Contacts of the helix formed by residues 444 - 459 (chain C) in PDB entry 3ZXR
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 444 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C SER* 3.9 14.8 + - - -
114C LYS* 4.0 10.3 - - - +
438C THR* 4.8 1.8 - - - -
441C GLY* 3.7 19.3 - - - +
442C VAL 4.2 0.6 + - - -
443C PHE* 1.3 78.2 - - - +
445C ASN* 1.3 65.9 + - - +
446C ASP* 2.5 28.7 + - - +
447C LEU* 3.1 21.4 + - - +
448C ILE* 3.2 15.5 + - - +
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Residues in contact with ASN 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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434C HIS* 3.5 24.1 + - - -
435C GLU* 6.1 0.2 - - - -
438C THR* 4.0 14.1 - - - +
444C THR* 1.3 73.2 - - - +
446C ASP* 1.3 57.1 + - - +
448C ILE* 3.3 5.4 + - - +
449C GLU* 2.8 49.1 + - - +
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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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105C SER* 2.6 27.6 + - - -
106C ARG* 2.8 26.9 + - - +
444C THR* 2.5 29.0 + - - -
445C ASN* 1.3 75.3 - - - +
447C LEU* 1.3 62.2 + - - +
449C GLU* 4.1 9.7 - - - +
450C THR* 2.7 34.0 + - - -
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Residues in contact with LEU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.9 29.4 - - + -
105C SER 3.9 10.5 - - - +
106C ARG* 4.0 14.1 - - + +
111C ILE* 3.5 35.9 - - + -
319C PHE* 4.7 5.8 - - + -
378C LEU* 4.4 11.7 - - + -
443C PHE* 3.6 30.7 - - + -
444C THR* 3.1 17.4 + - - +
446C ASP* 1.3 82.7 - - - +
448C ILE* 1.3 57.8 + - - +
450C THR* 3.3 2.8 + - - -
451C TRP* 2.9 30.6 + - + +
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Residues in contact with ILE 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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319C PHE* 4.6 9.6 - - + -
430C LEU* 4.1 15.9 - - + +
434C HIS* 3.7 45.1 - - + +
437C LEU* 4.4 7.4 - - + -
438C THR* 4.0 17.7 - - + -
443C PHE* 4.0 26.2 - - + -
444C THR 3.2 10.8 + - - +
445C ASN* 3.8 7.9 - - - +
447C LEU* 1.3 77.8 - - - +
449C GLU* 1.3 59.1 + - + +
451C TRP* 3.3 5.9 + - - +
452C ILE* 3.0 47.3 + - + +
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Residues in contact with GLU 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 ASN* 2.8 34.0 + - - +
446C ASP* 4.1 8.2 - - - +
448C ILE* 1.3 79.0 - - + +
450C THR* 1.3 56.3 + - - +
452C ILE* 3.5 10.4 + - + +
453C SER* 3.0 31.5 + - - -
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Residues in contact with THR 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.8 20.4 - - + -
60C GLY* 3.8 24.7 - - - +
106C ARG* 3.5 16.9 + - - +
446C ASP 2.7 22.8 + - - -
447C LEU 3.6 3.8 - - - -
449C GLU* 1.3 72.9 - - - +
451C TRP* 1.3 60.3 + - - +
453C SER* 3.7 4.5 - - - -
454C PHE* 2.8 35.1 + - + +
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Residues in contact with TRP 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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28C LEU* 3.4 46.2 - - + +
29C PRO* 4.1 15.0 - - + -
318C ALA 2.9 29.5 + - - -
319C PHE* 3.4 35.9 - + + -
322C PRO* 3.7 12.8 - - + -
375C ASN* 4.7 4.7 - - + -
378C LEU* 3.6 19.1 - - + -
427C ILE* 4.1 9.0 - - + +
430C LEU* 4.0 14.4 - - + -
447C LEU* 2.9 17.8 + - + +
448C ILE* 3.5 7.0 - - - +
450C THR* 1.3 77.7 - - - +
452C ILE* 1.3 63.6 + - - +
454C PHE* 3.8 6.7 - + + +
455C LYS* 3.0 61.2 + - - +
