Contacts of the helix formed by residues 438 - 451 (chain C) in PDB entry 1IV4
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 438 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C TYR* 3.3 20.0 - - + +
420C LEU* 3.4 6.6 + - - -
421C CYS 3.0 19.6 + - - -
422C GLY* 2.8 31.2 + - - -
436C ASP* 2.9 25.0 + - - +
437C GLY* 1.3 71.1 - - - +
439C ALA* 1.3 63.2 + - - +
440C ALA 3.2 4.7 + - - -
441C MET* 3.1 20.7 + - - +
442C HIS* 3.0 27.7 + - - -
472C ARG* 5.2 0.3 + - - -
473C SER* 4.0 6.6 - - - +
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Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ASP* 3.4 29.8 - - + +
410C HIS* 4.3 9.2 - - + -
420C LEU* 4.2 4.1 - - + +
437C GLY 2.9 7.2 + - - -
438C ASP* 1.3 72.7 + - - +
440C ALA* 1.3 63.1 + - - +
443C ALA* 3.0 19.9 + - - +
542C VAL* 4.3 26.0 - - + +
544C ALA* 3.3 24.9 - - + +
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Residues in contact with ALA 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 4.2 4.4 - - + +
421C CYS* 3.7 28.5 - - - +
438C ASP* 3.2 9.2 + - - +
439C ALA* 1.3 80.9 - - - +
441C MET* 1.3 63.6 + - - +
443C ALA* 3.8 1.6 - - - +
444C LEU* 3.1 29.9 + - + +
496C LEU* 3.9 8.4 - - + +
498C LEU* 3.7 22.7 - - + -
544C ALA* 3.9 9.8 - - - +
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Residues in contact with MET 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C CYS* 4.2 7.9 - - - -
422C GLY* 3.8 14.6 - - - +
438C ASP* 3.1 27.7 + - - +
440C ALA* 1.3 74.7 - - - +
442C HIS* 1.3 55.8 + - - +
444C LEU* 3.4 6.4 + - - +
445C THR* 2.7 38.3 + - - -
473C SER* 3.8 20.2 - - - +
474C GLU* 3.2 39.9 - - + +
477C LEU* 3.0 40.5 - - + +
516C LEU* 4.6 8.5 - - - -
519C LEU* 4.1 11.0 - - + -
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Residues in contact with HIS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C GLU 5.0 0.2 - - - -
408C ASP* 2.9 20.5 + - - +
410C HIS* 3.6 3.8 + - - -
435C SER* 3.5 24.0 + - - -
438C ASP 3.0 16.8 + - - +
441C MET* 1.3 73.7 - - - +
443C ALA* 1.3 61.4 + - - +
445C THR* 3.1 7.9 + - - -
446C ASP* 2.8 33.9 + - - +
457C ILE* 3.7 24.6 - - + +
473C SER* 2.7 35.3 + - - -
476C PHE* 4.2 16.8 - + - -
1563C MG 2.0 30.0 - - - -
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Residues in contact with ALA 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLY* 3.6 17.2 - - - +
407C GLU 4.0 15.5 - - - +
408C ASP* 3.9 0.8 - - - +
439C ALA 3.0 19.0 + - - +
440C ALA 3.8 3.6 - - - +
442C HIS* 1.3 78.5 - - - +
444C LEU* 1.3 56.6 + - - +
446C ASP* 3.4 0.4 + - - -
447C ALA* 2.9 29.8 + - - +
496C LEU* 5.6 0.4 - - + -
544C ALA* 3.8 28.3 - - + +
546C ALA* 4.1 10.5 - - + -
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Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C ALA 3.1 20.6 + - - +
441C MET* 3.6 8.3 - - - +
443C ALA* 1.3 70.8 - - - +
445C THR* 1.3 61.1 + - - +
447C ALA* 3.3 3.3 + - - +
448C LEU* 3.0 32.9 + - - +
477C LEU* 3.9 7.2 - - + -
494C ALA* 3.8 19.3 - - + -
496C LEU* 4.0 20.9 - - + -
516C LEU* 3.7 31.2 - - + -
520C MET* 3.4 32.1 - - + -
546C ALA* 3.9 19.1 - - + -
548C VAL* 4.4 6.1 - - + +
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Residues in contact with THR 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C MET 2.7 23.5 + - - -
