Contacts of the helix formed by residues 353 - 374 (chain H) 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 ASN 353 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H PRO* 5.0 5.6 - - + +
351H HIS 4.1 2.0 + - - -
352H ILE* 1.3 72.1 - - - +
354H LYS* 1.3 67.3 + - - +
355H SER* 3.0 34.3 + - - -
356H ILE* 3.2 30.7 + - + +
357H ILE* 3.3 12.5 + - - +
403H VAL* 5.6 6.1 - - - +
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Residues in contact with LYS 354 (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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330H LEU* 4.2 25.0 - - + +
333H TRP* 3.6 60.8 - - + +
352H ILE* 3.3 11.8 + - - -
353H ASN* 1.3 70.7 + - - +
355H SER* 1.3 68.8 + - - +
357H ILE* 3.0 8.4 + - - +
358H GLN* 2.9 42.5 + - + +
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Residues in contact with SER 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H ASN* 3.0 22.6 + - - -
354H LYS* 1.3 80.1 - - - +
356H ILE* 1.3 76.7 + - - +
358H GLN* 2.9 24.5 + - - +
359H THR* 2.9 19.2 + - - -
403H VAL* 4.4 13.3 - - - +
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Residues in contact with ILE 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H GLU 5.0 2.0 - - - +
284H LEU* 4.1 21.3 - - + -
287H PRO* 4.5 17.3 - - + -
353H ASN* 3.2 29.9 + - + +
355H SER* 1.3 81.0 + - - +
357H ILE* 1.3 71.6 + - + +
359H THR* 3.3 7.0 + - - -
360H MET* 3.0 45.0 + - + +
403H VAL* 5.2 8.1 - - + -
405H ASP* 4.2 25.4 - - + +
406H ILE* 4.7 13.2 - - + +
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Residues in contact with ILE 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H PRO* 4.1 24.9 - - + +
288H ILE* 5.7 0.7 - - - -
291H CYS* 4.0 22.9 - - - -
326H LEU* 4.1 34.1 - - + +
329H ILE* 5.5 3.1 - - + -
330H LEU* 3.2 24.5 - - + -
333H TRP* 6.1 2.2 - - + -
352H ILE* 3.9 19.3 - - + -
353H ASN 3.3 11.6 + - - +
354H LYS* 3.0 9.2 + - - +
356H ILE* 1.3 81.3 - - + +
358H GLN* 1.3 65.1 + - - +
359H THR 3.0 1.7 + - - -
360H MET* 3.0 17.9 + - - +
361H VAL* 3.1 14.2 + - - +
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Residues in contact with GLN 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H LEU* 3.8 26.7 - - + +
354H LYS* 2.9 46.3 + - - +
355H SER* 3.2 23.4 - - - +
357H ILE* 1.3 71.6 - - - +
359H THR* 1.3 61.6 + - - +
361H VAL* 3.8 8.0 - - + +
362H ASN* 3.3 23.4 + - - +
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Residues in contact with THR 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H SER* 2.9 21.8 + - - -
356H ILE* 3.8 6.3 - - - -
358H GLN* 1.3 78.1 - - - +
360H MET* 1.3 65.5 + - - +
362H ASN* 2.9 20.8 + - + +
363H ILE* 3.0 22.4 + - + +
402H ASP* 6.5 0.2 - - - -
403H VAL* 5.9 2.1 - - - +
406H ILE* 3.6 32.2 - - + +
410H LYS* 5.8 2.0 - - - +
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Residues in contact with MET 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H PHE* 3.3 39.5 - - + -
284H LEU* 3.8 19.5 - - + -
287H PRO* 5.8 1.3 - - - -
288H ILE* 4.3 16.2 - - + -
322H THR* 5.2 0.7 - - + -
326H LEU* 4.3 22.7 - - + -
356H ILE* 3.0 36.2 + - + +
357H ILE* 3.0 8.9 + - - +
359H THR* 1.3 78.0 - - - +
361H VAL* 1.3 59.3 + - - +
363H ILE* 3.9 8.4 - - - +
