Contacts of the helix formed by residues 392 - 409 (chain C) in PDB entry 4ZTZ
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 THR 392 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389C ARG* 3.1 45.7 + - - +
390C GLY 2.7 21.3 + - - -
391C PRO* 1.3 73.4 + - - +
393C LEU* 1.3 69.2 + - + +
394C GLU* 4.0 16.6 - - + +
395C LEU* 3.3 22.4 + - - +
396C ARG* 3.4 16.2 + - - +
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Residues in contact with LEU 393 (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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236A THR* 5.4 8.1 - - + +
836A LEU* 5.9 7.4 - - + -
392C THR* 1.3 77.3 - - + +
394C GLU* 1.3 59.3 + - + +
396C ARG* 3.1 24.5 + - + +
397C GLN* 2.9 52.2 + - + +
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Residues in contact with GLU 394 (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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234A SER* 2.8 30.8 + - - +
236A THR* 5.8 1.3 - - - +
238A GLN* 5.3 4.3 - - - +
389C ARG* 5.0 3.3 + - - -
392C THR* 3.3 15.1 - - + +
393C LEU* 1.3 78.1 - - + +
395C LEU* 1.3 57.8 + - - +
397C GLN* 3.1 15.4 + - - +
398C VAL* 2.9 33.9 + - - +
448C LEU* 3.3 29.6 - - + +
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Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C VAL* 3.9 23.1 - - + -
389C ARG* 3.6 39.3 - - + +
390C GLY 3.4 25.4 - - - +
391C PRO* 4.9 0.2 - - + -
392C THR* 3.5 19.5 - - - +
393C LEU 3.3 0.2 - - - -
394C GLU* 1.3 76.7 - - - +
396C ARG* 1.3 58.4 + - - +
398C VAL* 3.8 5.0 - - - +
399C CYS* 2.9 36.8 + - - -
443C VAL* 4.1 9.4 - - + +
444C THR 3.5 25.6 - - - +
445C GLU* 4.5 0.2 - - - -
448C LEU* 3.8 15.3 - - + -
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Residues in contact with ARG 396 (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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387C VAL* 5.0 1.5 - - - +
391C PRO* 5.2 13.7 - - - +
392C THR 3.4 11.7 + - - +
393C LEU* 3.1 26.8 + - + +
395C LEU* 1.3 76.8 - - - +
397C GLN* 1.3 60.2 + - - +
399C CYS* 3.8 5.5 - - - +
400C GLN* 2.9 33.1 + - + +
417C TYR* 2.8 37.0 + - + +
418C LEU* 2.6 41.2 + - - +
419C GLU* 4.8 3.8 - - - +
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Residues in contact with GLN 397 (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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234A SER* 3.4 29.2 + - - -
235A TRP 5.7 0.2 - - - -
236A THR* 3.2 28.3 + - - +
393C LEU* 2.9 40.2 + - + +
394C GLU* 3.3 11.8 - - - +
396C ARG* 1.3 74.2 - - - +
398C VAL* 1.3 60.6 + - + +
400C GLN* 3.3 6.8 + - - +
401C GLY* 2.9 24.4 + - - -
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 4.3 17.5 - - - +
234A SER* 5.8 5.8 - - - -
394C GLU* 2.9 21.0 + - + +
395C LEU* 3.8 4.0 - - - +
397C GLN* 1.3 75.5 - - + +
399C CYS* 1.3 59.2 - - - +
401C GLY* 3.0 3.9 + - - +
402C LEU* 2.9 26.5 + - - +
443C VAL* 4.1 19.7 - - + -
447C THR* 4.6 4.3 - - + -
448C LEU* 4.1 22.2 - - + -
468C ILE* 3.8 25.7 - - + +
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Residues in contact with CYS 399 (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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385C LEU* 3.6 20.5 - - + +
386C ASP 4.0 1.8 - - - -
387C VAL* 3.6 22.9 - - - -
395C LEU 2.9 25.1 + - - +
396C ARG 3.9 0.4 - - - +
398C VAL* 1.3 77.3 - - - +
400C GLN* 1.3 58.6 + - - +
402C LEU* 3.4 3.2 + - - +
403C PHE* 2.9 28.1 + - - +
417C TYR* 3.5 30.5 - - + -
443C VAL* 3.6 29.4 - - - -
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Residues in contact with GLN 400 (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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123B GLU* 4.1 19.1 + - - +
396C ARG* 2.9 21.7 + - + +
397C GLN* 3.6 6.5 - - - +
399C CYS* 1.3 73.4 - - - +
401C GLY* 1.3 60.5 + - - +
403C PHE* 3.3 12.6 - - - +
404C ASN* 2.9 61.7 + - - +
417C TYR* 2.8 25.5 + - - +
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Residues in contact with GLY 401 (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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397C GLN 2.9 13.7 + - - -
398C VAL* 3.0 5.6 + - - -
