Contacts of the helix formed by residues 403 - 412 (chain C) in PDB entry 1JFZ
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 MET 403 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400C GLY 4.3 5.6 - - - +
401C MET* 3.0 37.2 - - + -
402C LYS* 1.3 80.0 - - - +
404C LEU* 1.3 67.5 + - + +
406C GLN* 3.1 22.2 + - - +
491C LYS* 3.4 34.8 - - + +
492C PHE* 2.9 64.8 - - + -
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Residues in contact with LEU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C GLY* 3.1 32.1 - - - +
401C MET 3.8 3.8 - - - +
403C MET* 1.3 77.0 - - + +
405C GLU* 1.3 66.0 + - - +
407C LEU* 2.6 33.9 + - + +
408C GLU* 2.8 21.2 + - - +
418C LYS* 4.6 17.9 - - + +
421C LEU* 3.9 25.1 - - + -
422C GLU* 3.7 35.7 - - + +
425C LEU* 4.2 17.7 - - + -
492C PHE* 4.9 4.0 - - + +
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Residues in contact with GLU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C MET 3.0 16.2 - - - +
402C LYS* 3.6 32.5 - - + +
404C LEU* 1.3 86.3 - - - +
406C GLN* 1.3 61.0 + - - +
408C GLU* 3.2 25.7 + - - +
409C LYS* 3.1 22.7 + - - +
418C LYS* 4.5 15.5 + - - +
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Residues in contact with GLN 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C LYS 3.9 6.9 + - - +
403C MET* 3.1 28.4 + - - +
404C LEU 3.0 0.8 - - - -
405C GLU* 1.3 74.9 - - - +
407C LEU* 1.3 65.3 + - - +
409C LYS* 3.3 22.1 + - - +
410C LYS* 3.0 35.9 + - - +
488C GLU* 3.0 19.1 + - - +
491C LYS* 4.4 7.2 + - - +
492C PHE* 3.3 25.2 - - + -
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C MET 3.2 1.6 + - - -
404C LEU* 2.6 18.0 + - - +
406C GLN* 1.3 72.4 - - - +
408C GLU* 1.3 62.6 + - - +
410C LYS* 3.0 5.5 + - + -
411C LEU* 2.8 28.9 + - + +
421C LEU* 3.7 33.7 - - + -
425C LEU* 3.8 24.9 - - + -
487C LEU* 4.4 26.0 - - + +
489C LEU* 4.1 19.3 - - + -
492C PHE* 4.0 24.5 - - + -
512C LEU* 4.3 15.7 - - + -
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Residues in contact with GLU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C LEU* 2.8 18.9 + - - +
405C GLU* 3.2 38.0 - - - +
407C LEU* 1.3 72.0 - - - +
409C LYS* 1.3 63.1 + - - +
411C LEU* 3.1 3.3 + - + -
412C GLY* 2.9 20.3 + - - -
413C TYR 3.0 31.3 + - - +
414C THR* 3.8 19.2 - - - +
415C PHE* 3.1 19.0 + - + +
418C LYS* 2.9 29.7 + - - +
421C LEU* 4.1 15.4 - - + +
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Residues in contact with LYS 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C GLU 3.1 12.9 + - - +
406C GLN* 3.3 35.0 + - - +
407C LEU 3.2 0.2 - - - -
408C GLU* 1.3 77.2 - - - +
410C LYS* 1.3 81.2 + - - +
411C LEU 3.2 0.3 + - - -
412C GLY* 3.4 9.3 + - - -
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C GLN* 3.0 46.0 + - + +
407C LEU* 3.0 8.9 + - - +
409C LYS* 1.3 90.1 - - - +
411C LEU* 1.3 60.3 + - - +
486C LYS 4.8 8.2 + - - +
487C LEU* 3.4 43.0 - - + +
488C GLU* 3.3 27.2 + - + +
492C PHE* 4.4 3.4 - - + -
534C LEU* 3.7 15.8 - - - +
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Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C LEU* 2.8 19.7 + - + +
408C GLU* 3.6 5.2 - - - +
410C LYS* 1.3 77.3 - - - +
412C GLY* 1.3 62.8 + - - +
413C TYR* 4.0 22.9 - - + +
415C PHE* 4.1 11.2 - - + -
421C LEU* 6.2 0.2 - - + -
487C LEU* 3.9 21.8 - - + -
512C LEU* 4.2 16.8 - - + -
513C TRP* 3.9 34.3 - - + -
516C VAL* 3.7 24.9 - - + -
530C LEU* 3.7 16.0 - - + +
533C LYS* 5.9 0.2 - - - -
534C LEU* 3.7 15.7 - - + +
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Residues in contact with GLY 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLU 2.9 5.6 + - - -
409C LYS* 3.4 6.9 + - - -
410C LYS 3.4 3.2 - - - -
411C LEU* 1.3 79.3 - - - +
413C TYR* 1.3 63.4 + - - +
526C PHE* 5.1 2.6 - - - -
530C LEU* 3.8 14.8 - - - +
533C LYS* 5.5 8.6 - - - -
534C LEU* 5.7 0.4 - - - -
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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