1 - + + -
320G ASN* 4.0 28.5 - - + -
367G PHE 3.0 20.4 + - - +
368G GLU* 2.5 26.9 + - - +
370G ILE* 1.3 69.5 - - - +
372G LYS* 1.3 65.3 + - + +
374G LEU* 3.3 11.1 + - + +
375G GLN* 3.3 24.2 + - - +
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Residues in contact with LYS 372 (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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495B SER* 4.0 27.2 + - - +
496B LYS* 4.6 12.7 - - - +
368G GLU* 2.8 33.2 + - + +
369G ARG* 3.7 11.2 - - - +
371G PHE* 1.3 73.4 - - + +
373G GLU* 1.3 64.7 + - + +
375G GLN* 2.8 33.6 + - - +
376G THR* 3.6 6.1 + - - -
1I A 3.6 39.5 - - + +
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Residues in contact with GLU 373 (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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500B THR* 3.1 36.5 + - - +
503B PHE* 5.4 0.9 - - + -
504B PHE* 3.8 29.4 - - + -
369G ARG* 2.8 52.3 + - + +
370G ILE 3.9 3.6 - - - +
372G LYS* 1.3 75.6 - - - +
374G LEU* 1.3 60.9 + - + +
376G THR* 2.8 28.0 + - - -
381G SER* 4.0 9.5 - - - -
384G PHE* 4.4 13.3 - - + +
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Residues in contact with LEU 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B PHE* 6.2 0.2 - - + -
266G SER* 3.5 30.3 - - - +
267G SER* 4.1 11.2 - - - +
270G LEU* 5.6 2.0 - - + -
370G ILE* 3.1 44.4 + - + +
371G PHE* 3.7 7.0 - - + +
372G LYS 3.1 0.8 + - - -
373G GLU* 1.3 76.7 - - + +
375G GLN* 1.3 54.3 + - - +
376G THR 3.5 0.6 - - - +
381G SER* 4.8 1.7 - - - +
384G PHE* 5.3 4.3 - - + +
385G VAL* 4.1 11.2 - - + +
388G SER* 4.2 12.3 - - - +
421G TRP* 4.2 14.8 - - + -
566G ALA* 3.4 41.3 + - + +
567G SER* 2.6 27.7 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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