Contacts of the helix formed by residues 438 - 449 (chain C) in PDB entry 1Z6T
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 438 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C ALA* 4.6 4.0 - - + -
157C GLY* 3.8 10.4 - - - -
265C ARG* 5.3 1.8 - - - -
322C LEU* 4.0 16.6 - - + +
425C PHE* 4.1 11.8 - + + -
436C TYR* 5.6 1.6 - - - -
437C LEU* 1.3 75.4 - - - +
439C ASP* 1.3 72.9 + - + +
440C LEU* 3.1 49.6 + - + +
441C GLN* 2.8 30.8 + - + +
442C VAL* 3.1 8.9 + - - +
902C ADP 2.8 57.6 + - - -
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Residues in contact with ASP 439 (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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189C LYS* 6.1 0.2 - - - +
244C ASP* 3.9 11.9 - - - +
246C TRP* 4.5 6.8 + - - -
265C ARG* 3.3 28.8 + - - +
391C LYS* 3.7 39.1 + - + +
392C ASP* 3.4 25.2 + - - +
437C LEU 3.7 1.8 + - - +
438C HIS* 1.3 79.5 + - + +
440C LEU* 1.3 64.1 + - + +
442C VAL* 3.2 5.2 + - - +
443C ASP* 3.1 28.2 + - - +
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Residues in contact with LEU 440 (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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156C ALA* 4.1 15.7 - - + +
157C GLY* 4.3 4.7 - - - -
265C ARG* 5.4 4.0 - - - +
320C SER* 5.5 1.1 - - - +
322C LEU* 4.7 8.3 - - + -
359C TYR* 3.3 63.3 - - + +
361C TYR* 4.1 11.5 - - + +
364C LEU* 3.2 26.7 - - + +
438C HIS* 3.1 28.2 + - + +
439C ASP* 1.3 81.9 - - + +
441C GLN* 1.3 57.0 + - - +
443C ASP* 3.5 11.9 - - - +
444C PHE* 3.1 20.4 + - - +
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Residues in contact with GLN 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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322C LEU* 3.9 19.5 - - + +
326C LEU* 4.3 0.6 - - - +
364C LEU* 5.1 0.4 - - + -
368C MET* 3.7 32.5 - - + -
422C SER 2.9 27.3 + - - -
423C LEU* 3.8 10.3 - - - +
425C PHE* 3.3 15.5 - - - -
437C LEU* 3.7 20.2 - - + +
438C HIS* 2.8 31.9 + - + +
440C LEU* 1.3 74.4 - - - +
442C VAL* 1.3 65.5 + - - +
444C PHE* 3.4 7.2 + - - +
445C LEU* 3.0 30.8 + - - +
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Residues in contact with VAL 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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387C SER 5.5 1.7 - - - +
389C LEU 4.0 24.7 - - - +
390C GLN* 4.2 4.0 - - - +
391C LYS* 3.8 41.3 - - + +
437C LEU* 3.8 29.4 - - + +
438C HIS 3.1 7.3 + - - +
439C ASP* 3.2 7.6 + - - +
441C GLN* 1.3 76.8 - - - +
443C ASP* 1.3 57.5 + - - +
445C LEU* 3.3 3.7 + - - +
446C THR* 2.9 40.0 + - - +
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Residues in contact with ASP 443 (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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352C ARG* 3.5 8.6 + - - +
354C ARG* 4.2 14.4 + - - -
361C TYR* 2.5 39.6 + - + +
391C LYS* 3.0 32.0 + - - -
439C ASP* 3.1 17.5 + - - +
440C LEU* 3.5 15.5 - - - +
442C VAL* 1.3 73.6 - - - +
444C PHE* 1.3 65.5 + - - +
446C THR* 3.9 6.7 - - - +
447C GLU* 3.1 24.8 + - - +
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Residues in contact with PHE 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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350C PHE* 3.6 26.2 - + - -
352C ARG* 3.8 9.3 - - - +
364C LEU* 5.4 0.9 - - + -
365C ASP* 3.1 44.4 - - - +
368C MET* 3.6 40.6 - - + -
369C SER* 3.5 23.8 - - - -
372C VAL* 4.3 5.8 - - + -
440C LEU 3.1 11.6 + - - +
441C GLN 3.6 6.1 - - - +
442C VAL 3.4 0.2 - - - -
443C ASP* 1.3 79.1 - - - +
445C LEU* 1.3 68.1 + - + +
447C GLU* 3.3 2.6 + - - +
448C LYS* 2.8 58.6 + - + +
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Residues in contact with LEU 445 (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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368C MET* 4.8 0.2 - - + -
372C VAL* 5.2 0.9 - - + -
383C TYR* 3.7 45.5 - - + +
384C THR* 5.3 0.7 - - - -
386C LEU* 4.4 1.8 - - + +
387C SER* 3.6 31.7 + - - +
437C LEU* 3.8 29.2 - - + -
441C GLN 3.0 17.0 + - - +
442C VAL* 3.9 4.0 - - - +
444C PHE* 1.3 91.0 - - + +
446C THR* 1.3 61.5 + - - +
448C LYS* 4.4 2.5 - - + -
449C ASN* 2.9 53.9 + - - +
453C LEU* 4.6 0.2 - - - +
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Residues in contact with THR 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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354C ARG* 6.0 7.4 - - - +
387C SER 4.3 8.3 + - - -
442C VAL* 2.9 29.5 + - - +
443C ASP* 3.9 6.3 - - - +
445C LEU* 1.3 78.2 - - - +
447C GLU* 1.3 58.2 + - - +
450C CYS* 3.0 32.2 + - + +
453C LEU* 4.1 24.9 - - + +
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Residues in contact with GLU 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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350C PHE* 3.9 23.1 - - + -
351C LYS 3.5 7.3 - - - +
352C ARG* 3.7 21.6 + - - +
353C ILE* 2.8 49.9 + - - +
354C ARG* 3.4 21.8 + - - +
443C ASP 3.1 18.2 + - - +
444C PHE 3.5 3.8 - - - +
446C THR* 1.3 75.4 - - - +
448C LYS* 1.3 66.4 + - - +
449C ASN 3.3 0.7 + - - -
450C CYS* 3.4 15.5 + - - +
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Residues in contact with LYS 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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350C PHE* 4.0 23.3 - - + -
369C SER* 5.9 2.9 - - - +
372C VAL* 4.0 25.0 - - + +
384C THR* 4.7 8.1 + - - -
444C PHE* 2.8 45.7 + - + +
445C LEU* 4.9 1.3 - - + -
447C GLU* 1.3 75.8 - - - +
449C ASN* 1.3 85.8 + - - +
450C CYS 3.8 0.5 + - - -
452C GLN* 5.4 2.0 + - - +
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Residues in contact with ASN 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C THR* 3.7 19.5 + - + +
387C SER* 3.0 30.9 + - - +
445C LEU* 2.9 38.5 + - - +
446C THR 3.8 2.5 - - - -
448C LYS* 1.3 103.9 + - - +
450C CYS* 1.4 64.1 + - - +
451C SER* 3.2 4.0 - - - -
452C GLN* 3.0 39.5 + - + +
453C LEU* 3.2 13.3 + - + +
456C LEU* 5.0 0.7 - - + -
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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