Contacts of the helix formed by residues 397 - 409 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A THR* 3.3 9.4 + - - -
396B GLU* 1.3 77.9 - - + +
398B LYS* 1.3 56.0 + - - +
399B ALA* 3.2 7.0 - - + +
400B ASP* 3.5 18.5 - - + +
401B ALA* 2.6 35.3 + - - +
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Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A TYR* 3.4 62.2 + - + -
428A THR* 3.8 6.4 - - - +
397B ASN* 1.3 71.5 - - - +
399B ALA* 1.3 61.3 + - - +
401B ALA* 2.9 23.0 - - - +
402B LYS* 2.9 30.7 + - + +
417B GLU* 5.5 5.2 - - - +
420B VAL* 4.3 8.5 - - + -
421B THR* 4.0 18.9 - - - +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ASN* 4.0 6.2 - - + +
398B LYS* 1.3 80.4 - - + +
400B ASP* 1.3 65.9 + - - +
402B LYS* 3.1 13.5 + - - +
403B GLU* 2.9 23.9 + - - +
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B SER* 4.4 2.7 - - - -
396B GLU* 4.1 14.8 - - + +
397B ASN* 3.2 29.7 + - + +
399B ALA* 1.3 76.1 - - - +
401B ALA* 1.3 63.7 + - - +
403B GLU* 3.2 8.4 + - - +
404B ASN* 2.9 25.3 + - - +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A TYR* 5.0 1.8 - - + -
428A THR* 4.0 6.5 - - - +
391B LEU* 4.0 2.4 - - - +
392B ILE* 4.2 18.8 - - + -
395B SER* 3.5 21.7 - - - -
397B ASN 2.6 16.5 + - - +
398B LYS* 2.9 19.1 - - - +
400B ASP* 1.3 74.8 - - - +
402B LYS* 1.3 61.4 + - - +
404B ASN* 3.3 9.2 + - - +
405B LEU* 3.0 20.2 + - + +
420B VAL* 4.6 8.5 - - + -
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B LYS* 2.9 39.6 + - + +
399B ALA* 3.4 11.7 - - - +
401B ALA* 1.3 76.1 - - - +
403B GLU* 1.3 63.2 + - - +
405B LEU* 3.1 24.3 + - - +
406B LYS* 3.1 13.1 + - - +
413B GLU* 4.9 14.1 - - - +
416B ALA* 4.3 17.1 - - + +
417B GLU* 4.5 16.6 - - + +
420B VAL* 3.9 20.0 - - + -
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B ALA 2.9 18.6 + - - +
400B ASP* 3.8 7.6 - - - +
402B LYS* 1.3 73.8 - - - +
404B ASN* 1.3 57.0 + - - +
406B LYS* 4.0 6.8 - - - +
407B VAL* 3.1 27.5 + - - +
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Residues in contact with ASN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B LEU* 3.9 17.5 - - + -
395B SER* 4.0 11.2 - - - +
400B ASP 2.9 16.9 + - - +
401B ALA 3.7 4.7 - - - +
402B LYS 3.2 0.2 - - - -
403B GLU* 1.3 76.3 - - - +
405B LEU* 1.3 59.4 + - - +
407B VAL* 3.5 4.8 + - - +
408B SER* 2.9 32.7 + - - -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B VAL* 3.8 30.3 - - + -
391B LEU* 3.7 18.8 - - + +
392B ILE* 4.0 10.5 - - + -
401B ALA 3.0 26.6 + - - +
402B LYS* 3.1 17.9 + - - +
404B ASN* 1.3 73.5 - - - +
406B LYS* 1.3 68.1 + - - +
408B SER 4.6 0.2 - - - +
409B TYR* 3.0 29.5 + - + +
410B ASP 3.4 3.6 + - - -
411B PHE* 3.7 19.5 + - + -
416B ALA* 4.8 8.1 - - + -
419B ILE* 4.3 20.2 - - + -
420B VAL* 3.9 16.8 - - + -
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B LYS 3.1 12.8 + - - +
403B GLU* 4.0 8.1 - - - +
405B LEU* 1.3 77.8 - - - +
407B VAL* 1.3 61.8 + - - +
410B ASP* 3.0 22.7 - - - +
411B PHE* 3.7 23.4 - - - +
412B THR 4.9 7.0 - - - +
413B GLU* 6.1 1.1 - - - -
416B ALA* 5.6 2.0 - - + +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B GLU 3.1 18.9 + - - +
404B ASN* 3.8 5.8 - - - +
405B LEU 3.3 0.2 - - - -
406B LYS* 1.3 79.1 - - - +
408B SER* 1.3 62.8 + - - +
410B ASP* 4.1 3.1 + - - +
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 4.5 7.9 - - - -
404B ASN 2.9 21.4 + - - -
407B VAL* 1.3 77.6 - - - +
409B TYR* 1.3 79.5 + - - +
410B ASP* 3.2 4.1 + - - +
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Residues in contact with TYR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ARG* 2.6 34.4 + - - +
384B ILE* 3.6 29.6 - - + -
387B GLU* 3.1 32.6 + - + +
388B VAL* 4.0 12.6 - - + -
391B LEU* 5.0 11.6 - - + +
405B LEU* 3.0 11.8 + - + +
408B SER* 1.3 88.0 - - - +
410B ASP* 1.3 67.2 - - - +
411B PHE* 2.8 30.9 + + + -
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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