Contacts of the helix formed by residues 369 - 380 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368E GLY* 1.3 75.3 - - - +
370E LEU* 1.3 62.1 + - - +
371E LEU* 3.7 17.2 + - - +
372E THR* 3.0 28.3 + - - -
373E THR* 2.7 38.9 + - - -
419E ASP* 5.3 0.7 - - - -
420E ASN* 3.9 4.3 - - - +
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Residues in contact with LEU 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E ASP* 1.3 74.6 - - - +
371E LEU* 1.3 79.3 + - + +
374E ALA* 3.2 26.4 + - + +
398E GLN* 3.5 23.1 + - - +
400E ALA* 4.8 2.0 - - + -
401E ILE* 3.8 29.8 - - + -
405E TRP* 4.4 22.9 - - + -
419E ASP* 3.5 49.0 - - + +
96G ILE* 4.9 7.9 - - + -
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Residues in contact with LEU 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E ASP* 3.1 14.8 + - - +
370E LEU* 1.3 95.8 - - + +
372E THR* 1.3 63.5 + - - +
374E ALA* 3.5 7.9 + - + +
375E LYS* 3.1 20.3 + - - +
96G ILE* 6.1 2.5 - - + -
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Residues in contact with THR 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366E VAL* 4.4 4.5 - - + -
367E ASP 4.5 0.4 - - - +
368E GLY* 3.8 18.5 - - - -
369E ASP* 3.0 24.4 + - - -
371E LEU* 1.3 74.6 - - - +
373E THR* 1.3 71.5 + - - +
375E LYS* 2.7 29.9 + - + +
376E PHE* 3.1 5.9 + - - +
445E ILE* 4.1 31.4 - - + +
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Residues in contact with THR 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366E VAL* 3.8 18.1 - - + +
369E ASP 2.7 23.0 + - - -
372E THR* 1.3 74.7 - - - +
374E ALA* 1.3 62.0 + - - +
376E PHE* 3.0 18.5 + - - +
377E VAL* 3.3 7.6 + - - +
398E GLN* 3.2 24.5 - - - +
419E ASP 3.4 2.9 + - - +
420E ASN* 3.3 31.8 + - - +
422E VAL* 3.3 31.2 - - + -
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Residues in contact with ALA 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LEU* 3.2 18.5 + - + +
371E LEU* 3.5 8.7 - - + +
372E THR 3.1 0.4 - - - -
373E THR* 1.3 77.7 - - - +
375E LYS* 1.3 64.5 + - - +
377E VAL* 3.0 7.0 + - - +
378E ASP* 2.9 26.6 + - - +
398E GLN* 3.3 13.8 + - - +
401E ILE* 5.1 0.4 - - + -
92G THR* 3.4 34.3 - - + +
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Residues in contact with LYS 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E LEU 3.1 14.0 + - - +
372E THR* 2.7 24.5 + - + +
374E ALA* 1.3 72.0 - - - +
376E PHE* 1.3 59.5 + - - +
378E ASP* 3.5 10.0 + - + +
379E ALA* 3.2 22.2 + - - +
444E SER* 3.9 29.1 - - - +
445E ILE* 4.7 8.7 - - + +
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Residues in contact with PHE 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364E PHE* 3.6 36.6 - + - -
366E VAL* 3.9 14.1 - - + -
372E THR 3.1 3.6 + - - -
373E THR* 3.0 13.6 + - - +
374E ALA 3.0 0.8 - - - -
375E LYS* 1.3 74.7 - - - +
377E VAL* 1.3 72.2 + - + +
379E ALA* 3.2 14.3 + - - +
380E LEU* 3.5 29.7 + - + +
396E VAL* 5.6 0.4 - - + -
422E VAL* 4.4 9.2 - - + -
424E PHE* 5.5 1.3 - + - -
438E ILE* 3.7 12.1 - - + -
441E ALA* 3.4 36.3 - - + +
442E LEU* 3.6 23.8 - - + -
444E SER* 6.3 0.4 - - - -
445E ILE* 3.6 26.4 - - + +
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Residues in contact with VAL 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373E THR 3.3 15.5 - - - +
374E ALA* 3.0 3.3 + - - +
376E PHE* 1.3 82.5 - - + +
378E ASP* 1.3 72.5 + - - +
380E LEU* 3.3 35.0 + - + +
385E ILE* 4.2 25.2 - - + +
396E VAL* 4.9 9.8 - - + +
397E ASP* 5.6 5.2 - - - +
398E GLN* 4.0 14.8 - - + +
422E VAL* 4.4 18.2 - - + -
92G THR* 3.1 26.9 - - - +
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Residues in contact with ASP 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E ALA* 2.9 20.2 + - - +
375E LYS* 3.7 9.2 - - + +
377E VAL* 1.3 80.5 - - - +
379E ALA* 1.3 60.2 + - - +
380E LEU 3.6 6.6 + - - +
385E ILE* 3.9 5.1 - - - +
90G ASN 5.5 2.6 - - - +
91G LYS* 3.6 17.7 - - + +
92G THR* 2.8 45.0 + - - -
93G SER* 4.5 2.8 + - - -
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Residues in contact with ALA 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375E LYS 3.2 13.2 + - - +
376E PHE 3.5 9.9 - - - +
377E VAL 3.1 0.8 - - - -
378E ASP* 1.3 74.7 - - - +
380E LEU* 1.3 66.7 + - - +
381E LYS* 3.5 15.4 - - - +
440E GLN* 3.7 13.8 + - - +
441E ALA* 4.0 22.0 - - - +
444E SER* 4.0 17.3 - - - +
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Residues in contact with LEU 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E PHE* 3.6 22.2 - - + +
377E VAL* 3.3 28.9 + - - +
378E ASP 3.6 8.1 - - - +
379E ALA* 1.3 82.1 - - - +
381E LYS* 1.3 60.9 + - - +
383E PRO* 4.0 17.6 - - + +
396E VAL* 3.8 34.8 - - + -
424E PHE* 4.2 11.4 - - + -
437E ASP* 3.8 11.4 - - - +
438E ILE* 3.9 19.1 - - + -
441E ALA* 3.5 20.6 - - + -
67H ARG* 5.2 2.3 + - - -
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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