Contacts of the helix formed by residues 431 - 444 (chain F) in PDB entry 4E2I
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 GLY 431 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393F TRP* 5.2 3.4 - - - -
397F LEU* 3.9 11.5 - - - +
430F SER* 1.3 79.5 - - - +
432F LYS* 1.3 62.1 + - - +
433F THR 3.6 1.3 - - - -
434F THR* 3.2 20.8 + - - -
435F LEU* 2.9 26.7 + - - +
547F PHE* 3.3 17.1 - - - -
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Residues in contact with LYS 432 (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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418E LYS* 4.5 5.7 - - - +
540E ARG* 5.6 1.8 - - - +
424F PHE* 3.9 16.5 - - + +
426F GLY 3.1 28.7 - - - +
427F PRO 2.9 21.6 + - - -
428F ILE* 4.8 0.4 - - - +
429F ASP* 3.6 15.4 - - - +
430F SER* 3.0 22.4 + - - +
431F GLY* 1.3 72.3 - - - +
433F THR* 1.3 66.0 + - - +
434F THR 2.9 5.9 + - - -
435F LEU* 3.0 1.4 + - - +
436F ALA* 2.7 38.6 + - - +
474F ASP* 4.7 3.4 - - - -
527F THR* 4.9 8.3 - - + -
528F MET 3.9 3.4 - - - +
529F ASN* 3.3 20.9 - - - +
547F PHE* 3.4 25.5 - - + -
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Residues in contact with THR 433 (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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418E LYS* 5.2 6.0 + - - -
499E ASP* 5.4 1.6 - - - -
502E ASP* 3.7 28.2 + - + +
504E SER* 3.7 22.5 - - - +
505E VAL* 5.4 2.0 - - + -
540E ARG* 4.2 9.3 + - - -
432F LYS* 1.3 86.4 + - - +
434F THR* 1.3 58.0 + - - +
436F ALA* 4.6 0.2 - - - -
437F ALA* 3.1 25.6 + - + +
473F GLU* 3.1 34.7 + - - +
474F ASP* 4.4 5.2 + - - -
527F THR* 5.8 0.8 - - - -
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Residues in contact with THR 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E SER* 5.3 1.3 - - - -
393F TRP* 3.9 13.9 - - + -
394F LEU* 4.8 1.6 - - + -
397F LEU* 5.3 0.9 - - + -
431F GLY* 3.4 21.8 - - - -
432F LYS 2.9 0.6 - - - -
433F THR* 1.3 80.5 - - - +
435F LEU* 1.3 59.6 + - - +
437F ALA 4.1 0.2 - - - -
438F ALA* 3.5 8.1 + - - +
569F ILE* 3.2 50.9 - - + +
570F GLN* 3.5 26.6 - - + +
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Residues in contact with LEU 435 (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 LEU* 5.5 6.1 - - + -
397F LEU* 4.4 6.5 - - + -
398F LEU* 4.1 4.0 - - + -
401F MET* 3.8 33.9 - - + -
404F VAL* 6.4 1.6 - - + -
405F VAL* 5.5 1.6 - - + -
424F PHE* 3.5 29.4 - - + -
431F GLY 2.9 15.7 + - - +
434F THR* 1.3 74.4 - - - +
436F ALA* 1.3 63.1 + - - +
437F ALA 2.9 4.5 - - - -
438F ALA* 3.1 2.8 + - + +
439F LEU* 2.9 52.4 + - + +
545F ILE* 5.6 1.8 - - + -
547F PHE* 3.6 14.4 - - + -
569F ILE 5.4 0.2 - - - -
575F LEU* 4.2 19.5 - - + -
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Residues in contact with ALA 436 (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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424F PHE* 3.8 13.2 - - + -
432F LYS 2.7 21.3 + - - +
433F THR* 4.6 0.4 - - - -
435F LEU* 1.3 73.3 - - - +
437F ALA* 1.3 58.1 + - - +
439F LEU* 4.2 6.0 - - - +
440F LEU* 3.7 14.6 + - - +
471F VAL* 3.7 23.2 - - + +
473F GLU* 3.8 12.1 - - - +
525F ILE* 4.6 6.3 - - + +
527F THR* 3.7 27.6 - - + -
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Residues in contact with ALA 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E SER* 3.1 32.4 - - - +
505E VAL* 3.6 16.6 - - + -
433F THR 3.1 22.2 + - - +
434F THR 4.1 3.4 - - - +
435F LEU 2.9 0.4 - - - -
436F ALA* 1.3 79.6 - - - +
438F ALA* 1.3 66.1 + - - +
439F LEU 3.2 0.2 - - - -
440F LEU* 3.0 19.8 + - - +
441F GLU* 3.4 6.2 + - - +
473F GLU* 5.2 0.2 + - - -
570F GLN* 4.3 6.7 - - + +
