Contacts of the helix formed by residues 404 - 421 (chain B) in PDB entry 4OE4
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 HIS 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B PHE* 5.5 1.4 - + - -
238B THR* 3.9 27.6 - - + -
402B VAL* 3.6 1.3 - - - +
403B ILE* 1.3 96.3 - - + +
405B GLU* 1.3 60.1 + - - +
406B GLN* 3.4 27.6 + - + +
407B SER* 3.1 40.6 + - - -
408B PHE* 3.0 26.0 + - - +
438B TRP* 3.6 17.8 - - - +
1000B NAD 5.1 7.8 + - - -
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B HIS* 1.3 73.1 - - - +
406B GLN* 1.3 69.7 + - - +
408B PHE* 3.1 1.3 + - - +
409B ASP* 2.7 48.0 + - - +
434B LYS* 5.6 1.6 - - - +
438B TRP* 3.4 43.1 - - + -
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B HIS* 3.4 32.5 + - + +
405B GLU* 1.3 88.8 - - - +
407B SER* 1.3 56.8 + - - +
409B ASP* 3.2 8.7 + - - +
410B LYS* 2.9 28.8 + - - +
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLN* 4.5 1.9 + - - -
402B VAL* 3.8 10.2 - - - +
403B ILE* 4.3 10.5 - - - -
404B HIS* 3.1 27.4 + - - -
406B GLN* 1.3 78.6 - - - +
408B PHE* 1.3 63.3 + - - +
410B LYS* 3.3 7.1 + - - +
411B LEU* 3.1 39.8 + - - +
459B PHE 5.4 0.5 + - - -
460B PHE 4.3 9.2 + - - -
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B VAL* 4.1 6.5 - - - +
404B HIS 3.0 14.7 + - - +
405B GLU 3.3 8.7 - - - +
407B SER* 1.3 77.8 + - - +
409B ASP* 1.3 63.3 + - - +
411B LEU* 3.3 5.1 + - - +
412B VAL* 3.0 47.1 + - + +
432B TYR* 3.9 15.3 - + + -
433B ASP 3.7 12.8 - - - -
434B LYS* 3.4 52.0 - - + -
438B TRP* 3.7 30.5 - + + -
439B PHE 3.4 27.6 - - - -
440B VAL* 3.7 15.9 - - + +
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Residues in contact with ASP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLU* 2.7 30.5 + - - +
406B GLN* 3.7 7.4 - - - +
408B PHE* 1.3 75.5 - - - +
410B LYS* 1.3 66.5 + - - +
412B VAL* 3.2 7.7 + - - +
413B LYS* 3.0 22.9 + - - +
434B LYS* 3.2 28.0 + - - -
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLN 2.9 17.3 + - - +
407B SER* 3.7 8.1 - - - +
409B ASP* 1.3 76.0 - - - +
411B LEU* 1.3 59.3 + - + +
413B LYS* 3.4 10.8 + - - +
414B VAL* 3.0 32.4 + - + +
459B PHE 5.8 2.9 - - - +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B VAL* 3.7 31.4 - - + -
407B SER* 3.1 28.1 + - - +
408B PHE 3.7 4.0 - - - +
409B ASP 3.2 0.2 - - - -
410B LYS* 1.3 73.9 - - + +
412B VAL* 1.3 61.0 + - - +
414B VAL* 3.2 7.2 + - + +
415B ILE* 2.9 34.5 + - - +
440B VAL* 3.9 25.1 - - + -
459B PHE* 3.6 27.8 - - + +
460B PHE 4.6 0.2 - - - +
461B GLY* 3.7 20.9 - - - -
462B PRO* 4.2 2.9 - - + -
463B ILE* 3.9 20.8 - - + +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 3.0 43.7 + - + +
409B ASP* 3.2 10.1 + - - +
411B LEU* 1.3 74.1 - - + +
413B LYS* 1.3 56.5 + - - +
415B ILE* 3.1 7.8 + - - +
416B GLU* 2.7 41.0 + - + +
432B TYR* 3.6 43.7 - - + +
440B VAL* 5.4 0.7 - - + -
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Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ASP 3.0 11.9 + - - +
