Contacts of the helix formed by residues 409 - 426 (chain C) in PDB entry 2B4J
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 SER 409 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C VAL* 3.8 17.7 - - - +
374C ILE* 4.3 0.3 - - - +
406C PHE* 3.1 16.6 + - - +
407C LYS 3.2 0.4 - - - -
408C VAL* 1.3 80.1 - - - +
410C GLN* 1.3 58.2 + - - +
411C VAL* 3.4 12.5 + - - +
412C ILE* 3.2 41.1 + - - +
413C MET* 3.0 23.3 + - - +
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Residues in contact with GLN 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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407C LYS* 3.3 32.5 + - - +
408C VAL 4.3 0.4 - - - -
409C SER* 1.3 72.8 - - - +
411C VAL* 1.3 59.6 + - + +
413C MET* 3.5 33.7 - - - +
414C GLU* 2.9 30.8 + - - +
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Residues in contact with VAL 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ILE* 3.8 21.1 - - + -
409C SER* 3.1 8.9 + - - +
410C GLN* 1.3 80.2 - - + +
412C ILE* 1.3 63.1 + - - +
414C GLU* 3.4 11.2 + - + +
415C LYS* 3.1 52.1 + - + +
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Residues in contact with ILE 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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363C LEU* 4.0 3.1 - - + -
370C VAL* 3.8 16.4 - - + +
373C CYS* 3.8 26.0 - - + -
374C ILE* 3.6 18.8 - - + -
377C LEU* 3.9 21.9 - - + +
403C ILE* 4.0 24.7 - - + +
406C PHE* 3.9 29.2 - - + -
409C SER* 3.2 28.0 + - - +
411C VAL* 1.3 71.7 - - - +
413C MET* 1.3 65.3 + - - +
415C LYS* 4.7 0.2 - - - -
416C SER* 2.8 30.3 + - - -
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Residues in contact with MET 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE 3.8 4.5 - - - +
404C ARG 3.2 24.5 - - - +
405C ARG* 4.7 3.1 - - - -
406C PHE 3.2 33.9 - - - +
407C LYS* 3.7 25.8 - - + -
409C SER 3.0 9.6 + - - +
410C GLN* 3.5 44.2 - - - +
412C ILE* 1.3 76.0 - - - +
414C GLU* 1.3 57.1 + - - +
416C SER* 3.3 1.4 + - - -
417C THR* 2.7 34.8 + - - -
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Residues in contact with GLU 414 (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 GLN 2.9 20.3 + - - +
411C VAL* 3.8 10.6 - - - +
412C ILE 3.3 0.2 - - - -
413C MET* 1.3 72.6 - - - +
415C LYS* 1.3 60.7 + - + +
417C THR* 3.4 6.5 + - - -
418C MET* 3.1 28.7 + - + +
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Residues in contact with LYS 415 (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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374C ILE* 3.8 18.2 - - + -
377C LEU* 4.1 23.1 - - + -
378C ASP* 2.8 31.2 + - - +
411C VAL* 3.1 43.6 + - + +
414C GLU* 1.3 79.0 - - + +
416C SER* 1.3 61.1 + - - +
418C MET* 3.3 8.7 + - - +
419C LEU* 2.9 35.8 + - + +
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Residues in contact with SER 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 4.2 3.6 - - - +
400C LEU* 3.7 17.2 - - - +
403C ILE* 3.4 31.0 - - - -
404C ARG* 3.3 20.5 + - - +
412C ILE 2.8 22.6 + - - -
413C MET 3.3 4.3 + - - -
415C LYS* 1.3 73.4 - - - +
417C THR* 1.3 61.6 + - - +
419C LEU* 3.7 8.5 - - - +
420C TYR* 2.8 32.2 + - - +
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Residues in contact with THR 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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404C ARG* 3.5 31.2 + - + +
413C MET 2.7 23.9 + - - -
414C GLU* 3.5 7.6 - - - -
415C LYS 3.3 0.2 - - - -
416C SER* 1.3 73.7 + - - +
418C MET* 1.3 65.0 + - - +
420C TYR* 3.8 1.7 - - - +
421C ASN* 3.0 44.7 + - - +
