Contacts of the helix formed by residues 393 - 404 (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 HIS 393 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348C MET* 5.9 0.2 - - + -
349C ASP* 2.8 53.8 + - + -
352C LEU* 3.6 25.2 - - + +
353C GLN* 4.4 11.0 - - - -
389C GLN* 3.1 24.5 - - + +
390C ALA* 3.0 12.8 + - - +
392C LYS* 1.3 87.1 - - + +
394C THR* 1.3 62.6 + - - +
396C MET* 3.2 21.1 + - + +
397C ILE* 3.3 12.3 + - - +
443C GOL 2.7 38.9 + - - +
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Residues in contact with THR 394 (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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390C ALA 4.4 2.5 - - - +
391C GLN* 3.6 30.1 + - + +
392C LYS 3.7 1.1 - - - -
393C HIS* 1.3 74.2 - - - +
395C GLU* 1.3 71.4 + - - +
397C ILE* 3.2 13.7 + - + +
398C THR* 2.8 33.3 + - - -
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Residues in contact with GLU 395 (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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356C HIS* 3.5 14.3 + - + -
392C LYS 4.2 4.3 - - - +
393C HIS* 4.0 1.6 - - - -
394C THR* 1.3 90.7 + - - +
396C MET* 1.3 57.1 + - - +
398C THR* 3.3 9.9 + - - -
399C THR* 2.9 31.9 + - - -
443C GOL 2.8 34.9 + - - +
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Residues in contact with MET 396 (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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352C LEU* 3.7 48.0 - - + +
355C ILE* 4.4 7.0 - - - -
356C HIS* 3.5 31.4 - - + -
359C ILE* 5.1 4.5 - - + -
380C LEU* 4.2 26.5 - - + -
390C ALA* 6.2 1.1 - - - -
393C HIS* 3.2 21.5 + - + +
395C GLU* 1.3 75.5 - - - +
397C ILE* 1.3 65.0 + - + +
399C THR* 3.1 4.9 + - - +
400C LEU* 3.0 30.6 + - + +
423C PHE* 4.2 18.8 - - + -
443C GOL 3.1 14.7 + - - +
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ALA* 3.6 29.2 - - + +
393C HIS 3.3 6.5 + - - +
394C THR* 3.2 15.7 + - + +
396C MET* 1.3 85.1 - - + +
398C THR* 1.3 56.1 + - - +
400C LEU* 3.3 8.8 + - + +
401C LYS* 2.9 27.0 + - - +
420C TYR* 3.9 25.0 - - + -
423C PHE* 4.1 45.3 - - + +
424C LYS 5.7 0.7 - - - +
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Residues in contact with THR 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C THR* 2.8 17.5 + - - -
395C GLU* 3.4 13.1 - - - +
397C ILE* 1.3 77.0 - - - +
399C THR* 1.3 61.6 + - - +
401C LYS* 3.3 11.9 + - + +
402C LYS* 3.1 23.3 + - + +
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Residues in contact with THR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C HIS* 2.7 35.6 + - + +
359C ILE* 3.9 29.2 - - + -
360C LYS* 4.0 20.2 + - + +
363C LEU* 5.9 0.2 - - + -
395C GLU 2.9 8.9 + - - -
396C MET 3.1 5.4 + - - +
398C THR* 1.3 74.1 - - - +
400C LEU* 1.3 64.6 + - - +
402C LYS* 3.2 8.6 + - + +
403C ILE* 3.1 31.0 + - + +
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Residues in contact with LEU 400 (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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359C ILE* 4.3 12.8 - - + -
377C LEU* 3.6 31.2 - - + -
380C LEU* 4.0 12.1 - - + -
396C MET* 3.0 21.9 + - + +
397C ILE* 3.5 13.0 - - + +
399C THR* 1.3 73.9 - - - +
401C LYS* 1.3 63.6 + - - +
403C ILE* 3.2 18.8 + - + +
404C ARG* 3.4 16.0 + - - +
416C SER* 3.7 17.2 - - - +
419C LEU* 4.0 14.6 - - + -
420C TYR* 4.3 8.3 - - + +
423C PHE* 3.7 36.8 - - + -
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Residues in contact with LYS 401 (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 2.9 9.5 + - - +
398C THR* 3.6 13.9 - - + +
399C THR 3.3 0.2 - - - -
400C LEU* 1.3 76.8 - - - +
402C LYS* 1.3 62.5 + - - +
404C ARG* 2.7 50.9 + - - +
405C ARG* 4.9 1.9 + - - +
420C TYR* 3.5 41.6 + - + +
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Residues in contact with LYS 402 (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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168A GLN* 3.9 28.7 + - - +
131B TRP* 4.5 27.8 - - + -
132B TRP* 5.5 1.4 - - - +
398C THR* 3.1 14.2 + - + +
399C THR* 3.5 11.7 - - - +
400C LEU 3.2 0.4 - - - -
401C LYS* 1.3 79.7 - - - +
403C ILE* 1.3 66.1 + - + +
404C ARG 3.2 1.9 + - - -
405C ARG* 3.4 17.7 + - - +
406C PHE 4.3 0.9 + - - -
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Residues in contact with ILE 403 (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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131B TRP* 5.8 4.3 - - + -
359C ILE* 3.8 24.9 - - + -
363C LEU* 3.6 23.1 - - + -
373C CYS* 4.4 0.4 - - - -
377C LEU* 4.2 12.8 - - + -
399C THR* 3.1 25.7 + - + +
400C LEU* 3.2 6.3 + - + +
402C LYS* 1.3 83.4 - - + +
404C ARG* 1.3 64.8 + - - +
405C ARG 3.0 2.0 - - - -
406C PHE* 3.0 31.5 + - + +
412C ILE* 4.0 15.4 - - + +
413C MET* 3.8 6.6 - - - -
416C SER* 3.4 31.1 + - - +
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Residues in contact with ARG 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 LEU 3.4 7.8 + - - +
401C LYS* 2.7 58.1 + - - +
402C LYS 3.2 0.2 - - - -
403C ILE* 1.3 78.5 - - - +
405C ARG* 1.3 65.8 + - + +
413C MET* 3.2 27.1 - - - +
416C SER* 3.3 9.4 + - - -
417C THR* 3.5 40.8 + - - +
420C TYR* 3.6 33.4 - - - +
421C ASN* 4.9 2.6 + - - -
424C LYS* 4.7 7.5 - - - +
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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