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Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ILE* 3.7 21.4 - - + +
430C LEU* 3.9 15.7 - - + -
431C GLU* 3.6 40.4 - - + +
434C HIS* 5.7 0.4 - - + -
448C ILE* 3.0 38.0 + - + +
449C GLU* 3.8 10.1 - - + +
451C TRP* 1.3 75.0 - - - +
453C SER* 1.3 64.7 + - - +
455C LYS* 3.4 2.3 + - - +
456C ARG* 3.1 60.8 + - - +
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Residues in contact with SER 453 (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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449C GLU 3.0 19.0 + - - -
450C THR* 3.7 6.1 - - - -
452C ILE* 1.3 80.2 - - - +
454C PHE* 1.3 63.5 + - - +
456C ARG* 3.3 6.0 + - - +
457C GLU* 3.0 48.3 + - - +
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Residues in contact with PHE 454 (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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28C LEU* 5.8 2.7 - - + -
29C PRO* 3.8 27.6 - - + -
59C ARG* 3.9 40.8 - - + -
60C GLY* 4.8 9.6 - - - -
450C THR* 2.8 26.8 + - + +
451C TRP* 3.8 7.0 - + + +
453C SER* 1.3 74.6 + - - +
455C LYS* 1.3 68.2 + - + +
457C GLU* 5.7 0.4 - - - -
458C ASN* 2.9 72.7 + - + +
459C GLU* 3.3 26.0 - - + -
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Residues in contact with LYS 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 5.5 6.0 + - - +
322C PRO* 2.7 38.7 + - - +
323C THR* 4.4 4.8 - - - +
373C SER 5.4 1.2 + - - -
374C GLY* 5.8 0.6 - - - -
423C LEU* 4.3 3.1 - - + -
427C ILE* 3.9 29.8 - - + -
451C TRP* 3.0 54.1 + - - +
452C ILE 3.9 3.4 - - - +
454C PHE* 1.3 85.9 - - + +
456C ARG* 1.3 58.9 + - - +
459C GLU* 2.9 38.6 + - - +
460C ILE* 2.9 31.1 + - + +
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Residues in contact with ARG 456 (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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427C ILE* 3.6 8.5 - - + +
428C ASP* 2.9 35.5 + - - +
431C GLU* 2.9 42.0 + - - +
452C ILE* 3.1 36.1 + - - +
453C SER* 3.8 5.6 - - - +
455C LYS* 1.3 77.6 - - - +
457C GLU* 1.3 64.2 + - + +
460C ILE* 3.9 22.8 - - + +
461C GLU* 3.0 34.1 + - - +
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Residues in contact with GLU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C SER* 3.0 36.5 + - - +
454C PHE* 5.7 0.3 - - - -
456C ARG* 1.3 79.6 - - + +
458C ASN* 1.3 70.0 + - - +
459C GLU 3.7 0.2 - - - -
461C GLU* 4.6 14.6 - - - +
462C PRO* 3.4 16.6 - - - +
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Residues in contact with ASN 458 (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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454C PHE* 2.9 64.5 + - + +
457C GLU* 1.3 87.3 + - - +
459C GLU* 1.3 62.7 + - + +
462C PRO* 3.5 15.5 - - - +
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Residues in contact with GLU 459 (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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29C PRO* 5.7 0.5 - - - +
322C PRO 3.4 9.2 - - - +
323C THR* 3.7 19.1 - - - +
324C VAL* 4.2 11.9 + - + -
423C LEU* 3.9 3.2 - - + +
454C PHE* 3.3 19.6 - - + -
455C LYS* 2.9 48.4 + - - +
458C ASN* 1.3 88.3 - - + +
460C ILE* 1.3 69.5 + - - +
461C GLU 3.5 1.1 - - - -
462C PRO* 3.5 3.0 - - - +
463C VAL* 3.2 28.8 + - - +
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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
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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