364H LEU* 2.9 37.2 + - + +
406H ILE* 4.4 11.4 - - + -
409H LEU* 4.6 5.6 - - + -
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Residues in contact with VAL 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H TYR* 4.3 20.2 - - + +
326H LEU* 4.1 25.4 - - + -
327H ARG* 4.4 22.4 - - - +
330H LEU* 4.1 22.9 - - + -
357H ILE 3.1 15.3 + - - +
358H GLN* 3.8 9.9 - - + +
360H MET* 1.3 75.0 - - - +
362H ASN* 1.3 64.4 + - - +
364H LEU* 3.0 2.8 + - - -
365H ASP* 2.6 39.1 + - + +
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Residues in contact with ASN 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H GLN 3.3 12.2 + - - +
359H THR* 2.9 17.0 + - + +
361H VAL* 1.3 85.0 - - - +
363H ILE* 1.3 62.8 + - + +
365H ASP* 3.4 17.7 + - - +
366H GLY 3.9 1.4 + - - -
395H ILE* 5.9 0.7 - - - +
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Residues in contact with ILE 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H THR* 3.0 29.2 + - + +
360H MET* 3.9 7.2 - - - +
362H ASN* 1.3 76.2 - - + +
364H LEU* 1.3 64.2 + - + +
365H ASP 2.8 0.4 + - - -
366H GLY* 2.7 31.9 + - - -
367H PHE* 3.4 30.7 + - + -
395H ILE* 4.0 26.1 - - + +
396H CYS* 5.4 0.4 - - - -
406H ILE* 4.7 9.4 - - + -
409H LEU* 5.1 10.8 - - + -
410H LYS* 3.8 33.2 - - + -
413H ILE* 4.8 9.9 - - + -
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Residues in contact with LEU 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H LEU* 4.0 24.9 - - + -
278H PHE* 4.0 25.1 - - + -
320H ASN* 3.3 22.8 + - - +
322H THR* 4.8 4.5 - - + -
323H TYR* 3.6 43.3 - - + +
326H LEU* 5.5 1.8 - - + -
360H MET* 2.9 32.1 + - + +
361H VAL* 3.0 0.8 + - - -
363H ILE* 1.3 87.8 - - + +
365H ASP* 1.3 64.6 + - - +
366H GLY 3.1 0.2 - - - -
367H PHE* 2.9 21.1 + - + +
368H GLU* 3.0 9.5 + - - +
409H LEU* 6.3 1.3 - - + -
413H ILE* 5.9 1.3 - - + -
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Residues in contact with ASP 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H TYR* 3.5 26.7 + - + -
327H ARG* 5.3 4.1 + - - -
361H VAL* 2.6 23.2 + - + +
362H ASN* 3.4 17.1 + - - +
363H ILE 2.8 1.0 + - - -
364H LEU* 1.3 69.1 - - - +
366H GLY* 1.3 60.9 + - - +
368H GLU* 3.0 25.5 - - - +
369H ARG* 3.5 5.5 + - - +
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Residues in contact with GLY 366 (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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362H ASN 3.9 1.8 + - - -
363H ILE 2.7 11.6 + - - -
365H ASP* 1.3 78.0 + - - +
367H PHE* 1.3 61.5 + - - -
368H GLU 3.0 5.7 + - - -
369H ARG* 3.2 8.7 + - - +
370H ILE* 3.0 27.9 + - - +
391H LYS* 6.1 2.7 - - - -
395H ILE* 5.2 12.6 - - - -
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Residues in contact with PHE 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H LEU* 3.9 22.2 - - + +
273H VAL* 5.0 1.8 - - + -
274H LEU* 3.5 39.9 - - + -
320H ASN* 4.0 11.0 - - - +
363H ILE* 3.4 31.6 - - + -
364H LEU* 2.9 16.8 + - + +
366H GLY* 1.3 75.5 - - - +
368H GLU* 1.3 56.6 + - - +
370H ILE* 3.7 12.1 - - + +
371H PHE* 2.9 37.3 + - + -
392H VAL* 4.0 19.3 - - + -
395H ILE* 4.5 15.3 - - + -
396H CYS* 4.7 0.7 - - - -
413H ILE* 3.9 36.1 - - + -
