Contacts of the helix formed by residues 412 - 423 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F GLY* 6.5 0.7 - - - -
380F TYR* 4.0 22.9 - - + -
410F GLY 3.3 9.9 - - - +
411F CYS* 1.3 83.7 - - - +
413F PRO* 1.3 72.6 - - + +
414F ALA 3.2 0.2 - - - -
415F VAL* 3.0 27.3 + - + +
416F TYR 3.1 8.7 + - - -
448F LEU 3.2 21.5 - - - +
449F HIS* 3.3 36.3 - - + +
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Residues in contact with PRO 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411F CYS 3.1 7.8 - - - +
412F PRO* 1.3 83.8 - - + +
414F ALA* 1.3 56.3 + - - +
416F TYR* 3.0 13.2 + - + +
417F ASP* 2.8 37.6 + - - +
448F LEU 4.9 3.1 - - - +
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Residues in contact with ALA 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F PRO 3.2 0.4 - - - -
413F PRO* 1.3 79.1 - - - +
415F VAL* 1.3 61.5 + - - +
417F ASP* 3.1 26.8 + - - +
418F VAL* 3.2 11.3 + - - +
443F ILE* 3.8 16.8 - - + +
448F LEU* 3.9 37.9 - - + +
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Residues in contact with VAL 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 4.9 4.5 - - + -
376F LEU* 5.1 7.4 - - + -
380F TYR* 3.7 41.7 - - + +
411F CYS* 4.4 2.2 - - - -
412F PRO* 3.0 27.7 + - + +
414F ALA* 1.3 75.3 - - - +
416F TYR* 1.3 63.7 + - - +
418F VAL* 3.0 20.7 + - + +
419F MET* 3.2 22.8 + - + +
440F LEU* 5.2 4.3 - - + -
443F ILE* 3.8 29.4 - - + -
449F HIS* 4.7 2.0 - - + -
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Residues in contact with TYR 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404F LYS* 4.8 5.2 - - - +
405F MET 3.3 17.4 + - - -
406F ASP* 4.0 4.7 + - - -
407F ALA* 3.3 42.5 + - + -
411F CYS* 3.8 17.3 - - - -
412F PRO 3.1 6.0 + - - +
413F PRO* 3.0 14.2 + - + +
415F VAL* 1.3 73.3 - - - +
417F ASP* 1.3 67.1 + - - +
419F MET* 3.3 17.3 + - - +
420F LYS* 3.1 61.7 + - + +
423F TRP* 4.3 13.4 - + - -
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Residues in contact with ASP 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413F PRO* 2.8 26.9 + - - +
414F ALA* 3.2 15.8 + - - +
416F TYR* 1.3 77.3 - - - +
418F VAL* 1.3 58.6 + - + +
420F LYS* 3.4 30.1 + - - +
421F ASN* 2.9 27.7 + - - +
439F GLN* 5.2 0.4 - - - -
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Residues in contact with VAL 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F PHE* 5.1 0.9 - - + -
376F LEU* 3.8 21.5 - - + -
414F ALA 3.5 14.6 - - - +
415F VAL* 3.0 9.6 + - - +
417F ASP* 1.3 74.2 - - - +
419F MET* 1.3 67.7 + - - +
421F ASN* 2.7 15.1 + - - +
422F CYS* 3.0 13.4 + - - -
436F LEU* 3.9 24.9 - - + -
439F GLN* 3.7 25.8 - - + +
440F LEU* 4.0 17.7 - - + -
443F ILE* 3.9 19.3 - - + -
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Residues in contact with MET 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F GLY* 4.0 18.8 - - - +
376F LEU* 3.9 27.8 - - + +
377F TRP* 3.8 29.4 - - - -
380F TYR* 4.1 7.6 - - + -
408F PRO* 4.2 3.1 - - + -
411F CYS* 3.8 28.7 - - - -
415F VAL* 3.6 23.1 - - + +
416F TYR* 3.4 20.6 - - + +
418F VAL* 1.3 76.6 - - - +
420F LYS* 1.3 59.1 + - - +
422F CYS* 2.8 22.8 + - - +
423F TRP* 3.2 38.7 + - + -
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Residues in contact with LYS 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F LYS* 4.4 21.0 - - + +
416F TYR* 3.1 54.1 + - + +
417F ASP* 3.6 30.6 + - - +
419F MET* 1.3 78.5 - - - +
421F ASN* 1.3 62.2 + - - +
423F TRP* 3.2 32.4 + - + +
424F HIS* 4.1 7.5 + - - -
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Residues in contact with ASN 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F ASP 2.9 12.7 + - - +
418F VAL 2.7 18.1 + - - +
420F LYS* 1.3 74.0 - - - +
422F CYS* 1.3 57.4 + - - +
424F HIS* 2.9 38.8 + - - -
429F THR 5.7 0.6 + - - -
430F ARG* 4.1 0.5 - - - -
431F PRO* 3.1 36.5 - - + +
439F GLN* 3.0 35.7 - - - +
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Residues in contact with CYS 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369F VAL* 3.5 35.2 - - + +
370F TRP* 3.5 9.9 - - - -
372F PHE* 3.8 19.1 - - - +
373F GLY* 4.2 9.9 - - - -
418F VAL* 3.0 17.6 + - - -
419F MET 2.8 10.4 + - - +
421F ASN* 1.3 78.2 - - - +
423F TRP* 1.3 60.1 + - + +
424F HIS 3.4 0.7 - - - -
430F ARG* 2.9 25.6 + - - -
431F PRO* 4.2 0.2 - - - -
436F LEU* 3.6 26.5 - - - -
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Residues in contact with TRP 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F TRP* 3.4 48.3 + + + -
372F PHE 4.4 1.4 + - - -
373F GLY 4.0 2.7 - - - -
374F ILE* 3.3 36.5 - - + +
377F TRP* 4.5 8.5 - + + -
404F LYS* 3.5 43.1 + - + -
405F MET* 4.0 38.1 - - + -
416F TYR* 4.3 15.7 - + - -
419F MET* 3.2 51.5 + - + -
420F LYS* 3.2 18.3 + - + +
421F ASN 3.2 1.6 - - - -
422F CYS* 1.3 82.7 - - + +
424F HIS* 1.3 59.5 + - - +
425F LEU* 3.7 2.9 + - - +
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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