Contacts of the helix formed by residues 397 - 409 (chain A) in PDB entry 3KSA
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A GLU* 1.3 78.0 - - + +
398A LYS* 1.3 56.0 + - - +
399A ALA* 3.2 7.2 - - + +
400A ASP* 3.5 17.6 - - + +
401A ALA* 2.6 35.7 + - - +
428B THR* 3.4 9.4 + - - -
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Residues in contact with LYS 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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397A ASN* 1.3 70.8 - - - +
399A ALA* 1.3 59.0 + - - +
401A ALA* 2.9 22.5 - - - +
402A LYS* 2.9 18.2 + - + +
420A VAL* 4.8 3.3 - - + +
425B TYR* 3.4 49.1 - - + -
428B THR* 3.8 6.2 - - - +
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Residues in contact with ALA 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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397A ASN* 3.2 6.0 - - + +
398A LYS* 1.3 76.3 - - - +
400A ASP* 1.3 66.5 + - - +
402A LYS* 3.1 14.9 + - - +
403A GLU* 2.9 23.3 + - - +
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Residues in contact with ASP 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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395A SER* 4.4 2.7 - - - -
396A GLU* 4.1 14.4 - - + +
397A ASN* 3.1 28.6 + - + +
399A ALA* 1.3 77.1 - - - +
401A ALA* 1.3 63.0 + - - +
403A GLU* 3.2 7.8 + - - +
404A ASN* 2.9 26.0 + - - +
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Residues in contact with ALA 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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391A LEU* 4.0 2.5 - - - +
392A ILE* 4.2 18.8 - - + -
395A SER* 3.6 17.4 - - - -
397A ASN 2.6 17.4 + - - +
398A LYS* 2.9 18.8 - - - +
400A ASP* 1.3 75.1 - - - +
402A LYS* 1.3 59.1 + - - +
404A ASN* 3.3 9.0 + - - +
405A LEU* 2.9 21.3 + - - +
420A VAL* 4.6 8.3 - - + -
425B TYR* 5.0 1.8 - - + -
428B THR* 4.0 11.2 - - - +
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Residues in contact with LYS 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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398A LYS* 2.9 19.8 + - + +
399A ALA* 3.4 13.5 - - - +
401A ALA* 1.3 74.6 - - - +
403A GLU* 1.3 63.3 + - - +
405A LEU* 3.1 24.4 + - - +
406A LYS* 3.1 14.1 + - - +
413A GLU* 4.9 15.0 - - - +
416A ALA* 4.3 16.2 - - + +
417A GLU* 4.5 19.7 - - + +
420A VAL* 3.9 22.0 - - + -
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Residues in contact with GLU 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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399A ALA 2.9 19.4 + - - +
400A ASP* 3.8 7.6 - - - +
402A LYS* 1.3 73.2 - - - +
404A ASN* 1.3 57.4 + - - +
406A LYS* 3.7 7.5 + - - +
407A VAL* 3.1 27.5 + - - +
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Residues in contact with ASN 404 (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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391A LEU* 3.9 16.7 - - + +
395A SER* 4.0 12.3 - - - +
400A ASP 2.9 16.4 + - - +
401A ALA 3.6 4.7 - - - +
402A LYS 3.2 0.4 + - - -
403A GLU* 1.3 75.8 - - - +
405A LEU* 1.3 58.8 + - - +
407A VAL* 3.4 5.2 + - - +
408A SER* 2.9 32.9 + - - -
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Residues in contact with LEU 405 (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* 3.8 29.2 - - + -
391A LEU* 3.7 17.9 - - + -
392A ILE* 4.1 11.2 - - + -
401A ALA 2.9 27.1 + - - +
402A LYS* 3.1 18.1 + - - +
404A ASN* 1.3 73.5 - - - +
406A LYS* 1.3 67.5 + - - +
409A TYR* 3.0 29.7 + - + +
410A ASP 3.4 3.8 + - - -
411A PHE* 3.7 18.9 + - + -
416A ALA* 4.7 8.1 - - + -
419A ILE* 4.3 21.3 - - + -
420A VAL* 3.9 15.9 - - + -
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Residues in contact with LYS 406 (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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402A LYS 3.1 12.6 + - - +
403A GLU* 3.9 8.3 - - - +
405A LEU* 1.3 79.9 - - - +
407A VAL* 1.3 62.0 + - - +
410A ASP* 3.0 22.5 - - - +
411A PHE* 3.7 22.0 - - - +
412A THR 4.9 7.4 - - - +
413A GLU* 6.1 0.9 - - - -
416A ALA* 5.5 2.4 - - + +
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Residues in contact with VAL 407 (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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403A GLU 3.1 19.1 + - - +
404A ASN* 3.7 6.1 - - - +
406A LYS* 1.3 78.6 - - - +
408A SER* 1.3 63.8 + - - +
410A ASP* 4.1 3.5 + - - +
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Residues in contact with SER 408 (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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391A LEU* 4.5 8.5 - - - -
404A ASN 2.9 20.8 + - - -
407A VAL* 1.3 76.7 - - - +
409A TYR* 1.3 80.0 + - - +
410A ASP* 3.2 4.5 + - - +
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Residues in contact with TYR 409 (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 ARG* 2.6 36.6 + - - +
384A ILE* 3.6 29.8 - - + -
387A GLU* 3.0 32.5 + - + +
388A VAL* 4.0 15.5 - - + -
391A LEU* 5.0 12.1 - - + +
405A LEU* 3.0 10.1 + - + +
408A SER* 1.3 88.8 - - - +
410A ASP* 1.3 65.4 + - - +
411A PHE* 2.8 27.5 + + + -
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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