Contacts of the helix formed by residues 416 - 428 (chain C) in PDB entry 3J8B
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 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414C GLY 3.8 4.4 + - - -
415C LEU* 1.3 69.4 - - - +
417C LYS* 1.3 67.9 + - - +
418C ASP 3.1 1.8 - - - -
419C ALA* 3.0 6.3 + - - +
420C HIS* 3.0 27.3 + - - +
479C SER* 4.6 18.2 - - - -
482C LEU* 5.1 12.6 - - - -
483C LEU* 6.2 2.0 - - - -
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Residues in contact with LYS 417 (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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415C LEU* 6.2 0.2 - - + -
416C THR* 1.3 78.7 - - - +
418C ASP* 1.3 60.3 + - - +
420C HIS* 4.4 4.0 - - - +
421C ASN* 3.5 19.2 + - - +
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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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410C ALA* 4.6 11.9 - - + -
415C LEU* 3.8 24.3 + - + +
416C THR 3.1 0.4 - - - -
417C LYS* 1.3 78.7 - - - +
419C ALA* 1.3 65.8 + - - +
421C ASN* 3.0 9.8 + - - +
422C ALA* 2.9 22.2 + - - +
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Residues in contact with ALA 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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407C GLY* 4.1 20.5 - - - +
410C ALA* 4.9 3.6 - - - +
411C PHE* 4.2 13.5 - - + +
415C LEU 3.3 16.6 + - - +
416C THR* 3.0 7.2 + - - +
418C ASP* 1.3 79.6 - - - +
420C HIS* 1.3 64.6 + - - +
422C ALA* 3.0 9.9 + - - +
423C LEU* 3.0 26.4 + - - +
476C TYR* 6.5 0.2 - - - -
479C SER* 4.9 9.0 - - - -
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Residues in contact with HIS 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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416C THR 3.0 15.6 + - - +
417C LYS* 4.4 4.7 - - - +
419C ALA* 1.3 76.1 - - - +
421C ASN* 1.3 63.0 + - - +
423C LEU* 4.8 2.2 - - - +
424C LEU* 3.7 22.9 + - - +
476C TYR* 6.4 0.9 - - - +
479C SER* 4.4 18.0 - - - -
480C ALA* 5.2 6.7 - - - +
483C LEU* 5.5 8.1 - - + -
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Residues in contact with ASN 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 LYS 3.5 13.3 + - - +
418C ASP* 3.0 12.5 + - - +
420C HIS* 1.3 81.1 - - - +
422C ALA* 1.3 61.8 + - - +
424C LEU* 4.1 7.1 + - - +
425C ASP 5.4 0.5 + - - -
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Residues in contact with ALA 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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403C MET* 5.0 11.7 - - + +
406C LEU* 5.4 1.3 - - + -
407C GLY* 4.2 23.3 - - - +
418C ASP 2.9 11.8 + - - +
419C ALA* 3.0 9.1 + - - +
421C ASN* 1.3 81.3 - - - +
423C LEU* 1.3 61.7 + - - +
424C LEU 3.6 0.7 + - - -
425C ASP* 4.7 5.4 + - - +
426C ILE* 5.4 0.9 + - - +
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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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403C MET 6.1 1.3 - - - -
404C VAL* 6.6 0.2 - - - -
407C GLY* 5.7 5.4 - - - -
419C ALA 3.0 14.9 + - - +
420C HIS* 5.0 1.6 - - - +
422C ALA* 1.3 77.6 - - + +
424C LEU* 1.3 65.3 + - - +
425C ASP 3.4 0.9 - - - -
426C ILE* 3.3 8.0 + - - +
427C GLN* 2.9 27.4 + - + +
476C TYR* 4.8 19.5 - - + -
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Residues in contact with LEU 424 (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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420C HIS 3.7 16.9 + - - +
421C ASN 4.1 4.5 + - - +
422C ALA 3.5 2.8 - - - -
423C LEU* 1.3 77.0 - - - +
425C ASP* 1.3 64.6 + - - +
427C GLN* 3.8 3.0 - - - +
428C SER* 3.1 26.5 + - - -
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Residues in contact with ASP 425 (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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421C ASN 5.4 0.6 + - - -
422C ALA 4.7 3.7 + - - +
423C LEU 3.4 0.8 - - - -
424C LEU* 1.3 80.5 - - - +
426C ILE* 1.3 62.2 + - + +
427C GLN 3.6 0.2 + - - -
428C SER* 3.6 13.4 + - - -
429C SER* 4.3 3.6 + - - -
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Residues in contact with ILE 426 (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 ASN* 5.5 13.7 - - + +
403C MET* 5.7 9.0 - - + -
422C ALA 5.4 0.6 + - - +
423C LEU* 3.3 8.9 + - - +
425C ASP* 1.3 79.8 - - + +
427C GLN* 1.3 59.2 + - - +
428C SER 3.3 1.1 - - - -
429C SER* 3.5 18.9 - - - -
432C ALA* 4.0 10.2 - - - +
435C LEU* 5.8 1.0 - - - +
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Residues in contact with GLN 427 (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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423C LEU* 2.9 26.7 + - + +
424C LEU* 3.8 2.7 - - - +
426C ILE* 1.3 75.5 - - - +
428C SER* 1.3 59.3 + - - +
429C SER 3.1 10.1 + - - +
432C ALA* 5.3 3.8 - - - -
473C GLU* 6.6 0.2 - - - -
476C TYR* 5.1 12.1 - - + -
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Residues in contact with SER 428 (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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424C LEU 3.1 17.1 + - - -
425C ASP* 3.7 9.2 - - - -
426C ILE 3.3 0.6 - - - -
427C GLN* 1.3 78.4 - - - +
429C SER* 1.3 61.8 + - - +
430C GLY 3.5 2.4 + - - -
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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