Contacts of the helix formed by residues 383 - 400 (chain A) in PDB entry 1E3Q
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 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LYS* 6.0 0.2 - - - +
380A ASP* 3.4 28.4 + - - +
381A ASP 3.6 1.8 - - - -
382A ASN* 1.3 75.9 - - - +
384A GLY* 1.3 77.4 + - - +
385A ILE* 3.4 16.4 + - - +
386A LYS* 3.2 44.3 - - + +
387A ASN* 2.9 29.6 + - - +
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Residues in contact with GLY 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A LYS* 3.6 27.1 - - - +
347A ILE 3.1 31.2 + - - +
382A ASN 3.6 4.4 + - - -
383A ASN* 1.3 77.4 + - - +
385A ILE* 1.3 61.1 + - - +
388A ARG* 3.1 12.0 + - - +
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 5.1 2.7 - - - +
346A LYS* 3.6 37.5 - - + +
383A ASN* 3.3 13.2 + - - +
384A GLY* 1.3 72.2 - - - +
386A LYS* 1.3 64.3 + - + +
388A ARG* 3.0 42.0 + - - +
389A ASP* 2.7 43.1 + - - +
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 5.3 0.2 - - - -
375A TYR 5.5 1.0 - - - +
377A ASP* 2.9 36.5 + - + +
379A MET* 6.2 0.2 - - - +
380A ASP* 3.7 24.2 + - - +
383A ASN* 3.2 39.7 + - + +
385A ILE* 1.3 77.8 - - + +
387A ASN* 1.3 60.5 + - - +
389A ASP* 4.8 4.0 - - - -
390A GLY* 2.8 29.6 + - - -
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Residues in contact with ASN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ILE* 3.3 30.4 + - + +
349A ARG* 3.7 36.3 + - - +
352A PHE* 3.3 40.8 - - + -
376A THR* 5.2 3.1 - - - +
381A ASP* 4.0 5.7 + - - +
382A ASN* 4.0 8.5 - - - +
383A ASN 2.9 28.2 + - - +
386A LYS* 1.3 79.8 - - - +
388A ARG* 1.3 61.2 + - - +
391A LEU* 3.3 15.6 + - - +
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.7 22.1 - - + -
344A GLU* 3.3 29.7 + - - -
345A SER 3.0 26.0 + - - +
347A ILE* 4.0 9.4 - - + +
384A GLY 3.1 13.9 + - - +
385A ILE* 3.0 40.3 + - - +
387A ASN* 1.3 74.6 - - - +
389A ASP* 1.3 106.9 + - - +
391A LEU* 3.0 16.2 + - - +
392A ASP* 3.1 12.6 + - - +
435A TRP* 3.4 42.1 + - + +
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE* 2.7 35.2 + - - +
386A LYS* 4.3 3.1 - - - +
388A ARG* 1.3 102.8 + - - +
390A GLY* 1.3 61.2 + - - +
392A ASP* 3.2 13.0 + - - +
393A ASP* 3.1 26.2 + - - +
435A TRP 4.6 4.5 - - - +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.7 4.5 - - - -
375A TYR* 3.7 18.6 - - - -
386A LYS 2.8 23.6 + - - -
387A ASN 4.2 0.7 - - - -
389A ASP* 1.3 74.1 - - - +
391A LEU* 1.3 58.8 + - - +
393A ASP* 3.5 11.0 + - - +
394A ILE* 3.1 30.5 + - - +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LEU* 3.8 16.8 - - + -
339A PHE* 3.9 26.0 - - + -
347A ILE* 4.7 3.8 - - + -
351A ASP 4.6 1.8 - - - +
352A PHE* 3.8 27.1 - - + -
355A GLY* 4.0 19.5 - - - -
356A VAL* 3.7 37.2 - - + +
359A SER* 5.3 2.0 - - - +
387A ASN 3.3 17.0 + - - +
388A ARG 3.0 6.4 + - - +
390A GLY* 1.3 76.6 - - - +
392A ASP* 1.3 65.3 + - - +
394A ILE* 3.1 20.1 + - + +
395A VAL* 3.1 19.4 + - + +
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Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A LYS 5.3 0.2 - - - +
326A ASP* 3.2 31.6 - - - +
327A GLU 4.1 6.2 + - - -
328A GLY* 3.5 8.3 + - - -
329A SER* 3.4 27.4 + - - +
332A LEU* 3.5 17.4 - - + +
339A PHE* 6.2 0.2 - - + -
388A ARG* 3.1 11.7 + - - +
389A ASP* 3.3 15.2 - - - +
391A LEU* 1.3 77.0 - - - +
393A ASP* 1.3 60.9 + - - +
395A VAL 3.6 0.2 + - - -
396A GLY* 3.0 24.3 + - - -
435A TRP* 4.8 6.9 - - + +
