Contacts of the helix formed by residues 393 - 403 (chain A) in PDB entry 3I5G
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 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A ALA* 4.2 0.7 - - - -
392A VAL* 1.3 81.1 - - - +
394A ALA* 1.3 56.7 + - - +
395A GLY* 3.1 3.4 - - - +
396A ASP* 2.7 49.1 + - - +
397A LEU* 2.9 11.8 + - - +
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Residues in contact with ALA 394 (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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380A THR* 5.6 4.9 - - + +
383A ALA* 3.9 14.4 - - + +
384A GLU* 4.0 15.5 - - + +
387A ALA* 3.4 28.7 - - + +
392A VAL 3.6 0.2 + - - -
393A ASN* 1.3 69.2 - - - +
395A GLY* 1.3 64.2 + - - +
397A LEU* 4.2 5.6 - - - -
398A LEU* 2.9 32.9 + - + +
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Residues in contact with GLY 395 (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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393A ASN* 2.9 4.1 + - - +
394A ALA* 1.3 78.7 - - - +
396A ASP* 1.3 57.5 + - - +
398A LEU* 4.0 4.5 - - - +
399A LYS* 3.0 33.9 + - - +
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Residues in contact with ASP 396 (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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393A ASN* 2.7 38.3 + - + +
395A GLY* 1.3 69.2 - - - -
397A LEU* 1.3 67.5 + - - +
399A LYS* 2.8 11.4 + - - +
400A CYS* 2.7 26.9 + - - +
611A LEU* 4.1 22.9 - - + +
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Residues in contact with LEU 397 (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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363A LEU* 6.0 1.8 - - + -
366A MET* 4.8 4.7 - - + -
383A ALA* 4.2 8.1 - - + +
386A VAL* 3.8 29.6 - - + -
387A ALA* 4.5 9.6 - - + +
390A LEU* 6.0 5.2 - - + -
392A VAL* 5.3 4.3 - - + -
393A ASN 2.9 12.4 + - - +
394A ALA* 3.7 9.0 - - - +
396A ASP* 1.3 77.9 - - - +
398A LEU* 1.3 65.9 + - - +
400A CYS* 2.9 10.2 + - - -
401A LEU* 2.9 47.3 + - + +
429A LEU* 5.0 8.3 - - + -
608A VAL* 4.3 20.6 - - + -
611A LEU* 3.7 13.9 - - + +
612A LEU* 5.7 6.3 - - + -
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Residues in contact with LEU 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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366A MET* 4.3 4.0 - - + -
368A TRP* 3.5 35.2 - - + -
377A ALA* 4.0 20.6 - - + -
380A THR* 4.6 16.2 - - + +
383A ALA* 3.7 31.4 - - + -
394A ALA* 2.9 23.0 + - + +
395A GLY* 4.0 4.7 - - - +
397A LEU* 1.3 72.9 - - + +
399A LYS* 1.3 55.2 + - - +
401A LEU* 4.3 4.5 - - + -
402A LEU* 2.7 47.9 + - + +
403A LYS* 5.3 0.4 - - - +
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Residues in contact with LYS 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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395A GLY 3.0 22.9 + - - +
396A ASP* 2.8 20.9 + - - +
398A LEU* 1.3 77.6 - - + +
400A CYS* 1.3 51.8 + - - +
403A LYS* 2.7 79.5 + - + +
405A LYS* 5.7 12.4 - - - +
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Residues in contact with CYS 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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396A ASP* 2.7 24.5 + - - +
397A LEU* 3.2 15.3 - - - -
399A LYS* 1.3 71.8 - - - +
401A LEU* 1.3 60.6 + - - +
404A PRO* 3.4 28.5 - - + +
605A ASN* 5.9 0.5 - - - +
607A ASN* 3.8 27.3 - - + +
608A VAL* 4.4 11.7 - - - +
611A LEU* 3.4 33.2 - - - -
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Residues in contact with LEU 401 (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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363A LEU* 6.3 0.4 - - + -
366A MET* 4.2 22.9 - - + -
368A TRP* 4.5 11.0 - - + -
397A LEU* 2.9 42.5 + - + +
398A LEU* 3.8 4.7 - - - +
400A CYS* 1.3 81.2 - - - +
402A LEU* 1.3 64.1 + - - +
417A ARG* 3.4 19.9 - - - +
422A VAL* 4.0 12.9 - - + +
425A SER* 4.8 17.2 + - - +
426A ILE* 4.3 21.3 - - + -
429A LEU* 5.2 6.7 - - + -
608A VAL* 3.5 31.9 - - + -
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Residues in contact with LEU 402 (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 TRP* 3.5 29.8 - - + -
374A GLN* 2.9 23.1 + - - -
375A ALA* 3.1 29.2 - - + +
376A GLU* 3.3 17.7 - - + +
377A ALA* 3.5 22.7 - - + +
398A LEU* 2.7 32.0 + - + +
401A LEU* 1.3 75.3 - - - +
403A LYS* 1.3 78.5 + - + +
404A PRO* 4.0 0.4 - - - -
415A GLN 3.9 0.2 - - - +
417A ARG* 3.3 14.2 - - - +
422A VAL* 4.4 7.2 - - + -
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Residues in contact with LYS 403 (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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374A GLN* 4.6 6.1 - - + +
376A GLU* 6.4 0.2 - - - -
398A LEU* 5.3 0.6 - - - +
399A LYS* 2.7 62.3 + - + +
402A LEU* 1.3 101.6 - - + +
404A PRO* 1.3 70.6 - - - +
405A LYS* 4.3 10.2 - - - +
413A VAL* 4.4 5.1 - - + +
415A GLN* 3.2 39.3 - - + +
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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