Contacts of the helix formed by residues 412 - 423 (chain E) in PDB entry 1K9A
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 PRO 412 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288E GLY* 6.1 0.4 - - - -
380E TYR* 3.8 23.1 - - + -
410E GLY 3.4 9.0 - - - +
411E CYS* 1.3 81.3 - - - +
413E PRO* 1.3 62.2 - - + +
414E ALA* 3.1 1.1 - - + -
415E VAL* 2.7 37.4 + - + +
416E TYR 3.0 9.2 + - - -
448E LEU 3.3 23.1 - - - +
449E HIS* 3.2 37.0 - - + +
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Residues in contact with PRO 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411E CYS 3.2 8.4 - - - +
412E PRO* 1.3 83.1 - - + +
414E ALA* 1.3 52.0 + - - +
416E TYR* 3.1 10.0 + - + +
417E ASP* 2.7 44.5 + - - +
448E LEU 5.3 2.0 - - - +
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Residues in contact with ALA 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E PRO* 3.1 0.8 - - - +
413E PRO* 1.3 78.2 - - - +
415E VAL* 1.3 63.2 + - - +
417E ASP* 3.1 28.1 + - - +
418E VAL* 3.2 12.1 + - - +
443E ILE* 3.5 32.0 - - + +
448E LEU* 4.6 22.4 - - + +
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Residues in contact with VAL 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E LEU* 4.8 4.9 - - + -
376E LEU* 4.3 10.5 - - + -
380E TYR* 3.7 43.7 - - + +
411E CYS* 3.9 6.3 - - - -
412E PRO* 2.7 29.6 + - + +
414E ALA* 1.3 69.5 - - - +
416E TYR* 1.3 64.5 + - - +
418E VAL* 3.2 15.2 + - - +
419E MET* 3.2 29.0 + - + +
440E LEU* 5.5 2.7 - - + -
443E ILE* 4.1 24.7 - - + -
449E HIS* 4.7 2.2 - - + -
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Residues in contact with TYR 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E LYS* 4.3 10.6 + - - +
405E MET 2.9 25.1 + - - -
406E ASP* 4.0 2.7 - - - -
407E ALA* 3.3 45.5 + - + -
411E CYS* 3.8 8.2 - - - +
412E PRO 3.0 7.7 + - - +
413E PRO* 3.1 12.5 + - + +
415E VAL* 1.3 77.5 - - - +
417E ASP* 1.3 67.6 + - - +
419E MET* 3.1 22.4 + - + +
420E LYS* 2.9 55.1 + - + +
423E TRP* 4.0 14.3 - + - -
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Residues in contact with ASP 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E PRO* 2.7 26.9 + - - +
414E ALA* 3.1 19.3 - - - +
416E TYR* 1.3 79.7 - - - +
418E VAL* 1.3 56.3 + - + +
420E LYS* 3.1 20.1 + - - +
421E ASN* 2.8 29.3 + - - +
439E GLN* 5.4 0.2 - - - -
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Residues in contact with VAL 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E PHE* 4.7 0.9 - - + -
376E LEU* 3.5 21.8 - - + -
414E ALA 3.2 13.4 + - - +
415E VAL* 3.2 8.5 + - - +
417E ASP* 1.3 75.2 - - + +
419E MET* 1.3 66.8 + - - +
421E ASN* 2.9 12.7 + - - +
422E CYS* 2.9 12.3 + - - -
436E LEU* 3.5 29.8 - - + -
439E GLN* 3.6 26.2 - - + +
440E LEU* 4.0 23.8 - - + -
443E ILE* 4.2 9.6 - - + -
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Residues in contact with MET 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373E GLY* 3.7 26.5 - - - +
376E LEU* 4.0 24.9 - - + +
377E TRP* 3.7 32.1 - - - -
380E TYR* 4.2 4.9 - - + -
408E PRO* 4.3 3.8 - - + -
411E CYS* 3.8 19.7 - - - -
415E VAL* 3.2 32.8 + - + +
416E TYR* 3.1 20.1 + - - +
418E VAL* 1.3 76.8 - - - +
420E LYS* 1.3 57.0 + - - +
422E CYS* 2.7 26.5 + - - +
423E TRP* 3.1 30.4 + - + -
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Residues in contact with LYS 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E LYS* 4.1 26.3 + - + +
416E TYR* 2.9 51.0 + - + +
417E ASP* 3.2 20.6 - - - +
419E MET* 1.3 78.9 - - - +
421E ASN* 1.3 56.5 + - - +
423E TRP* 2.9 36.1 + - + +
424E HIS* 3.7 4.0 + - - -
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Residues in contact with ASN 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417E ASP 2.8 15.7 + - - +
418E VAL* 2.9 11.4 + - - +
420E LYS* 1.3 73.4 - - - +
422E CYS* 1.3 61.0 + - - +
424E HIS* 3.1 36.8 + - - -
429E THR 4.0 5.0 - - - +
430E ARG* 3.9 1.9 - - - -
431E PRO* 3.3 28.6 - - + +
439E GLN* 4.3 20.0 + - - +
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Residues in contact with CYS 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E VAL* 3.5 31.9 - - - +
370E TRP* 3.5 11.1 - - - -
372E PHE* 4.0 12.8 - - - -
373E GLY* 3.8 15.7 - - - -
418E VAL* 2.9 17.7 + - - -
419E MET 2.7 12.9 + - - +
421E ASN* 1.3 73.7 - - - +
423E TRP* 1.3 59.5 + - + +
424E HIS 3.3 0.9 - - - -
430E ARG* 3.4 23.7 - - - -
431E PRO* 4.2 6.1 - - - -
436E LEU* 3.8 27.1 - - - -
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Residues in contact with TRP 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E TRP* 3.1 47.8 + + + -
373E GLY 3.5 22.2 - - - -
374E ILE* 3.5 30.8 - - + +
377E TRP* 4.2 6.7 - + + -
387E TYR* 5.7 2.6 + - - -
404E LYS* 3.5 42.5 + - + +
405E MET* 4.0 40.8 - - + -
416E TYR* 4.0 9.9 - + - -
419E MET* 3.4 44.2 - - + -
420E LYS* 2.9 14.3 + - + +
422E CYS* 1.3 83.1 - - + +
424E HIS* 1.3 65.2 - - - +
425E LEU* 3.3 4.3 + - - +
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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