Contacts of the helix formed by residues 417 - 423 (chain C) in PDB entry 3KHU
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 TRP 417 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C GLY* 4.3 0.4 - - - -
337C ALA* 4.4 2.5 - - + -
340C LYS* 4.0 7.1 - - - +
341C ASP* 3.2 50.7 - - - -
342C THR 3.3 24.5 - - - -
368C ASP* 2.8 35.6 + - - -
369C PRO* 3.4 27.4 - - + -
370C LYS* 3.6 17.7 - - + -
415C THR* 2.9 24.4 + - + +
416C GLU* 1.3 77.2 - - - +
418C ASP* 1.3 67.1 + - - +
419C MET* 4.1 14.1 - - + -
420C PHE* 3.1 41.1 + + + +
421C LYS 4.5 0.9 + - - -
444C VAL* 4.7 3.8 - - - +
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Residues in contact with ASP 418 (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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340C LYS* 3.1 35.0 + - - +
341C ASP* 4.9 5.7 + - - +
416C GLU 3.2 4.0 + - - +
417C TRP* 1.3 75.1 - - - +
419C MET* 1.3 63.5 + - - +
420C PHE 3.1 1.0 + - - -
421C LYS* 3.2 42.7 + - - +
422C GLU* 3.9 7.4 - - - +
444C VAL* 6.0 1.3 - - - -
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Residues in contact with MET 419 (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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367C TYR* 3.8 40.6 - - + +
369C PRO* 3.9 17.9 - - + -
401C PRO* 3.9 17.7 - - + -
417C TRP* 4.1 10.7 - - + +
418C ASP* 1.3 80.3 - - - +
420C PHE* 1.3 77.9 + - + +
422C GLU* 3.1 22.1 + - - +
423C LEU* 3.5 23.3 + - + +
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Residues in contact with PHE 420 (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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334C LEU* 3.5 30.5 - - + -
335C GLY* 3.6 17.5 - - - -
367C TYR* 4.0 25.4 - + - -
369C PRO* 4.6 1.1 - - + -
401C PRO* 5.2 0.7 - - + -
413C ILE* 3.8 22.7 - - + -
415C THR 3.3 26.7 - - - -
416C GLU 5.0 0.2 - - - -
417C TRP* 3.1 32.3 + + - +
418C ASP 3.1 0.2 + - - -
419C MET* 1.3 96.3 - - + +
421C LYS* 1.3 60.9 + - - +
422C GLU 3.2 0.4 + - - -
423C LEU* 3.7 20.1 + - + +
425C TYR* 2.6 34.7 + - - +
444C VAL* 4.8 4.0 - - + -
445C LEU* 3.8 2.4 - - - +
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Residues in contact with LYS 421 (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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417C TRP 4.5 0.8 + - - +
418C ASP* 3.2 37.9 + - - +
420C PHE* 1.3 78.0 - - - +
422C GLU* 1.3 78.3 + - - +
423C LEU 3.4 2.1 + - - +
425C TYR* 4.4 4.0 - - - -
444C VAL* 3.8 31.4 - - + +
445C LEU* 3.8 12.8 - - + -
448C LEU* 3.8 22.2 - - + +
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Residues in contact with GLU 422 (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 TYR* 5.0 0.2 + - - -
418C ASP 3.9 12.7 - - - +
419C MET* 3.1 13.5 + - - +
421C LYS* 1.3 104.4 - - - +
423C LEU* 1.3 66.5 + - - +
424C ASP 3.7 0.5 + - - -
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Residues in contact with LEU 423 (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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334C LEU* 3.8 25.4 - - + -
401C PRO* 4.0 26.7 - - + -
402C TYR* 3.6 25.6 - - + +
419C MET* 3.8 20.9 - - + +
420C PHE* 3.7 11.9 + - + +
421C LYS 3.4 3.6 - - - +
422C GLU* 1.3 83.6 - - - +
424C ASP* 1.3 60.4 + - - +
425C TYR* 3.1 46.3 + - + +
428C ILE* 4.2 14.1 - - + -
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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