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Residues in contact with GLU 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H TRP 4.4 2.9 - - - +
320H ASN* 3.0 38.1 + - - +
323H TYR* 3.1 33.5 - - + +
324H THR* 4.9 7.2 - - - +
364H LEU 3.0 5.2 + - - +
365H ASP* 3.0 11.7 - - - +
366H GLY 3.0 0.2 - - - -
367H PHE* 1.3 73.5 - - - +
369H ARG* 1.3 55.1 + - - +
370H ILE 3.0 0.7 - - - -
371H PHE* 2.6 30.5 + - - +
372H LYS* 2.7 36.9 + - + +
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Residues in contact with ARG 369 (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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365H ASP 3.5 4.2 + - - +
366H GLY* 3.2 10.4 + - - +
368H GLU* 1.3 78.8 - - - +
370H ILE* 1.3 63.2 + - + +
372H LYS* 3.3 10.7 + - - -
373H GLU* 2.9 60.3 + - + +
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Residues in contact with ILE 370 (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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270H LEU* 3.4 25.6 - - + -
366H GLY 3.0 17.0 + - - +
367H PHE* 3.7 13.2 - - + +
368H GLU 3.0 0.6 - - - -
369H ARG* 1.3 76.6 - - + +
371H PHE* 1.3 65.7 + - - +
373H GLU* 2.9 18.6 + - - +
374H LEU* 3.0 20.9 + - + +
388H SER* 3.8 36.1 - - - +
391H LYS* 3.7 35.9 - - + -
392H VAL* 4.1 15.0 - - + +
395H ILE* 5.3 1.3 - - + -
421H TRP* 4.6 0.4 - - + -
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Residues in contact with PHE 371 (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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267H SER* 3.3 27.4 - - - -
270H LEU* 3.7 20.9 - - + -
271H SER* 3.7 26.0 - - - -
274H LEU* 3.9 14.1 - - + -
319H TRP* 3.7 37.9 - + + -
320H ASN* 3.9 29.2 - - + -
367H PHE 2.9 24.9 + - - +
368H GLU* 2.6 22.0 + - - +
370H ILE* 1.3 74.5 - - - +
372H LYS* 1.3 60.1 + - + +
374H LEU* 3.6 6.0 + - + +
375H GLN* 3.2 32.1 + - - +
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Residues in contact with LYS 372 (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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368H GLU* 2.7 34.8 + - + +
369H ARG* 3.7 15.3 - - - +
371H PHE* 1.3 73.2 - - + +
373H GLU* 1.3 66.8 + - + +
375H GLN* 2.9 27.1 + - - +
376H THR* 3.5 9.1 + - - -
1K A 3.0 60.8 + - - +
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Residues in contact with GLU 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H ARG* 2.9 55.6 + - + +
370H ILE* 2.9 6.3 + - - +
372H LYS* 1.3 76.3 - - - +
374H LEU* 1.3 64.1 + - + +
376H THR* 3.2 26.5 + - - -
381H SER* 4.1 9.4 - - - -
384H PHE* 5.6 12.6 - - + +
388H SER* 5.8 1.6 - - - +
1K A 6.5 0.2 - - - -
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Residues in contact with LEU 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H SER* 3.8 37.0 - - - +
267H SER* 3.9 12.1 - - - +
270H LEU* 5.0 3.1 - - + -
370H ILE* 3.0 29.0 + - + +
371H PHE* 3.9 4.7 - - + +
373H GLU* 1.3 79.3 - - + +
375H GLN* 1.3 53.4 + - - +
376H THR 3.3 4.3 + - - +
381H SER* 4.9 1.3 - - - +
384H PHE* 4.6 7.0 - - + +
385H VAL* 4.4 23.3 - - + +
388H SER* 3.7 20.2 - - - +
421H TRP* 4.1 13.0 - - + -
566H ALA* 4.0 14.4 - - + +
567H SER* 2.6 33.7 + - - +
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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