Contacts of the helix formed by residues 430 - 442 (chain H) 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 430 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E SER* 2.8 40.0 + - - +
58E GLY* 4.7 6.8 + - - -
59E SER* 3.0 11.8 + - - +
311E HIS* 4.8 7.2 + - - -
315E GLN* 5.5 4.2 + - - -
316H GLN* 4.5 6.1 + - - +
429H GLU* 1.3 71.4 - - - +
431H PHE* 1.3 70.1 + - - +
432H ASP* 4.4 15.5 + - + +
433H ASP* 2.9 18.5 + - + +
434H LEU* 3.0 10.6 + - - +
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Residues in contact with PHE 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316H GLN* 4.6 4.9 - - - +
320H THR* 3.8 27.1 - - + +
323H ARG* 3.1 63.9 - - + +
324H MET* 3.5 30.7 - - + -
327H ILE* 3.8 21.8 - - + -
429H GLU 3.3 5.6 + - - -
430H ASP* 1.3 72.6 + - - +
432H ASP* 1.3 65.9 + - - +
434H LEU* 3.0 8.2 + - - +
435H LYS* 2.6 54.0 + - + +
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Residues in contact with ASP 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E SER* 6.5 0.2 - - - -
430H ASP* 3.2 13.7 + - + +
431H PHE* 1.3 92.4 - - - +
433H ASP* 1.3 63.7 + - - +
435H LYS* 3.9 16.1 + - - +
436H ALA* 3.0 28.2 + - - +
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Residues in contact with ASP 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE 3.2 14.1 - - - +
54E LEU* 4.3 1.8 - - - -
55E ASN* 3.0 32.5 + - - +
56E SER* 2.9 29.1 + - - -
59E SER* 2.9 25.6 + - - +
382H ILE* 3.3 22.3 - - + +
430H ASP* 2.9 11.1 + - - +
432H ASP* 1.3 78.8 - - - +
434H LEU* 1.3 61.8 + - + +
436H ALA* 3.9 3.7 + - - +
437H ASP* 3.3 15.8 + - - +
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Residues in contact with LEU 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320H THR* 3.9 26.9 - - + +
324H MET* 5.6 0.2 - - + -
382H ILE* 3.9 22.9 - - + -
383H PRO* 5.2 0.2 - - + -
394H SER* 3.4 24.9 - - - +
424H PHE* 4.8 8.3 - - + -
426H PHE* 4.4 15.9 - - + -
427H GLY 4.8 4.0 - - - +
429H GLU* 3.3 44.2 - - + +
430H ASP 3.0 8.7 + - - +
431H PHE* 3.0 6.6 + - + +
433H ASP* 1.3 76.2 - - - +
435H LYS* 1.3 66.4 + - - +
437H ASP* 2.9 14.4 + - - +
438H ILE* 3.0 19.0 + - + +
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Residues in contact with LYS 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H MET* 3.7 26.7 - - - +
327H ILE* 3.7 25.2 - - + +
431H PHE* 2.6 37.5 + - + +
432H ASP* 3.9 13.7 + - - +
434H LEU* 1.3 73.9 - - - +
436H ALA* 1.3 65.4 + - - +
438H ILE* 3.3 2.1 + - - +
439H LEU* 3.0 49.3 + - + +
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Residues in contact with ALA 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432H ASP 3.0 19.0 + - - +
433H ASP* 4.1 4.5 - - - +
435H LYS* 1.3 80.1 - - - +
437H ASP* 1.3 57.4 + - - +
439H LEU* 3.6 7.9 - - - +
440H GLN* 2.8 33.4 + - - +
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Residues in contact with ASP 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 5.7 4.1 - - + +
380H LEU* 3.7 8.2 - - - +
381H LYS* 3.1 26.9 + - - +
382H ILE* 3.2 33.5 + - + +
383H PRO* 3.3 13.5 - - - +
433H ASP 3.3 13.1 + - - +
434H LEU* 2.9 11.1 + - + +
436H ALA* 1.3 79.0 - - - +
438H ILE* 1.3 65.5 + - - +
440H GLN* 2.8 37.9 - - - +
441H ALA* 2.9 11.4 + - - +
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Residues in contact with ILE 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H MET* 3.6 19.3 - - + -
328H LEU* 4.0 17.0 - - + -
364H PHE* 5.4 1.1 - - + -
376H PHE* 3.7 15.3 - - + -
380H LEU* 3.8 11.2 - - + -
424H PHE* 3.9 27.4 - - + -
426H PHE* 3.4 36.3 - - + -
434H LEU* 3.0 15.0 + - + +
435H LYS 3.8 5.8 - - - +
437H ASP* 1.3 75.8 - - + +
439H LEU* 1.3 57.3 + - + +
441H ALA 3.5 0.3 + - - -
442H LEU* 3.0 50.6 + - + +
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Residues in contact with LEU 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H MET* 6.1 1.3 - - + -
327H ILE* 4.5 18.4 - - + -
328H LEU* 6.2 0.7 - - + -
331H HIS* 4.0 27.8 + - + +
435H LYS* 3.0 47.5 + - + +
436H ALA* 3.6 6.3 - - - +
438H ILE* 1.3 76.1 - - + +
440H GLN* 1.3 58.8 + - - +
442H LEU* 2.7 29.3 + - + +
443H ASP* 3.3 15.5 + - - +
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Residues in contact with GLN 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379H ALA* 3.5 22.5 + - - +
381H LYS* 4.1 23.2 - - - +
436H ALA 2.8 20.8 + - - +
437H ASP* 2.8 38.9 - - - +
439H LEU* 1.3 74.0 - - - +
441H ALA* 1.3 63.6 + - - +
443H ASP* 3.5 22.3 + - - +
444H SER* 3.6 9.7 + - - -
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Residues in contact with ALA 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376H PHE* 3.6 20.3 - - + +
379H ALA* 3.6 30.8 - - + +
380H LEU* 3.7 27.1 - - + +
437H ASP 2.9 16.2 + - - +
439H LEU 3.0 0.2 - - - -
440H GLN* 1.3 75.6 - - - +
442H LEU* 1.3 57.2 + - - +
443H ASP 3.0 9.3 + - - -
444H SER* 3.4 15.6 + - - -
445H ILE* 4.4 3.1 + - - +
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Residues in contact with LEU 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328H LEU* 3.9 13.7 - - + -
331H HIS* 3.8 34.0 - - + +
333H LYS* 3.1 39.5 + - + +
334H VAL* 4.7 13.5 - - + -
364H PHE* 5.4 0.7 - - + -
366H VAL* 5.1 6.5 - - + -
376H PHE* 3.6 27.8 - - + -
438H ILE* 3.0 41.3 + - + +
439H LEU* 2.7 12.3 + - + +
441H ALA* 1.3 76.8 - - - +
443H ASP* 1.3 59.9 - - - +
445H ILE* 4.3 12.4 + - + +
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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