Contacts of the helix formed by residues 404 - 419 (chain H) in PDB entry 4P0S
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 SER 404 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325H ILE* 5.1 0.3 - - - +
368H LYS* 6.0 2.7 - - - -
403H VAL* 1.3 86.5 + - - +
405H ARG* 1.4 61.0 + - - +
406H VAL* 3.6 4.1 + - - +
407H ASP* 3.6 23.0 + - - +
408H ALA* 3.1 25.3 + - - +
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Residues in contact with ARG 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407G GLU* 4.0 23.4 + - - -
368H LYS 5.6 5.9 + - - +
369H CYS* 5.3 1.8 - - - +
370H PHE* 3.8 52.6 - - - +
404H SER* 1.4 71.1 - - - +
406H VAL* 1.3 67.8 + - + +
407H ASP 3.3 0.2 - - - -
408H ALA* 3.7 8.7 - - - -
409H GLU* 3.1 57.5 + - + +
425H ILE* 6.0 1.1 - - - -
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Residues in contact with VAL 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G LEU* 5.6 3.7 - - + +
404H SER* 3.6 4.4 - - - +
405H ARG* 1.3 78.2 - - + +
407H ASP* 1.3 63.6 + - - +
409H GLU* 4.5 2.2 - - - +
410H GLU* 3.3 32.5 + - + +
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Residues in contact with ASP 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325H ILE* 3.6 20.1 - - + +
329H LYS* 4.7 28.5 - - + +
403H VAL* 4.7 6.7 + - - +
404H SER* 3.6 23.7 + - - +
405H ARG 3.3 0.2 - - - -
406H VAL* 1.3 81.5 - - - +
408H ALA* 1.3 61.8 + - - +
410H GLU* 3.9 11.6 + - - +
411H ALA* 3.4 21.5 + - - +
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Residues in contact with ALA 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PHE* 4.0 13.7 - - + -
322H VAL* 6.5 0.2 - - + -
325H ILE* 4.0 11.6 - - + +
369H CYS* 4.7 20.0 - - + -
404H SER 3.1 17.5 + - - +
405H ARG* 3.8 13.0 - - - +
406H VAL 3.3 0.4 - - - -
407H ASP* 1.3 74.9 - - - +
409H GLU* 1.4 63.7 + - + +
411H ALA* 3.2 18.1 + - - +
412H LEU* 3.4 15.2 + - + +
425H ILE* 5.9 4.5 - - + -
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Residues in contact with GLU 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400G LYS* 4.1 23.9 + - - -
407G GLU* 6.0 1.6 - - - -
414G LEU* 4.9 7.6 - - + -
370H PHE* 4.6 1.7 - - - +
405H ARG* 3.1 55.9 + - + +
406H VAL* 4.5 2.5 - - - +
408H ALA* 1.4 72.8 - - + +
410H GLU* 1.3 66.2 + - - +
412H LEU* 3.1 12.9 + - - +
413H VAL* 3.0 26.1 + - + +
425H ILE* 3.5 24.6 - - - +
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Residues in contact with GLU 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G LEU* 4.3 17.1 - - + +
421G ARG* 5.2 4.3 + - - -
329H LYS* 2.7 32.1 + - + +
406H VAL* 3.3 25.2 + - + +
407H ASP* 4.2 12.6 - - - +
409H GLU* 1.3 77.8 - - - +
411H ALA* 1.3 56.4 + - - +
413H VAL* 3.1 9.0 + - + +
414H ASP* 2.9 38.0 + - - +
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Residues in contact with ALA 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PHE* 3.9 5.2 - - + -
325H ILE* 3.6 32.1 - - + -
329H LYS* 5.3 5.8 - - + +
343H LEU* 3.8 13.9 - - + +
407H ASP 3.4 8.7 + - - +
408H ALA 3.2 11.4 + - - +
409H GLU 3.1 0.4 - - - -
410H GLU* 1.3 75.1 - - - +
412H LEU* 1.3 68.7 + - - +
414H ASP* 4.1 5.2 - - - +
415H LEU* 3.1 24.8 + - - +
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Residues in contact with LEU 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G PHE* 5.4 0.5 - - - -
400G LYS* 5.2 10.8 - - - +
321H PHE* 3.2 34.3 - - + -
361H LEU* 6.0 1.6 - - + -
363H ILE* 4.6 7.2 - - + -
408H ALA 3.4 13.8 + - - +
409H GLU* 3.1 20.5 + - - +
