Contacts of the helix formed by residues 382 - 393 (chain A) in PDB entry 1SQG
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A THR* 2.7 24.7 + - - +
376A SER* 2.9 26.7 + - - -
378A LEU 3.4 15.4 + - - +
379A PRO* 3.0 5.9 + - + +
380A GLU 3.3 0.2 - - - -
381A GLU* 1.3 88.9 - - - +
383A SER* 1.3 70.9 + - - +
384A LEU 3.3 0.2 - - - -
385A GLN* 3.1 3.8 + - - +
386A ILE* 3.1 24.9 + - - +
410A GLN* 2.8 25.7 + - - +
422A PHE* 3.3 32.4 - - + +
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Residues in contact with SER 383 (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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379A PRO* 3.4 11.9 + - - +
382A ASN* 1.3 81.4 - - - +
384A LEU* 1.3 75.4 + - - +
385A GLN 3.1 1.0 + - - -
386A ILE* 3.1 9.2 + - - -
387A LYS* 3.2 9.7 + - - +
406A GLN* 4.6 7.9 - - - -
407A PRO* 3.1 44.3 - - - +
422A PHE* 3.4 6.8 - - - -
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Residues in contact with LEU 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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379A PRO* 3.0 41.3 + - + +
380A GLU* 4.0 20.9 - - + +
383A SER* 1.3 79.8 + - - +
385A GLN* 1.3 61.9 + - - +
387A LYS* 3.5 9.2 + - + +
388A ALA* 3.2 21.0 + - - +
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Residues in contact with GLN 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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350A ALA* 2.7 35.3 + - - +
353A GLN* 3.0 26.5 + - - +
354A SER* 3.9 18.0 + - - -
357A LEU* 4.5 10.5 - - + +
372A TYR* 3.6 20.9 - - + +
380A GLU 3.6 10.0 + - - +
381A GLU 3.5 14.1 - - - +
382A ASN 3.1 10.7 + - - +
384A LEU* 1.3 76.3 - - - +
386A ILE* 1.3 69.0 + - - +
388A ALA* 3.0 21.1 + - - +
389A PHE* 3.1 12.1 + - - +
392A ARG* 5.1 1.6 + - - -
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Residues in contact with ILE 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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357A LEU* 4.6 10.3 - - + -
372A TYR* 3.3 41.1 - - + -
382A ASN 3.1 13.3 + - - +
383A SER 3.1 1.8 + - - +
385A GLN* 1.3 75.7 - - - +
387A LYS* 1.3 62.9 + - - +
389A PHE* 3.2 7.4 + - + -
390A LEU* 3.0 31.0 + - + +
398A LEU* 4.3 1.3 - - + -
407A PRO* 3.4 26.9 - - + -
422A PHE* 4.0 4.0 - - + -
424A ALA* 3.6 22.9 - - + -
426A LEU* 4.1 25.1 - - + -
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Residues in contact with LYS 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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383A SER 3.2 12.2 + - - +
384A LEU* 3.7 13.0 - - + +
385A GLN 3.1 0.4 - - - -
386A ILE* 1.3 78.4 - - - +
388A ALA* 1.3 62.5 + - - +
390A LEU* 3.3 7.1 + - + +
391A GLN* 3.0 25.3 + - + +
404A PRO 4.1 18.4 - - - +
405A GLU 5.0 3.6 - - - +
407A PRO* 3.8 15.1 - - + +
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Residues in contact with ALA 388 (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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384A LEU 3.2 9.6 + - - +
385A GLN* 3.0 16.2 + - - +
387A LYS* 1.3 79.4 - - - +
389A PHE* 1.3 61.8 + - - +
391A GLN* 3.3 17.9 + - - +
392A ARG* 3.3 36.3 + - - +
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Residues in contact with PHE 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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357A LEU* 4.3 32.3 - - + -
358A ASP* 5.6 1.6 - - - -
361A TRP* 4.0 22.9 - + + -
370A LEU* 5.3 0.2 - - + -
385A GLN* 3.1 11.8 + - - +
386A ILE* 3.2 17.3 - - + +
388A ALA* 1.3 78.1 - - - +
390A LEU* 1.3 90.9 + - + +
392A ARG* 3.2 24.6 + - - +
393A THR* 2.8 43.8 + - + -
396A ALA* 2.9 30.3 - - + -
426A LEU* 3.4 40.8 - - + -
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Residues in contact with LEU 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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386A ILE* 3.0 29.4 + - + +
387A LYS* 3.6 6.7 - - + +
389A PHE* 1.3 101.6 - - + +
391A GLN* 1.3 64.0 - - - +
393A THR 3.2 21.1 + - - +
394A ALA* 4.9 1.0 - - - -
396A ALA 3.8 21.9 - - - +
397A GLU* 4.3 0.2 - - - -
398A LEU* 3.9 31.4 - - + +
404A PRO* 5.1 9.2 - - + +
407A PRO* 4.1 16.4 - - + -
426A LEU* 4.1 1.6 - - + -
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Residues in contact with GLN 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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387A LYS* 3.0 13.5 + - + +
388A ALA* 3.5 20.0 + - - +
390A LEU* 1.3 79.7 - - - +
392A ARG* 1.3 58.1 + - - +
393A THR 3.8 0.3 + - - -
394A ALA* 5.4 0.5 + - - -
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Residues in contact with ARG 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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354A SER* 2.9 41.1 + - - +
357A LEU* 4.5 4.4 - - - +
358A ASP* 2.9 36.3 + - - -
385A GLN* 5.1 2.0 + - - -
388A ALA* 3.3 33.5 + - - +
389A PHE* 3.5 19.7 - - - +
390A LEU 3.2 0.2 - - - -
391A GLN* 1.3 78.5 - - + +
393A THR* 1.3 62.2 + - - +
394A ALA 4.0 1.9 + - - -
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Residues in contact with THR 393 (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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358A ASP* 4.7 4.2 + - - -
361A TRP* 3.5 41.1 - - + +
389A PHE* 2.8 38.2 + - + -
390A LEU 3.2 11.5 + - - +
391A GLN 3.5 0.4 - - - -
392A ARG* 1.3 88.4 + - - +
394A ALA* 1.3 66.4 + - - +
395A ASP* 3.6 5.8 - - - +
396A ALA* 3.1 17.7 + - + +
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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