Contacts of the helix formed by residues 414 - 426 (chain A) in PDB entry 1KB9
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 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A VAL* 4.8 3.4 - - - -
412A ALA 3.9 10.5 - - - +
413A ILE* 1.3 82.5 - - - +
415A VAL* 1.3 63.3 + - - +
416A LYS* 3.5 10.7 + - - +
417A ASP* 2.9 39.1 + - - +
418A VAL* 3.3 12.2 + - - +
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Residues in contact with VAL 415 (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 VAL* 3.7 22.9 - - + +
359A THR 4.1 1.1 - - - -
360A ASP* 3.3 40.4 - - - +
363A VAL* 3.7 27.9 - - + +
414A THR* 1.3 73.6 - - - +
416A LYS* 1.3 63.4 + - + +
417A ASP 3.2 0.3 + - - -
418A VAL* 3.2 5.2 + - - +
419A LYS* 3.0 43.0 + - + +
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Residues in contact with LYS 416 (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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414A THR* 3.1 11.1 + - - +
415A VAL* 1.3 81.2 - - - +
417A ASP* 1.3 62.2 + - - +
419A LYS* 3.6 10.9 + - + +
420A ALA* 3.1 24.3 + - - +
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Residues in contact with ASP 417 (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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274A ASN* 5.3 2.2 + - - +
277A VAL* 4.0 13.9 - - + +
412A ALA 3.8 5.2 - - - +
413A ILE* 3.4 19.9 - - + +
414A THR* 2.9 36.1 + - - +
416A LYS* 1.3 76.6 - - - +
418A VAL* 1.3 66.2 + - - +
420A ALA* 3.2 7.0 + - - +
421A TRP* 2.9 22.9 + - - +
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Residues in contact with VAL 418 (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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277A VAL* 3.9 14.1 - - + +
280A LEU* 4.1 20.4 - - + -
281A ALA* 4.8 6.5 - - + -
284A ILE* 4.7 6.1 - - + -
354A LEU* 4.0 38.6 - - + +
358A VAL* 4.3 9.2 - - + -
363A VAL* 4.4 10.3 - - + -
413A ILE* 4.1 15.3 - - + -
414A THR 3.3 10.7 + - - +
415A VAL* 3.2 7.9 + - - +
417A ASP* 1.3 74.8 - - - +
419A LYS* 1.3 57.7 + - - +
421A TRP* 3.3 3.5 + - + +
422A ALA* 2.8 28.4 + - - +
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Residues in contact with LYS 419 (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 LEU 3.2 19.7 - - - +
355A THR* 3.7 19.7 - - - +
356A ILE* 3.5 28.5 + - - +
357A SER* 4.3 3.5 - - - +
358A VAL* 4.2 10.7 + - + -
415A VAL* 3.0 39.2 + - + +
416A LYS* 3.8 10.8 - - + +
418A VAL* 1.3 77.7 - - - +
420A ALA* 1.3 57.3 + - - +
422A ALA* 3.9 0.7 - - - +
423A GLY* 2.9 27.7 + - - -
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Residues in contact with ALA 420 (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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416A LYS 3.1 18.3 + - - +
417A ASP* 3.2 6.0 + - - +
419A LYS* 1.3 76.3 - - - +
421A TRP* 1.3 63.7 + - - +
423A GLY* 3.7 2.2 + - - -
424A LYS* 3.5 21.1 + - - +
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Residues in contact with TRP 421 (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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267A GLY* 5.6 0.7 - - - -
268A GLU* 2.9 35.1 + - + +
274A ASN* 3.5 27.3 - - + +
277A VAL* 3.7 15.7 - - + -
278A ALA* 3.5 22.1 - - + +
281A ALA* 3.5 26.7 - - + -
328A TRP* 3.4 39.9 - + + -
354A LEU* 4.3 1.8 - - + -
417A ASP 2.9 13.4 + - - +
418A VAL* 3.5 9.2 - - + +
420A ALA* 1.3 75.0 - - - +
422A ALA* 1.3 76.4 + - + +
424A LYS* 3.0 8.1 + - + +
425A ARG* 2.8 45.7 + - + +
426A LEU* 3.8 26.0 - - + -
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Residues in contact with ALA 422 (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 LEU* 3.5 31.4 - - + +
355A THR* 3.4 14.6 - - - +
418A VAL 2.8 20.2 + - - +
419A LYS 4.0 0.4 - - - +
421A TRP* 1.3 85.1 - - + +
423A GLY* 1.3 57.6 + - - +
424A LYS 3.0 1.6 + - - -
426A LEU* 2.8 37.2 + - + +
427A TRP 3.0 9.7 + - - -
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Residues in contact with GLY 423 (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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355A THR* 3.4 19.0 + - - -
419A LYS 2.9 17.6 + - - -
420A ALA* 4.1 3.4 - - - -
421A TRP 3.2 0.4 - - - -
422A ALA* 1.3 75.9 - - - +
424A LYS* 1.3 62.2 + - - +
427A TRP* 4.1 19.2 - - - +
429A GLN* 5.2 1.6 + - - -
13I ARG* 5.6 4.9 - - - -
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Residues in contact with LYS 424 (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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420A ALA 3.5 12.4 + - - +
421A TRP* 3.0 8.5 + - - +
422A ALA 3.0 0.6 - - - -
423A GLY* 1.3 84.7 - - - +
425A ARG* 1.3 70.5 + - - +
429A GLN* 3.6 23.6 + - - +
13I ARG* 4.4 25.3 + - - +
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Residues in contact with ARG 425 (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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265A VAL* 3.5 22.2 - - + +
266A GLU* 3.3 49.0 + - - +
267A GLY* 3.3 16.1 + - - +
268A GLU* 2.9 35.8 + - - +
269A PRO* 4.6 5.7 - - - +
421A TRP* 2.8 39.5 + - + +
424A LYS* 1.3 91.3 + - - +
426A LEU* 1.3 65.3 + - + +
429A GLN* 3.5 13.8 - - - +
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Residues in contact with LEU 426 (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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265A VAL* 3.6 21.1 - - + -
328A TRP* 3.9 24.5 - - + -
351A TRP* 4.0 29.6 - - + +
354A LEU* 3.9 28.5 - - + -
355A THR* 5.1 1.3 - - - +
421A TRP* 3.8 27.8 - - + -
422A ALA* 2.8 20.0 + - + +
425A ARG* 1.3 79.8 - - - +
427A TRP* 1.3 63.2 + - - +
428A ASP 3.2 3.8 + - - -
429A GLN* 3.6 5.7 + - - +
452A MET* 3.3 29.3 - - + +
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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