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Residues in contact with MET 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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381C ALA* 5.0 10.5 - - + +
414C GLU* 3.1 14.3 + - + +
415C LYS* 3.6 9.6 - - - +
417C THR* 1.3 77.5 - - - +
419C LEU* 1.3 79.6 + - - +
421C ASN* 3.4 9.7 + - - +
422C LYS* 3.0 55.8 + - + +
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Residues in contact with LEU 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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377C LEU* 3.5 48.2 - - + +
380C LEU* 4.2 20.2 - - + +
381C ALA* 3.8 26.0 - - + +
400C LEU* 4.0 11.2 - - + -
415C LYS* 2.9 20.7 + - + +
416C SER 3.7 4.5 - - - +
417C THR 3.2 0.2 - - - -
418C MET* 1.3 98.2 - - - +
420C TYR* 1.3 60.8 + - - +
422C LYS* 3.2 14.1 + - - +
423C PHE* 2.9 35.9 + - + -
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Residues in contact with TYR 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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397C ILE* 3.9 28.0 - - + -
400C LEU* 4.3 9.8 - - + +
401C LYS* 3.5 47.6 + - + +
404C ARG* 3.6 39.5 - - - +
416C SER 2.8 17.7 + - - +
417C THR 3.8 2.7 - - - +
419C LEU* 1.3 75.1 - - - +
421C ASN* 1.3 59.0 + - - +
423C PHE* 3.3 7.0 + - - -
424C LYS* 2.7 63.4 + - + +
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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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404C ARG* 4.9 2.8 + - - -
417C THR* 3.0 38.9 + - - +
418C MET* 3.5 8.2 - - - +
420C TYR* 1.3 78.4 - - - +
422C LYS* 1.3 55.4 + - - +
424C LYS* 3.6 26.2 + - + +
425C ASN* 2.8 49.6 + - - +
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Residues in contact with LYS 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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380C LEU 5.5 1.8 - - - +
381C ALA* 4.4 14.8 + - - +
383C LEU 5.5 6.7 - - - +
418C MET* 3.0 43.6 + - + +
419C LEU* 3.2 23.8 + - + +
421C ASN* 1.3 74.9 - - - +
423C PHE* 1.3 67.8 + - + +
425C ASN* 3.9 6.3 - - - +
426C MET* 3.1 44.3 + - + +
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Residues in contact with PHE 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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380C LEU* 4.1 30.3 - - + -
385C VAL* 4.3 19.5 - - + -
390C ALA* 3.9 29.2 - - + -
396C MET* 4.2 12.8 - - + -
397C ILE* 4.1 28.8 - - + +
400C LEU* 3.7 27.1 - - + -
419C LEU* 2.9 31.2 + - + -
420C TYR* 3.7 4.9 - - - +
422C LYS* 1.3 83.6 - - + +
424C LYS* 1.3 64.9 + - - +
426C MET* 3.5 33.3 + - + +
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Residues in contact with LYS 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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397C ILE* 5.7 0.4 - - - +
404C ARG* 4.7 6.1 - - - +
420C TYR* 2.7 55.5 + - + +
421C ASN* 3.6 22.6 + - - +
423C PHE* 1.3 74.6 - - - +
425C ASN* 1.3 75.2 + - - +
426C MET 3.5 4.7 + - - +
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Residues in contact with ASN 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* 2.8 32.2 + - - +
422C LYS* 3.9 6.5 - - - +
424C LYS* 1.3 85.3 - - - +
426C MET* 1.3 65.9 + - - +
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Residues in contact with MET 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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385C VAL* 3.5 26.7 - - + +
386C THR 4.0 4.3 - - - +
387C MET* 3.7 38.2 - - + +
390C ALA* 3.9 28.3 - - - -
422C LYS* 3.1 32.6 + - + +
423C PHE* 3.6 33.2 - - + +
424C LYS 3.4 5.0 - - - +
425C ASN* 1.3 81.5 - - - +
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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