Contacts of the helix formed by residues 369 - 378 (chain C) in PDB entry 1I43
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 ASP 369 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C GLY* 1.3 74.9 - - - +
370C LEU* 1.3 69.2 + - - +
371C LEU* 3.7 18.1 + - - +
372C THR* 3.0 26.4 + - - -
373C THR* 2.7 26.9 + - - -
419C ASP* 4.3 2.9 - - - -
420C ASN* 4.0 2.7 - - - +
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Residues in contact with LEU 370 (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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96A ILE* 4.9 9.2 - - + -
369C ASP* 1.3 75.3 - - - +
371C LEU* 1.3 80.6 + - + +
374C ALA* 3.3 20.1 + - + +
398C GLN* 3.5 25.0 + - - +
400C ALA* 4.8 2.0 - - + -
401C ILE* 3.9 25.4 - - + -
405C TRP* 4.4 24.7 - - + -
419C ASP* 3.4 49.4 + - + +
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Residues in contact with LEU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 6.1 2.5 - - + -
369C ASP* 3.1 14.9 + - - +
370C LEU* 1.3 96.7 - - + +
372C THR* 1.3 66.1 + - - +
374C ALA* 3.4 8.5 + - + +
375C LYS* 3.1 20.1 + - - +
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Residues in contact with THR 372 (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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366C VAL* 4.4 1.8 - - + -
368C GLY* 3.7 17.1 - - - -
369C ASP* 3.0 25.3 + - - -
371C LEU* 1.3 73.3 - - - +
373C THR* 1.3 68.1 + - - +
375C LYS* 3.0 26.0 + - + +
376C PHE 3.1 4.9 + - - -
445C ILE* 3.3 41.6 + - + +
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Residues in contact with THR 373 (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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366C VAL* 4.0 12.6 - - + +
369C ASP 2.7 21.3 + - - -
372C THR* 1.3 75.6 - - - +
374C ALA* 1.3 61.5 + - - +
376C PHE* 2.9 23.7 + - - +
377C VAL* 3.2 6.5 + - + +
398C GLN* 3.1 28.0 - - + +
419C ASP 3.3 8.3 + - - +
420C ASN* 3.3 24.4 + - - +
422C VAL* 3.3 32.1 - - + -
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Residues in contact with ALA 374 (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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92A THR* 3.6 34.5 - - + +
370C LEU* 3.3 18.0 + - + +
371C LEU* 3.5 10.1 - - + +
372C THR 3.2 0.2 - - - -
373C THR* 1.3 78.3 - - - +
375C LYS* 1.3 52.3 + - - +
377C VAL* 3.1 7.2 + - - +
378C ASP* 2.8 38.4 + - - +
398C GLN* 3.4 12.3 + - - +
401C ILE* 5.1 0.2 - - + -
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Residues in contact with LYS 375 (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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371C LEU 3.1 9.4 + - - +
372C THR* 3.0 18.2 + - - +
374C ALA* 1.3 79.1 - - - +
376C PHE* 1.3 59.5 + - - +
378C ASP* 3.6 9.8 + - + +
379C ALA* 3.3 21.1 + - - +
444C SER* 4.4 31.8 - - - +
445C ILE* 4.8 6.5 - - - +
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Residues in contact with PHE 376 (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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364C PHE* 3.7 34.3 - + - -
366C VAL* 3.9 14.6 - - + -
372C THR 3.1 3.4 + - - -
373C THR* 2.9 10.8 + - - +
375C LYS* 1.3 75.6 - - - +
377C VAL* 1.3 70.1 + - + +
379C ALA* 2.9 25.9 + - - +
380C LEU* 3.4 23.1 + - + +
396C VAL* 5.6 0.4 - - + -
422C VAL* 4.4 8.3 - - + -
424C PHE* 5.5 0.9 - + - -
438C ILE* 3.7 17.3 - - + -
441C ALA* 3.5 29.4 - - + -
442C LEU* 3.6 31.9 - - + -
444C SER* 6.0 0.4 - - - -
445C ILE* 3.2 25.7 - - + +
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Residues in contact with VAL 377 (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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92A THR* 3.1 22.9 - - - +
373C THR 3.3 15.9 - - - +
374C ALA* 3.1 10.9 + - - +
376C PHE* 1.3 87.0 - - + +
378C ASP* 1.3 66.7 + - - +
379C ALA 3.1 1.1 + - - -
380C LEU* 3.4 34.3 + - + +
385C ILE* 4.2 23.9 - - + +
396C VAL* 5.1 8.9 - - + +
397C ASP* 5.5 6.3 - - - +
398C GLN* 4.3 11.4 - - + +
422C VAL* 4.3 17.7 - - + -
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Residues in contact with ASP 378 (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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90A ASN 5.8 1.3 - - - +
91A LYS* 3.7 23.1 - - + +
92A THR* 2.9 39.4 + - - -
93A SER* 4.6 3.1 + - - -
374C ALA* 2.8 18.4 + - - +
375C LYS* 3.8 11.3 - - + +
377C VAL* 1.3 79.2 - - - +
379C ALA* 1.3 58.7 + - - +
380C LEU 4.0 4.9 - - - +
385C ILE* 3.9 4.6 - - - +
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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