400C GLN* 1.3 76.7 - - - +
402C LEU* 1.3 55.9 + - - +
404C ASN* 3.3 8.4 + - - +
405C GLU* 2.9 41.9 + - - +
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Residues in contact with LEU 402 (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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385C LEU* 3.9 20.0 - - + -
398C VAL 2.9 14.3 + - - +
399C CYS* 3.9 5.4 - - - +
401C GLY* 1.3 75.3 - - - +
403C PHE* 1.3 56.6 + - - +
405C GLU* 4.3 17.0 - - + +
406C LEU* 2.9 51.4 + - + +
441C VAL* 4.2 3.6 - - + -
443C VAL* 4.9 3.8 - - + -
453C ILE* 3.7 30.5 - - + -
468C ILE* 3.7 21.2 - - + +
471C LEU* 3.7 28.5 - - + -
472C LYS* 5.8 1.3 - - + +
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Residues in contact with PHE 403 (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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120B VAL 4.7 3.1 - - - -
121B PHE 4.1 8.3 - - - -
123B GLU* 3.8 35.4 - - + -
385C LEU* 4.4 4.2 - - + +
399C CYS 2.9 18.9 + - - +
400C GLN* 3.3 15.0 - - - +
402C LEU* 1.3 77.8 - - - +
404C ASN* 1.3 69.5 + - - +
406C LEU* 3.9 1.6 - - - +
407C LEU* 2.9 57.5 + - + +
413C VAL* 3.6 45.0 - - + +
415C PRO* 4.0 14.4 - - + -
417C TYR* 3.7 23.1 - + + +
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Residues in contact with ASN 404 (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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121B PHE 5.1 4.0 - - - +
400C GLN* 2.9 47.3 + - - +
401C GLY* 3.8 6.2 - - - +
403C PHE* 1.3 83.7 - - - +
405C GLU* 1.3 58.5 + - + +
407C LEU* 3.4 5.7 + - - +
408C GLU* 2.9 38.2 + - - +
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Residues in contact with GLU 405 (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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401C GLY* 2.9 25.8 + - - +
402C LEU* 3.8 18.8 - - + +
404C ASN* 1.3 78.2 - - + +
406C LEU* 1.3 63.1 + - + +
408C GLU* 3.2 13.7 + - - +
409C ASN* 3.3 20.1 - - - +
468C ILE* 5.0 7.8 - - - +
469C SER* 5.8 1.6 - - - -
472C LYS* 4.8 11.9 - - + +
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Residues in contact with LEU 406 (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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383C VAL* 3.9 27.8 - - + -
385C LEU* 4.2 15.7 - - + -
402C LEU* 2.9 41.0 + - + +
403C PHE 3.9 2.2 - - - +
405C GLU* 1.3 77.3 - - - +
407C LEU* 1.3 61.2 + - - +
408C GLU 3.3 0.3 + - - -
409C ASN* 3.3 8.4 + - - +
411C ILE* 3.1 45.1 + - + +
413C VAL* 4.4 6.3 - - + -
471C LEU* 4.6 4.5 - - + -
472C LYS* 4.1 27.6 - - + +
475C LEU* 3.9 23.6 - - + -
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Residues in contact with LEU 407 (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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120B VAL* 3.3 47.5 - - + +
121B PHE* 3.7 29.9 - - + +
403C PHE* 2.9 49.1 + - + +
404C ASN* 4.0 6.1 - - - +
406C LEU* 1.3 75.5 - - - +
408C GLU* 1.3 62.6 + - - +
409C ASN 3.2 0.6 + - - -
410C GLY* 3.5 10.3 + - - -
411C ILE 3.3 24.5 - - - +
412C SER* 4.4 3.1 - - - -
413C VAL* 3.7 15.9 - - + +
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Residues in contact with GLU 408 (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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121B PHE* 4.6 19.2 - - - -
483B LYS* 5.9 0.7 + - - -
484B ASN* 5.8 0.9 + - - +
404C ASN* 2.9 23.4 + - - +
405C GLU* 3.3 11.4 - - - +
406C LEU 3.1 0.4 - - - -
407C LEU* 1.3 78.0 - - - +
409C ASN* 1.3 64.3 + - - +
410C GLY 3.4 1.4 + - - -
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Residues in contact with ASN 409 (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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405C GLU 3.3 10.2 - - - +
406C LEU 3.3 6.9 + - - +
407C LEU 3.2 0.4 - - - -
408C GLU* 1.3 85.7 + - - +
410C GLY* 1.3 61.6 + - - +
411C ILE* 3.6 8.4 - - + +
472C LYS* 3.2 31.9 + - + +
476C ILE* 3.6 31.8 - - + +
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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
------------------------------------------------------------
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