Contacts of the helix formed by residues 430 - 443 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316I GLN* 4.4 5.3 + - - +
429I GLU* 1.3 72.8 - - - +
431I PHE* 1.3 71.4 + - - +
432I ASP* 4.4 14.2 + - - +
433I ASP* 3.1 17.0 + - + +
434I LEU* 3.1 10.8 + - - +
56L SER* 2.7 41.5 + - - +
58L GLY* 4.7 6.3 + - - -
59L SER* 3.0 14.2 + - - +
311L HIS* 4.9 7.3 + - - -
315L GLN* 5.5 4.5 + - - -
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Residues in contact with PHE 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I GLN* 4.5 4.6 - - - +
320I THR* 4.7 18.4 - - + +
323I ARG* 2.9 76.5 - - + +
324I MET* 3.5 18.8 - - + -
327I ILE* 3.9 18.6 - - + -
429I GLU 3.4 4.3 + - - -
430I ASP* 1.3 73.6 - - - +
432I ASP* 1.3 73.7 + - - +
434I LEU* 2.8 10.8 + - + -
435I LYS* 2.7 52.5 + - + -
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Residues in contact with ASP 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430I ASP* 3.4 12.9 + - + +
431I PHE* 1.3 87.6 - - - +
433I ASP* 1.3 59.8 + - - +
435I LYS* 3.8 18.0 + - - +
436I ALA* 2.9 34.8 + - - +
56L SER* 6.4 0.4 - - - -
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Residues in contact with ASP 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382I ILE* 3.1 21.7 - - + +
429I GLU* 5.3 0.4 - - + -
430I ASP* 3.1 11.2 + - - +
431I PHE 3.0 0.2 + - - -
432I ASP* 1.3 80.7 - - - +
434I LEU* 1.3 62.4 + - + +
436I ALA* 3.8 4.4 + - - +
437I ASP* 3.3 13.9 + - - +
53L PHE 3.2 20.0 - - - +
54L LEU* 4.0 1.3 - - - -
55L ASN* 3.0 29.5 + - - +
56L SER* 3.1 28.0 + - - -
59L SER* 2.7 28.2 + - - +
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Residues in contact with LEU 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I THR* 3.8 25.1 - - + -
324I MET* 5.5 0.4 - - + -
382I ILE* 3.9 25.6 - - + -
383I PRO* 5.2 0.7 - - + -
394I SER* 3.4 25.1 - - - +
424I PHE* 4.5 15.7 - - + -
426I PHE* 4.2 11.2 - - + -
427I GLY 4.8 4.0 - - - +
429I GLU* 3.7 40.2 - - + +
430I ASP 3.1 7.9 + - - +
431I PHE* 2.8 11.9 + - + +
433I ASP* 1.3 71.3 - - - +
435I LYS* 1.3 65.5 + - - +
437I ASP* 3.0 6.3 + - - +
438I ILE* 2.9 28.0 + - - +
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Residues in contact with LYS 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I MET* 3.7 17.8 - - + +
327I ILE* 3.8 18.6 - - + +
431I PHE* 2.7 46.6 + - + +
432I ASP* 3.8 16.3 + - - +
434I LEU* 1.3 73.2 - - - +
436I ALA* 1.3 65.1 + - - +
438I ILE* 3.4 1.4 + - - +
439I LEU* 2.9 50.3 + - + +
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Residues in contact with ALA 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432I ASP 2.9 18.2 + - - +
433I ASP* 4.1 5.2 - - - +
435I LYS* 1.3 80.8 - - - +
437I ASP* 1.3 57.1 + - - +
439I LEU* 3.5 6.5 + - - +
440I GLN* 3.0 32.1 + - - +
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Residues in contact with ASP 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380I LEU* 3.7 8.4 - - - +
381I LYS* 3.0 38.9 + - - +
382I ILE* 3.2 24.2 + - + +
383I PRO* 3.4 12.8 - - - +
433I ASP 3.3 12.5 + - - +
434I LEU* 3.0 10.1 + - + +
436I ALA* 1.3 76.5 - - - +
438I ILE* 1.3 66.2 + - + +
440I GLN* 2.9 35.1 - - - +
441I ALA* 3.0 13.5 + - - +
53L PHE* 5.4 5.3 - - + +
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Residues in contact with ILE 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I MET* 3.4 27.1 - - + -
328I LEU* 3.9 28.7 - - + -
364I PHE* 5.4 1.3 - - + -
376I PHE* 3.8 13.5 - - + -
380I LEU* 3.9 11.4 - - + -
424I PHE* 4.0 24.9 - - + -
426I PHE* 3.5 29.8 - - + -
434I LEU 2.9 20.3 + - - +
435I LYS 3.9 3.1 - - - +
437I ASP* 1.3 77.3 - - + +
439I LEU* 1.3 65.0 + - + +
441I ALA 3.6 0.3 + - - -
442I LEU* 3.2 28.5 + - + +
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Residues in contact with LEU 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I MET* 5.8 1.6 - - + -
327I ILE* 4.3 19.7 - - + -
328I LEU* 6.1 0.9 - - + -
331I HIS* 3.9 28.5 + - + +
435I LYS* 2.9 45.5 + - + +
436I ALA* 3.8 6.5 - - - +
438I ILE* 1.3 80.2 - - + +
440I GLN* 1.3 62.6 + - - +
442I LEU* 3.1 17.4 + - + +
443I ASP* 3.2 19.3 + - - +
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Residues in contact with GLN 440 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379I ALA* 3.7 22.2 + - - +
381I LYS* 4.0 24.8 + - - +
436I ALA 3.0 16.0 + - - +
437I ASP* 2.9 33.8 - - - +
439I LEU* 1.3 75.8 - - - +
441I ALA* 1.3 65.8 + - - +
443I ASP* 3.1 20.9 + - - +
444I SER* 3.1 16.9 + - - +
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Residues in contact with ALA 441 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376I PHE* 3.6 29.9 - - + -
379I ALA* 3.4 31.1 - - + +
380I LEU* 3.7 15.5 - - + +
437I ASP 3.0 17.7 + - - +
438I ILE 3.9 0.2 - - - +
440I GLN* 1.3 79.2 - - - +
442I LEU* 1.3 60.7 + - - +
444I SER* 3.4 16.6 + - - -
445I ILE* 4.0 6.4 + - - +
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Residues in contact with LEU 442 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I LEU* 4.2 11.7 - - + -
331I HIS* 3.4 41.5 - - + +
333I LYS* 2.9 37.7 + - + +
334I VAL* 4.5 8.7 - - + -
364I PHE* 5.5 0.9 - - + -
366I VAL* 4.9 6.1 - - + -
376I PHE* 3.5 27.6 - - + -
438I ILE* 3.2 32.5 + - + +
439I LEU* 3.1 10.2 + - + +
441I ALA* 1.3 73.1 - - - +
443I ASP* 1.3 61.8 + - - +
444I SER 3.2 2.2 - - - -
445I ILE* 3.3 22.0 + - + +
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Residues in contact with ASP 443 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I HIS* 5.4 4.9 + - - -
333I LYS* 4.1 10.3 + - - +
439I LEU* 3.2 14.4 + - - +
440I GLN* 3.1 17.3 + - - +
442I LEU* 1.3 76.8 - - - +
444I SER* 1.3 58.2 + - - +
445I ILE 3.2 4.7 + - - -
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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
------------------------------------------------------------
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