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Residues in contact with ALA 438 (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 LEU* 5.8 0.9 - - + -
434F THR 3.5 12.1 + - - +
435F LEU* 3.1 5.3 + - + +
437F ALA* 1.3 78.7 - - - +
439F LEU* 1.3 58.3 + - - +
441F GLU* 3.1 3.0 + - - -
442F LEU* 2.9 24.4 + - - +
569F ILE 4.4 3.4 - - - +
570F GLN* 3.7 21.7 + - - -
571F SER 3.5 19.5 - - - +
572F GLY* 3.4 8.9 - - - +
575F LEU* 3.5 22.2 - - + -
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Residues in contact with LEU 439 (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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405F VAL* 4.4 14.8 - - + -
408F PHE* 4.4 28.0 - - + -
424F PHE* 3.6 20.2 - - + -
435F LEU* 2.9 35.0 + - + +
436F ALA 4.4 3.4 - - - +
438F ALA* 1.3 76.0 - - - +
440F LEU* 1.3 64.4 + - - +
442F LEU* 3.6 13.3 - - + +
443F CYS* 3.0 29.6 + - - +
469F LEU* 4.7 2.5 - - + +
525F ILE* 3.5 28.3 - - + -
575F LEU* 3.5 20.2 - - + -
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Residues in contact with LEU 440 (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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505E VAL* 4.4 15.5 - - + -
506E LYS* 5.0 8.1 - - + +
436F ALA 3.7 12.1 + - - +
437F ALA 3.0 15.2 + - - +
439F LEU* 1.3 79.6 - - - +
441F GLU* 1.3 55.3 + - + +
444F GLY* 2.8 30.1 + - - -
445F GLY 3.4 31.1 + - - +
446F LYS* 3.4 8.7 - - + +
447F ALA* 3.8 28.7 - - + +
469F LEU* 3.5 25.1 - - + -
471F VAL* 3.5 14.1 - - + +
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Residues in contact with GLU 441 (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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506E LYS* 5.2 11.6 + - - -
364F ARG* 2.8 49.7 + - - +
368F LEU* 3.7 6.2 - - + +
371F ARG* 3.4 24.4 + - - +
437F ALA 3.4 4.9 + - - +
438F ALA* 3.1 7.9 + - - +
440F LEU* 1.3 79.5 - - + +
442F LEU* 1.3 61.3 + - - +
443F CYS 3.3 0.2 - - - -
570F GLN 5.0 1.1 - - - +
571F SER* 3.5 11.4 + - - -
572F GLY* 2.8 31.1 + - - +
573F ILE* 4.1 3.0 + - - +
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Residues in contact with LEU 442 (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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364F ARG* 3.5 7.1 - - - +
365F PHE* 3.9 13.4 - - + -
368F LEU* 3.5 26.4 - - + +
405F VAL* 3.7 24.0 - - + -
409F LEU* 4.3 11.2 - - + -
438F ALA 2.9 16.2 + - - +
439F LEU* 3.2 11.4 + - + +
441F GLU* 1.3 78.3 - - - +
443F CYS* 1.3 60.8 + - - +
572F GLY* 3.6 20.6 - - - +
575F LEU* 3.6 26.9 - - + -
576F LEU* 3.8 12.1 - - + +
579F LEU* 3.8 24.2 - - + -
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Residues in contact with CYS 443 (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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360F MET 5.4 0.3 - - - +
361F LEU* 3.7 25.7 - - + +
364F ARG* 3.2 20.6 - - - +
408F PHE* 3.9 14.1 - - - -
409F LEU* 3.5 31.2 - - - -
412F MET* 5.2 0.2 - - - -
439F LEU* 3.0 15.0 + - - +
442F LEU* 1.3 84.4 - - - +
444F GLY* 1.3 58.7 + - - +
468F PHE* 3.8 10.2 - - + +
469F LEU* 3.5 29.8 - - + -
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Residues in contact with GLY 444 (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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364F ARG* 4.2 17.3 - - - -
440F LEU 2.8 22.2 + - - -
441F GLU 4.1 0.6 + - - -
442F LEU 3.8 0.4 - - - -
443F CYS* 1.3 75.1 - - - +
445F GLY* 1.3 57.9 + - - -
468F PHE* 3.3 23.4 - - - +
469F LEU* 3.4 13.6 - - - +
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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