Contacts of the helix formed by residues 387 - 398 (chain F) in PDB entry 4R8A
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 ASN 387 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385F VAL 3.0 3.4 + - - -
386F GLU* 1.3 74.7 - - - +
388F GLY* 1.3 61.0 + - - -
389F LEU 3.4 2.2 - - - -
390F ILE 4.4 2.0 - - - -
391F ASN* 2.8 39.7 + - - +
466F TYR* 4.5 11.7 - - - +
502F ARG* 3.6 4.0 + - - +
503F ALA* 3.2 18.7 - - - +
504F GLY 3.2 6.9 - - - +
505F LEU* 2.9 56.6 - - - +
3G A 3.8 2.9 - - - +
4G C 2.8 24.1 + - - +
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Residues in contact with GLY 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F VAL 3.0 3.6 + - - -
386F GLU 2.8 15.2 + - - -
387F ASN* 1.3 74.4 - - - +
389F LEU* 1.3 59.9 + - - +
392F SER* 2.7 32.4 + - - -
466F TYR* 3.6 25.8 - - - -
469F LEU* 4.0 16.1 - - - +
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Residues in contact with LEU 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F VAL* 3.4 27.0 + - + +
387F ASN 3.4 0.2 - - - -
388F GLY* 1.3 76.2 - - - +
390F ILE* 1.3 64.7 - - + +
392F SER* 3.7 2.7 - - - -
393F LEU* 3.1 44.0 + - + +
469F LEU* 4.8 2.5 - - - -
470F LEU* 4.2 15.0 - - + -
474F LEU* 4.1 24.7 - - + -
478F ALA* 4.2 13.5 - - + -
482F LEU* 4.5 10.3 - - + -
509F ILE* 3.8 29.2 - - + -
511F PHE* 3.9 23.1 - - + -
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Residues in contact with ILE 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F ASN 3.9 2.2 + - - -
389F LEU* 1.3 84.3 - - + +
391F ASN* 1.3 60.6 + - - +
393F LEU* 3.4 8.2 + - + +
394F PHE* 3.0 28.2 + - - +
482F LEU* 5.8 1.8 - - + -
487F LEU* 5.9 0.4 - - + -
490F TRP* 3.7 59.7 - - + -
491F PHE* 3.9 11.6 - - + -
494F LEU* 5.1 10.8 - - + -
505F LEU* 3.6 41.5 - - + -
509F ILE* 5.8 4.0 - - + -
520F MET* 4.4 9.2 - - + -
537F TRP* 5.8 0.7 - - + -
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Residues in contact with ASN 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F ASN* 2.8 30.6 + - - +
390F ILE* 1.3 76.2 - - - +
392F SER* 1.3 56.5 + - - +
394F PHE* 3.5 4.9 + - - +
395F GLY 2.8 22.7 + - - -
464F PHE* 3.2 37.9 - - - +
466F TYR* 4.0 5.8 - - + -
494F LEU* 3.7 20.1 - - - +
501F ASN 5.3 0.2 - - - +
502F ARG* 3.0 53.0 + - - +
505F LEU* 4.3 6.3 - - - +
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Residues in contact with SER 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F GLY 2.7 22.0 + - - -
389F LEU* 3.7 4.3 - - - -
390F ILE 3.2 0.6 - - - -
391F ASN* 1.3 76.0 - - - +
393F LEU* 1.3 60.4 + - - +
395F GLY* 3.1 1.0 + - - -
396F LEU* 2.9 36.4 + - - +
464F PHE 3.3 5.4 + - - -
465F VAL* 3.8 6.9 - - - +
466F TYR* 2.7 33.9 + - - +
470F LEU* 3.7 25.4 - - - +
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F LEU* 3.1 36.7 + - + +
390F ILE* 3.9 6.7 - - + +
392F SER* 1.3 76.5 - - - +
394F PHE* 1.3 61.7 + - - +
396F LEU* 3.6 2.1 + - - -
397F LEU* 3.3 23.9 + - - +
450F ILE* 3.9 17.2 - - + +
470F LEU* 4.8 6.5 - - + -
475F LEU* 4.1 26.2 - - + +
478F ALA* 4.3 8.5 - - + -
479F LEU* 5.4 6.7 - - + -
482F LEU* 3.7 30.3 - - + -
487F LEU* 4.2 15.0 - - + -
491F PHE* 3.8 15.1 - - + -
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Residues in contact with PHE 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390F ILE 3.0 17.1 + - - +
391F ASN 3.8 1.6 - - - +
393F LEU* 1.3 78.0 - - - +
395F GLY* 1.3 63.4 + - - +
397F LEU* 3.6 0.4 + - - -
398F CYS* 3.2 43.7 + - + +
402F ILE* 4.6 4.7 - - + -
426F PHE* 6.1 0.7 - + - -
434F PHE* 3.9 11.9 - + - -
438F LEU* 5.0 0.9 - - + -
464F PHE* 4.1 35.7 - + - -
491F PHE* 3.5 55.3 - + + -
494F LEU* 3.8 23.6 - - + -
495F LEU* 3.6 31.2 - - + -
498F ILE* 5.2 1.8 - - + -
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Residues in contact with GLY 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F ASN 2.8 17.7 + - - -
392F SER 3.1 3.3 + - - -
394F PHE* 1.3 78.3 - - - +
396F LEU* 1.3 59.6 + - - +
398F CYS 3.8 0.7 - - - -
399F TRP* 3.3 30.7 + - - -
402F ILE* 4.0 10.1 - - - +
464F PHE* 3.7 18.8 - - - -
465F VAL* 3.8 10.3 - - - -
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Residues in contact with LEU 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392F SER 2.9 20.5 + - - +
393F LEU* 4.1 1.8 - - - +
395F GLY* 1.3 76.5 - - - +
397F LEU* 1.3 64.8 + - - +
398F CYS 3.5 0.3 + - - -
399F TRP* 3.5 14.4 + - + +
450F ILE* 3.6 39.5 - - + +
453F ARG* 3.2 44.1 + - + +
454F TYR* 4.1 10.8 - - + +
457F LYS* 5.4 0.4 - - + -
465F VAL* 3.9 10.1 - - + -
467F TRP* 3.6 30.5 - - + -
470F LEU* 3.8 26.0 - - + -
475F LEU* 4.8 0.4 - - + -
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Residues in contact with LEU 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393F LEU 3.3 12.3 + - - +
394F PHE 3.6 2.2 + - - +
396F LEU* 1.3 79.9 - - - +
398F CYS* 1.3 61.0 + - - +
399F TRP 3.4 1.1 + - - -
400F GLU* 4.1 5.7 - - - +
437F CYS* 3.3 45.0 - - + +
438F LEU* 4.2 9.6 - - + -
440F ARG* 4.3 21.5 - - + -
441F LEU* 4.1 22.4 - - + -
446F TYR* 4.4 10.8 - - + -
449F ALA* 4.4 8.7 - - + -
450F ILE* 3.4 21.5 - - + +
453F ARG* 5.3 0.9 + - - -
491F PHE* 3.9 22.9 - - + -
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Residues in contact with CYS 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F PHE* 3.2 38.8 + - + +
395F GLY 3.8 3.4 - - - -
397F LEU* 1.3 82.6 - - - +
399F TRP* 1.3 57.5 + - - +
400F GLU 3.4 2.5 - - - -
401F ALA* 3.2 4.7 + - + -
402F ILE* 2.9 35.5 + - + +
434F PHE* 3.8 27.4 - - + -
437F CYS* 4.1 13.5 - - - -
438F LEU* 3.8 24.5 - - - -
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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