Contacts of the helix formed by residues 378 - 392 (chain A) in PDB entry 1IAX
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 THR 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A GLU* 2.6 32.1 + - + +
377A SER* 1.3 80.6 - - - +
379A PHE* 1.3 55.4 + - - +
380A ASP* 2.8 21.1 + - - +
381A SER* 2.7 56.8 + - - -
382A GLU 3.3 3.5 + - - -
408A PRO* 3.7 7.7 - - - +
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Residues in contact with PHE 379 (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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378A THR* 1.3 70.9 - - - +
380A ASP* 1.3 60.0 + - - +
381A SER 3.1 0.2 - - - -
382A GLU* 3.7 12.3 - - - +
383A MET* 3.1 34.0 + - + +
401A SER* 3.7 30.1 - - - +
405A CYS 3.2 28.0 - - - -
406A GLN* 3.4 24.5 - - - -
407A GLU 3.6 2.0 - - - -
408A PRO* 3.4 33.0 - - + +
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 2.8 18.9 + - - +
379A PHE* 1.3 80.8 + - - +
381A SER* 1.3 61.2 + - - +
383A MET* 4.1 5.9 - - - +
384A SER* 3.4 19.2 + - - -
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 3.5 12.3 - - - +
375A ARG* 4.2 10.9 - - - +
376A GLU* 3.0 39.4 + - - +
378A THR* 2.7 19.7 + - - -
380A ASP* 1.3 79.4 - - - +
382A GLU* 1.3 60.0 + - - +
383A MET 3.2 0.2 - - - -
384A SER* 3.2 7.0 + - - -
385A LEU* 2.9 30.0 + - - +
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 3.4 12.8 - - + +
378A THR 3.3 3.2 + - - -
379A PHE* 3.7 20.4 - - - +
381A SER* 1.3 78.9 - - - +
383A MET* 1.3 52.4 + - - +
385A LEU* 3.3 3.4 + - - +
386A TRP* 2.7 34.8 + - - +
399A PRO* 3.6 5.0 - - + +
400A GLY* 3.4 11.7 + - - -
401A SER* 2.7 44.9 + - - -
407A GLU 4.3 0.5 - - - +
408A PRO* 3.1 10.7 - - + +
409A GLY* 2.8 32.9 + - - +
410A TRP 3.9 5.1 + - - +
411A PHE* 3.7 20.2 - - + -
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Residues in contact with MET 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 4.8 7.4 - - + +
27A TYR* 3.5 37.2 - - + +
29A ASP* 5.4 1.6 - - - +
379A PHE* 3.1 20.9 + - + +
380A ASP* 4.3 5.8 - - - +
381A SER 3.2 0.2 - - - -
382A GLU* 1.3 74.3 - - - +
384A SER* 1.3 64.3 + - - +
386A TRP* 3.5 29.9 - - + +
387A ARG* 3.1 31.7 + - + +
399A PRO* 4.2 11.9 - - - -
401A SER* 3.9 12.1 - - - +
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Residues in contact with SER 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ARG* 6.6 0.2 - - - -
380A ASP 3.4 15.4 + - - -
381A SER* 3.2 12.5 + - - -
383A MET* 1.3 80.7 - - - +
385A LEU* 1.3 63.5 + - - +
387A ARG* 3.4 6.9 + - - +
388A VAL* 3.3 25.6 + - - +
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Residues in contact with LEU 385 (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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370A LEU* 3.9 28.9 - - + +
373A LEU* 3.8 30.5 - - + +
374A LEU* 4.4 10.1 - - + -
381A SER 2.9 15.3 + - - +
382A GLU* 3.5 4.3 - - - +
384A SER* 1.3 75.3 - - - +
386A TRP* 1.3 66.3 + - - +
388A VAL* 3.0 8.3 + - + -
389A ILE* 2.9 41.8 + - + +
411A PHE* 4.2 8.3 - - + -
433A PHE* 3.5 34.5 - - + -
437A GLU* 5.0 1.6 - - - +
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Residues in contact with TRP 386 (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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27A TYR* 3.3 39.9 - + - -
29A ASP* 3.8 22.7 - - + -
30A GLY* 3.6 25.6 - - - -
382A GLU 2.7 22.4 + - - +
383A MET* 3.5 31.6 - - + +
384A SER 3.3 0.2 - - - -
385A LEU* 1.3 72.6 - - - +
387A ARG* 1.3 66.4 + - + +
389A ILE* 3.1 6.2 + - + +
390A ILE* 2.9 43.0 + - + +
397A VAL* 3.2 38.4 + - + +
399A PRO* 3.5 21.0 - - + +
411A PHE* 3.5 28.3 - + + -
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Residues in contact with ARG 387 (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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26A PRO* 5.1 0.6 + - - +
29A ASP* 3.2 36.6 + - - +
383A MET* 3.1 17.4 + - + +
384A SER* 3.6 9.4 - - - +
385A LEU 3.2 0.2 - - - -
386A TRP* 1.3 80.7 - - + +
388A VAL* 1.3 64.7 + - + +
390A ILE* 3.0 9.4 + - + -
391A ASN* 2.8 46.3 + - - +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER* 3.4 17.3 - - - +
385A LEU* 3.0 12.7 + - + +
387A ARG* 1.3 76.6 - - + +
389A ILE* 1.3 63.0 + - - +
392A ASP* 3.1 41.1 + - + +
393A VAL* 3.2 9.1 + - + +
433A PHE* 3.3 37.9 - - + -
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Residues in contact with ILE 389 (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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368A MET* 5.3 4.0 - - + -
370A LEU* 3.6 30.7 - - + -
385A LEU* 2.9 35.8 + - + +
386A TRP* 3.4 6.5 - - + +
388A VAL* 1.3 76.8 - - - +
390A ILE* 1.3 57.9 + - + +
393A VAL* 3.3 14.0 - - + +
394A LYS 3.2 8.1 + - - -
395A LEU* 3.0 46.0 + - + +
397A VAL* 4.4 16.4 - - + -
411A PHE* 4.3 16.2 - - + -
433A PHE* 4.2 10.5 - - + -
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Residues in contact with ILE 390 (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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29A ASP* 3.5 36.3 - - + +
30A GLY* 3.6 20.0 - - - +
33A ALA* 3.9 15.6 - - + +
48A VAL* 4.3 11.5 - - + +
386A TRP* 2.9 49.1 + - + +
387A ARG* 3.0 19.7 + - + +
389A ILE* 1.3 77.6 - - + +
391A ASN* 1.3 71.4 + - - +
394A LYS* 4.3 4.0 - - - -
395A LEU 3.5 19.7 - - - +
396A ASN* 4.7 3.4 - - - -
397A VAL 4.7 0.2 - - - +
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Residues in contact with ASN 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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33A ALA* 5.0 5.9 - - - +
387A ARG* 2.8 45.6 + - - +
389A ILE 3.5 0.4 - - - -
390A ILE* 1.3 96.1 - - - +
392A ASP* 1.3 72.5 + - - +
393A VAL 3.6 0.4 - - - -
394A LYS* 3.3 32.5 + - - +
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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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388A VAL* 3.1 30.9 + - + +
391A ASN* 1.3 83.3 - - - +
393A VAL* 1.3 64.6 + - + +
394A LYS* 3.3 5.2 - - - +
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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