436A MET 4.6 0.3 - - - +
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS 5.4 3.5 - - - +
326A ASP* 5.3 2.6 - - - +
375A TYR* 3.6 20.7 - - + -
389A ASP 3.1 13.6 + - - +
390A GLY* 3.7 8.8 - - - +
391A LEU 3.2 0.2 - - - -
392A ASP* 1.3 81.5 - - - +
394A ILE* 1.3 60.2 + - - +
396A GLY* 5.0 0.7 - - - -
397A ASP* 2.8 38.4 + - - +
517A ARG* 3.7 23.0 + - - +
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.4 5.2 - - + -
356A VAL* 4.0 16.4 - - + -
359A SER* 4.3 19.7 - - - -
360A VAL* 4.6 2.0 - - + -
371A VAL* 4.1 13.0 - - + +
375A TYR* 3.4 40.2 - - + -
390A GLY 3.1 16.2 - - - +
391A LEU* 3.1 27.7 + - + +
393A ASP* 1.3 76.6 - - - +
395A VAL* 1.3 65.2 + - + +
397A ASP* 4.0 0.3 - - - +
398A HIS* 3.0 29.2 + - + +
524A TRP* 3.9 21.5 - - + -
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE* 4.1 6.5 - - + -
288A PHE* 3.9 17.9 - - + -
328A GLY* 3.6 25.4 - - - +
331A PHE* 4.2 8.5 - - + -
332A LEU* 3.5 29.2 - - + -
359A SER* 3.6 20.6 - - - +
391A LEU* 3.1 15.3 + - + +
394A ILE* 1.3 74.6 - - - +
396A GLY* 1.3 63.1 + - - +
398A HIS* 5.0 0.4 - - - -
399A ASN* 2.9 46.1 + - - +
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Residues in contact with GLY 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE* 6.1 0.2 - - - -
327A GLU* 3.9 11.2 - - - -
328A GLY* 3.6 19.4 - - - -
392A ASP* 3.0 14.9 + - - -
393A ASP* 3.9 0.7 - - - -
395A VAL* 1.3 76.9 - - - +
397A ASP* 1.3 56.4 + - - +
400A VAL* 2.8 33.7 + - - +
401A ILE* 3.2 13.2 + - - -
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Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TYR* 2.5 22.0 + - - -
393A ASP* 2.8 22.3 + - - +
394A ILE 4.0 0.2 - - - +
396A GLY* 1.3 70.3 - - - +
398A HIS* 1.3 64.1 + - - +
401A ILE* 4.0 17.5 - - - +
402A CYS* 3.0 38.4 + - - +
403A PRO* 3.3 1.9 - - - +
517A ARG* 2.5 46.2 + - - -
520A MET* 3.8 4.8 - - - +
524A TRP* 3.5 19.5 - - + +
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Residues in contact with HIS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PRO* 3.9 16.2 - - + +
289A ARG* 3.1 23.3 + - - -
359A SER* 3.5 21.5 - - - -
360A VAL* 4.9 1.3 - - + -
362A HIS* 3.5 24.9 - + - -
394A ILE* 3.0 18.0 + - + +
395A VAL* 4.1 0.9 - - - +
397A ASP* 1.3 79.0 - - - +
399A ASN* 1.3 79.8 + - - +
402A CYS* 5.1 0.6 - - - +
403A PRO* 3.2 20.4 - - - +
524A TRP* 3.5 45.2 - + + +
528A LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS* 3.3 11.6 - - - +
232A PRO* 3.6 8.6 - - - +
233A TRP* 2.9 28.9 + - + -
287A ILE* 4.9 1.0 + - - +
288A PHE* 3.5 40.8 - - + +
289A ARG* 2.6 30.6 + - - +
359A SER* 4.8 4.6 + - - -
395A VAL* 2.9 35.1 + - - +
398A HIS* 1.3 94.1 - - - +
400A VAL* 1.3 57.9 + - - +
403A PRO* 3.9 2.9 - - - -
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A SER* 3.8 28.9 - - - +
227A GLY* 4.2 2.7 - - - +
228A SER 5.5 0.3 + - - -
231A CYS* 4.6 4.3 - - - -
233A TRP* 4.8 2.9 - - + +
288A PHE* 4.1 24.7 - - + -
323A VAL* 3.9 4.9 - - + -
327A GLU* 3.4 42.0 - - + +
396A GLY* 2.8 16.9 + - - +
398A HIS 3.7 0.8 - - - -
399A ASN* 1.3 80.2 - - - +
401A ILE* 1.3 69.0 + - - +
403A PRO* 3.4 4.9 - - - +
404A LEU* 3.3 21.3 + - - +
440A HIS* 4.7 7.4 - - + +
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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
------------------------------------------------------------
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