411H ALA* 1.3 82.7 - - - +
413H VAL* 1.3 57.5 + - + +
415H LEU* 3.3 11.7 + - + +
416H GLN* 2.9 29.9 + - - +
423H ALA* 4.2 27.7 - - + +
424H GLN 5.4 1.8 - - - +
425H ILE* 3.9 33.7 - - + -
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Residues in contact with VAL 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411G TYR* 5.1 17.3 - - + -
414G LEU* 3.2 55.4 - - + +
415G LEU* 4.2 5.8 - - + +
418G GLY* 4.9 0.9 - - - -
409H GLU* 3.0 15.3 + - + +
410H GLU* 3.4 10.1 - - + +
412H LEU* 1.3 74.3 - - + +
414H ASP* 1.3 72.2 + - - +
415H LEU 3.0 1.3 - - - -
416H GLN* 3.0 19.3 + - - +
417H LEU* 3.2 25.0 + - + +
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Residues in contact with ASP 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G GLY* 4.9 6.2 - - - -
421G ARG* 2.7 34.0 + - - +
329H LYS* 2.4 38.6 + - - -
344H GLN* 4.1 15.9 + - - +
410H GLU* 2.9 22.7 + - - +
411H ALA* 4.3 4.9 - - - +
413H VAL* 1.3 79.7 - - - +
415H LEU* 1.3 61.7 + - - +
417H LEU* 3.4 4.8 + - - +
418H HIS* 3.3 31.8 + - - +
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Residues in contact with LEU 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PHE* 5.0 1.3 - - + -
343H LEU* 3.7 33.9 - - + -
344H GLN* 4.0 22.7 - - + +
347H VAL* 4.2 17.5 - - + -
361H LEU* 5.4 10.5 - - + -
411H ALA 3.1 19.4 + - - +
412H LEU* 3.4 20.2 - - + +
413H VAL 3.0 0.4 - - - -
414H ASP* 1.3 78.3 - - - +
416H GLN* 1.3 60.0 + - - +
419H THR* 2.3 53.0 + - + +
421H ALA* 4.9 9.9 - - + -
422H GLN 6.1 0.2 - - - +
423H ALA* 5.5 5.8 - - + -
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Residues in contact with GLN 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G HIS* 4.1 11.1 + - + +
363G ARG* 4.3 1.9 + - - -
365G VAL* 4.0 18.2 - - - +
398G PHE* 3.4 47.1 - - + -
411G TYR* 2.7 37.8 + - - -
415G LEU* 3.4 28.2 - - + +
412H LEU 2.9 17.1 + - - +
413H VAL* 3.0 9.8 + - - +
415H LEU* 1.3 77.6 - - - +
417H LEU* 1.3 61.5 + - + +
419H THR* 3.1 16.8 - - - +
421H ALA 4.8 2.7 - - - -
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Residues in contact with LEU 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G HIS* 3.7 23.3 - - + +
363G ARG* 4.0 0.7 + - - -
415G LEU* 3.7 30.3 - - + +
418G GLY* 3.3 41.1 - - - +
419G LEU* 3.8 16.6 - - + +
422G LEU* 3.5 19.9 - - + +
448G ASN* 3.2 26.2 + - - +
413H VAL* 3.2 23.6 + - + +
414H ASP* 4.0 5.8 - - - +
415H LEU 3.2 0.8 - - - -
416H GLN* 1.3 79.0 - - - +
418H HIS* 1.3 66.1 + - + +
419H THR 3.3 2.6 + - - -
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Residues in contact with HIS 418 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G ARG* 5.2 1.1 - - - -
418G GLY* 5.4 2.5 - - - -
421G ARG* 4.0 29.3 + - - -
422G LEU* 3.9 37.8 - - + +
448G ASN* 5.3 8.5 - - - +
344H GLN* 4.0 23.8 + - - +
414H ASP* 3.3 24.7 + - + +
417H LEU* 1.3 81.5 - - + +
419H THR* 1.3 67.5 + - + +
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Residues in contact with THR 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G ARG* 3.3 14.1 + - - -
344H GLN* 5.1 9.6 - - + +
347H VAL* 4.3 15.5 - - + -
348H THR* 6.1 0.4 - - - +
415H LEU* 2.3 47.8 + - + +
416H GLN* 3.1 21.3 - - - +
418H HIS* 1.3 91.9 - - + +
420H GLU* 1.3 60.2 + - - +
421H ALA* 3.3 22.1 + - - +
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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
------------------------------------------------------------
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