Contacts of the helix formed by residues 369 - 380 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368K GLY* 1.3 75.6 - - - +
370K LEU* 1.3 60.7 + - + +
371K LEU* 3.8 15.7 + - - +
372K THR* 3.1 28.0 + - - -
373K THR* 2.7 34.8 + - - -
419K ASP* 4.2 3.6 - - - -
420K ASN* 3.9 2.0 - - - +
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Residues in contact with LEU 370 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ILE* 4.9 9.6 - - + -
369K ASP* 1.3 76.0 - - + +
371K LEU* 1.3 80.8 + - + +
374K ALA* 3.2 21.6 + - + +
398K GLN* 3.5 25.9 + - - +
400K ALA* 4.9 1.6 - - + -
401K ILE* 3.7 26.0 - - + -
405K TRP* 4.4 23.3 - - + -
419K ASP* 3.5 45.6 + - + +
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Residues in contact with LEU 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ILE* 6.2 1.6 - - + -
369K ASP* 3.2 15.0 + - - +
370K LEU* 1.3 94.3 - - + +
372K THR* 1.3 65.6 + - - +
374K ALA* 3.2 9.3 + - + +
375K LYS* 3.0 20.1 + - - +
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Residues in contact with THR 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366K VAL* 4.6 2.7 - - + -
367K ASP 4.7 0.2 - - - +
368K GLY* 3.8 17.1 - - - -
369K ASP* 3.1 26.1 + - - -
371K LEU* 1.3 78.0 - - - +
373K THR* 1.3 67.4 + - - +
375K LYS* 2.8 27.9 + - + +
376K PHE* 3.1 6.1 + - - +
445K ILE* 3.8 41.3 + - + +
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Residues in contact with THR 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366K VAL* 4.0 16.0 - - + +
368K GLY 4.3 0.3 - - - -
369K ASP 2.7 23.3 + - - -
372K THR* 1.3 75.5 - - - +
374K ALA* 1.3 62.6 + - - +
376K PHE* 3.0 21.9 + - - +
377K VAL* 3.3 6.6 + - - +
398K GLN* 3.4 21.3 - - + +
419K ASP 3.5 2.4 + - - -
420K ASN* 3.4 31.1 + - - +
422K VAL* 3.3 33.4 - - + -
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Residues in contact with ALA 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I THR* 3.6 26.7 - - + -
370K LEU* 3.2 15.1 + - + +
371K LEU* 3.3 14.1 - - + +
373K THR* 1.3 77.7 - - - +
375K LYS* 1.3 64.0 + - - +
376K PHE 3.0 0.9 + - - -
377K VAL* 3.0 6.8 + - - +
378K ASP* 2.9 27.1 + - - +
398K GLN* 3.3 18.5 + - - +
401K ILE* 5.1 0.2 - - + -
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Residues in contact with LYS 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K LEU 3.0 11.9 + - - +
372K THR* 2.8 18.6 + - - +
374K ALA* 1.3 75.7 - - - +
376K PHE* 1.3 59.8 + - - +
378K ASP* 3.8 8.6 + - + +
379K ALA* 3.4 19.1 + - - +
444K SER* 3.4 35.3 - - - +
445K ILE* 4.5 11.0 - - + +
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Residues in contact with PHE 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364K PHE* 3.7 31.9 - + - -
366K VAL* 4.0 14.4 - - + -
372K THR 3.1 4.0 + - - +
373K THR* 3.0 13.0 + - - +
374K ALA 3.0 0.2 + - - -
375K LYS* 1.3 75.0 - - - +
377K VAL* 1.3 76.0 + - + +
379K ALA* 2.9 26.0 + - - +
380K LEU* 3.4 27.0 + - + +
422K VAL* 4.4 7.9 - - + -
424K PHE* 5.5 2.0 - + - -
438K ILE* 3.7 11.7 - - + -
441K ALA* 3.4 37.5 - - + -
442K LEU* 3.7 26.9 - - + -
444K SER* 6.3 0.4 - - - -
445K ILE* 3.7 23.3 - - + +
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Residues in contact with VAL 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I THR* 3.2 26.5 - - - +
373K THR 3.4 13.7 - - - +
374K ALA* 3.0 6.7 + - - +
376K PHE* 1.3 86.9 - - + +
378K ASP* 1.3 67.9 + - - +
380K LEU* 3.2 37.5 + - + +
385K ILE* 4.2 22.7 - - + +
396K VAL* 5.0 9.4 - - + +
397K ASP* 5.5 6.1 - - - +
398K GLN* 4.3 12.3 - - + +
422K VAL* 4.2 19.7 - - + -
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Residues in contact with ASP 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ASN 5.6 2.4 - - - +
91I LYS* 3.5 24.3 - - + +
92I THR* 2.8 40.4 + - - -
93I SER* 4.6 2.8 + - - -
374K ALA* 2.9 17.8 + - - +
375K LYS* 3.9 10.1 - - + +
376K PHE 3.1 0.2 - - - -
377K VAL* 1.3 79.9 - - - +
379K ALA* 1.3 60.9 + - - +
380K LEU 3.4 5.6 - - - +
385K ILE* 3.9 5.4 - - - +
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Residues in contact with ALA 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375K LYS 3.4 11.7 + - - +
376K PHE 2.9 12.9 + - - +
378K ASP* 1.3 77.4 - - - +
380K LEU* 1.3 67.4 + - - +
381K LYS* 3.4 15.1 - - - +
440K GLN* 3.7 13.6 + - - +
441K ALA* 4.0 22.4 - - + +
444K SER* 4.2 15.5 - - - +
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Residues in contact with LEU 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67J ARG* 5.2 2.8 + - - -
376K PHE* 3.7 24.7 - - + +
377K VAL* 3.2 29.7 + - + +
378K ASP 3.7 6.8 - - - +
379K ALA* 1.3 82.7 - - - +
381K LYS* 1.3 60.0 + - - +
383K PRO* 4.0 14.2 - - + +
396K VAL* 3.7 36.8 - - + -
424K PHE* 4.1 11.0 - - + -
437K ASP* 3.8 18.2 - - - +
438K ILE* 4.1 10.5 - - - -
441K ALA* 3.5 22.2 - - + -
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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