442C HIS* 3.5 6.9 - - - -
444C LEU* 1.3 73.5 - - - +
446C ASP* 1.3 64.9 + - - +
448C LEU* 3.2 6.4 + - - +
449C LEU* 2.9 24.9 + - + +
457C ILE* 3.5 23.3 - - + -
461C PHE* 4.1 7.6 - - + -
473C SER 4.8 1.0 + - - -
476C PHE* 3.7 27.4 - - + +
477C LEU* 3.5 24.8 + - - +
480C ALA* 3.9 10.1 - - + -
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Residues in contact with ASP 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B THR* 4.1 12.9 + - + +
332B LYS* 3.5 27.4 + - - +
406C GLY* 4.2 12.1 - - - -
407C GLU 3.9 3.9 - - - +
442C HIS 2.8 19.3 + - - +
443C ALA* 3.8 4.5 - - - +
445C THR* 1.3 73.5 - - - +
447C ALA* 1.3 58.3 + - - +
449C LEU* 3.9 3.6 - - - +
450C SER* 2.8 33.5 + - - -
456C ASP* 3.2 15.7 - - - +
457C ILE* 2.7 42.5 + - - +
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Residues in contact with ALA 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C GLY* 3.4 24.9 - - - +
405C TYR 3.8 11.4 - - - -
406C GLY* 3.6 15.2 - - - +
443C ALA 2.9 19.0 + - - +
444C LEU* 3.7 7.0 - - - +
445C THR 3.2 0.2 - - - -
446C ASP* 1.3 74.8 - - - +
448C LEU* 1.3 61.9 + - - +
450C SER* 3.3 0.3 + - - -
451C ALA 3.1 18.4 + - - -
546C ALA* 3.9 7.6 - - + +
548C VAL* 3.6 17.6 - - + +
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Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C LEU 3.0 14.0 + - - +
445C THR 3.6 6.1 - - - +
447C ALA* 1.3 73.9 - - - +
449C LEU* 1.3 67.1 + - - +
451C ALA* 3.3 14.1 + - - +
452C TYR 3.9 0.2 + - - -
477C LEU* 3.7 34.3 - - + +
480C ALA* 4.1 19.5 - - + +
481C MET* 4.4 12.8 - - + +
484C VAL* 3.6 28.7 - - + +
491C LEU* 4.0 33.9 - - + -
520C MET* 4.3 6.3 - - + -
548C VAL* 4.2 15.0 - - + -
550C LEU* 4.4 12.7 - - + +
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C THR* 2.9 24.0 + - + +
446C ASP* 3.9 3.4 - - - +
448C LEU* 1.3 76.8 - - - +
450C SER* 1.3 62.6 + - - +
452C TYR* 3.1 7.3 + - - -
454C LEU* 3.0 48.3 + - + +
455C GLY 3.8 11.7 - - - +
456C ASP* 3.7 28.0 - - - +
457C ILE 4.0 2.9 - - - +
460C LEU* 3.3 35.0 - - + -
461C PHE* 4.2 13.5 - - + -
480C ALA* 3.7 26.2 - - + +
483C LEU* 4.3 1.8 - - + -
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Residues in contact with SER 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLN* 4.3 3.3 - - - +
295B SER* 2.7 27.8 + - - -
296B LEU 4.7 0.2 + - - -
325B ASP 4.9 0.2 - - - +
327B ILE 4.5 0.2 - - - -
328B GLY* 3.0 40.0 + - - -
329B LEU 5.1 0.2 - - - +
330B THR* 4.0 10.1 - - - +
403C ILE 4.8 0.2 - - - +
405C TYR 3.9 10.8 + - - -
446C ASP 2.8 18.7 + - - -
447C ALA 3.6 4.7 - - - -
448C LEU 3.2 0.2 - - - -
449C LEU* 1.3 78.7 - - - +
451C ALA* 1.3 61.9 + - - +
452C TYR 3.1 0.2 - - - -
453C GLY* 3.1 12.2 + - - +
455C GLY 4.4 5.1 + - - -
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Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLN* 3.0 10.7 - - - +
325B ASP 4.3 0.2 - - - -
402C ARG* 2.9 27.7 + - + -
403C ILE 3.5 25.6 - - - +
404C GLY* 3.9 0.6 - - - +
447C ALA 3.1 11.9 + - - +
448C LEU 3.6 11.0 - - - +
449C LEU 3.2 0.8 - - - -
450C SER* 1.3 75.5 - - - +
452C TYR* 1.3 61.5 + - + +
550C LEU* 3.6 30.3 - - + -
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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