410B LYS* 3.5 12.3 - - - +
411B LEU 3.3 0.2 - - - -
412B VAL* 1.3 77.0 - - - +
414B VAL* 1.3 55.7 + - + +
416B GLU* 4.6 4.3 - - - -
417B ASP* 2.8 70.3 + - - +
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Residues in contact with VAL 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LYS* 3.0 21.4 + - + +
411B LEU* 3.4 11.0 - - + +
412B VAL 3.2 0.2 - - - -
413B LYS* 1.3 78.2 - - + +
415B ILE* 1.3 62.0 + - - +
417B ASP* 4.7 0.7 - - - -
418B ALA* 3.2 11.8 + - - +
445B ILE* 4.8 1.6 - - + -
454B TYR* 2.6 45.4 + - + +
459B PHE* 3.5 40.4 - - + -
463B ILE* 3.6 24.9 - - + -
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Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B LEU 2.9 22.2 + - - +
412B VAL 3.6 2.9 - - - +
414B VAL* 1.3 75.9 - - - +
416B GLU* 1.3 64.2 + - - +
418B ALA* 3.2 19.2 + - - +
419B LYS* 3.5 18.6 + - - +
426B ILE* 3.6 13.9 - - + +
430B GLY* 3.7 37.9 - - - +
432B TYR* 3.9 26.9 - - + -
440B VAL* 3.9 28.3 - - + -
443B THR* 4.3 9.2 - - + +
445B ILE* 5.2 1.8 - - + -
463B ILE* 4.0 14.4 - - + -
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B VAL* 2.7 30.1 + - + +
413B LYS* 4.0 4.3 - - - +
415B ILE* 1.3 74.4 - - - +
417B ASP* 1.3 63.4 + - - +
419B LYS* 2.9 53.9 + - - +
420B LYS* 3.6 29.3 + - - +
432B TYR* 2.8 30.7 + - + +
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Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LYS* 2.8 63.0 + - - +
414B VAL* 5.0 0.2 - - - -
416B GLU* 1.3 71.0 - - - +
418B ALA* 1.3 66.2 + - - +
419B LYS 3.1 0.7 - - - -
420B LYS* 3.2 21.6 + - - +
421B ASP* 3.0 24.6 + - - +
454B TYR* 3.6 15.2 + - + +
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B VAL 3.2 15.5 + - - +
415B ILE 3.4 11.0 - - - +
416B GLU 3.2 0.2 - - - -
417B ASP* 1.3 78.2 - - - +
419B LYS* 1.3 61.3 + - - +
421B ASP 3.4 17.3 - - - +
424B LEU* 3.7 31.7 - - + +
425B GLU* 5.2 0.7 - - - -
426B ILE* 3.9 13.9 + - + +
445B ILE* 3.8 27.1 - - + -
454B TYR* 3.6 0.4 + - - -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B ILE* 3.7 18.2 - - - +
416B GLU* 2.9 45.8 + - - +
417B ASP 3.1 0.4 - - - -
418B ALA* 1.3 79.3 - - - +
420B LYS* 1.3 62.9 + - + +
421B ASP 4.4 2.4 - - - +
426B ILE* 3.8 22.9 - - + -
430B GLY* 5.0 5.2 + - - -
432B TYR* 5.0 1.4 + - - -
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 3.7 31.2 + - - +
417B ASP* 3.2 22.7 + - - +
419B LYS* 1.3 78.2 - - + +
421B ASP* 1.3 61.0 + - - +
422B PRO* 3.4 9.4 - - - +
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Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ASP 3.0 15.8 + - - +
418B ALA 3.4 5.6 - - - +
419B LYS 3.3 2.5 - - - +
420B LYS* 1.3 77.3 - - - +
422B PRO* 1.3 65.4 - - - +
423B GLU* 2.9 33.6 + - - +
424B LEU* 2.9 39.9 + - + +
452B HIS* 3.0 29.4 + - - -
454B TYR* 5.3 1.4 - - - -
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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