Contacts of the helix formed by residues 465 - 478 (chain C) in PDB entry 1Z5S
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 465 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C ASP* 3.9 2.6 - - - +
464C SER* 1.3 81.2 - - - +
466C PRO* 1.3 73.3 - - + +
467C GLU* 3.4 23.2 + - - +
468C LYS* 3.2 42.3 + - - +
469C VAL* 3.4 10.6 + - - +
507C PHE* 3.7 2.0 - - - -
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Residues in contact with PRO 466 (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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465C ASP* 1.3 86.2 - - + +
467C GLU* 1.3 65.0 + - - +
469C VAL* 2.8 4.5 + - - +
470C VAL* 2.8 27.3 + - + +
507C PHE* 3.2 32.5 - - + -
508C ASN* 3.8 22.2 - - + +
511C THR* 3.8 28.7 - - + +
512C PHE* 3.9 17.9 - - + -
515C ARG* 5.5 0.4 - - + -
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Residues in contact with GLU 467 (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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465C ASP* 3.2 14.9 + - - +
466C PRO* 1.3 79.0 - - - +
468C LYS* 1.3 60.4 + - + +
470C VAL* 3.4 6.8 + - - +
471C SER* 3.1 24.9 + - - -
515C ARG* 2.9 54.1 + - + +
519C HIS* 3.2 21.2 + - - -
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Residues in contact with LYS 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C THR* 4.3 8.1 - - + +
462C ASP* 3.2 49.2 + - + +
465C ASP* 3.2 28.4 + - - +
466C PRO 3.2 0.6 - - - -
467C GLU* 1.3 77.6 - - + +
469C VAL* 1.3 67.1 + - - +
471C SER* 3.1 8.6 + - - -
472C ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C THR* 5.1 3.6 - - - -
462C ASP 4.6 0.2 + - - -
463C THR* 4.2 19.3 - - - +
465C ASP 3.4 16.2 - - - +
466C PRO 2.8 6.2 + - - +
468C LYS* 1.3 78.0 - - - +
470C VAL* 1.3 64.5 + - - +
472C ALA* 3.1 5.5 + - - +
473C PHE* 2.9 23.6 + - - +
497C LEU* 4.6 12.1 - - + -
498C MET* 4.0 21.8 - - + -
501C ALA* 4.3 11.4 - - + -
507C PHE* 3.5 28.9 - - + -
512C PHE* 3.9 17.7 - - + -
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Residues in contact with VAL 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C PRO 2.8 16.6 + - - +
467C GLU* 3.4 9.0 - - - +
469C VAL* 1.3 76.6 - - - +
471C SER* 1.3 62.7 + - - +
473C PHE* 3.8 1.7 - - - +
474C LEU* 3.0 37.8 + - + +
512C PHE* 3.2 37.2 - - + +
515C ARG* 3.7 14.6 - - + +
516C LEU* 3.9 23.6 - - + +
519C HIS* 3.6 28.0 - - + -
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Residues in contact with SER 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C GLU 3.1 11.4 + - - -
468C LYS* 3.1 12.8 + - - -
470C VAL* 1.3 80.5 - - - +
472C ALA* 1.3 65.1 + - - +
474C LEU* 4.0 6.1 - - - +
475C LYS* 3.0 43.5 + - - +
519C HIS* 5.6 3.6 - - - -
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Residues in contact with ALA 472 (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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438C LEU* 5.0 10.1 - - + -
457C ILE* 5.6 3.1 - - + -
461C THR* 3.6 31.4 - - + +
468C LYS 3.0 6.4 + - - +
469C VAL 3.5 3.8 - - - +
471C SER* 1.3 75.0 - - - +
473C PHE* 1.3 67.5 + - - +
475C LYS* 2.7 22.7 + - - +
476C VAL* 2.9 15.5 + - + +
497C LEU* 3.4 22.0 - - + -
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Residues in contact with PHE 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C VAL 2.9 20.5 + - - +
470C VAL* 3.8 3.8 - - - +
472C ALA* 1.3 73.4 - - - +
474C LEU* 1.3 83.1 + - + +
476C VAL* 3.6 5.6 + - - +
477C SER* 2.5 51.6 + - - -
494C VAL* 3.9 14.9 - - + +
497C LEU* 3.4 13.1 - - + +
498C MET* 4.4 9.4 - - + -
512C PHE* 4.7 5.8 - + + -
516C LEU* 4.1 15.7 - - + -
538C PRO* 4.3 6.5 - - + -
541C ALA* 3.6 20.0 - - + -
542C LEU* 3.6 24.2 - - + -
545C MET* 3.2 35.0 - - + -
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Residues in contact with LEU 474 (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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470C VAL* 3.0 29.5 + - + +
471C SER* 4.0 4.3 - - - +
473C PHE* 1.3 96.1 - - + +
475C LYS* 1.3 57.9 + - + +
477C SER* 3.0 4.9 + - - -
478C SER* 2.7 35.7 + - - -
516C LEU* 3.7 13.7 - - + -
519C HIS* 3.6 33.4 - - + +
520C MET* 4.2 7.6 - - + -
532C ILE* 4.6 19.1 - - + -
538C PRO* 3.9 23.8 - - + +
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Residues in contact with LYS 475 (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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437C PHE* 4.9 2.9 - - + -
438C LEU* 3.1 53.1 + - + +
439C ALA 4.3 6.9 + - - -
441C PRO* 4.0 22.5 - - + +
471C SER* 3.0 36.6 + - - +
472C ALA* 2.7 14.3 + - - +
474C LEU* 1.3 71.4 - - + +
476C VAL* 1.3 60.4 + - - +
478C SER* 2.4 28.5 + - - -
479C VAL* 4.5 1.2 - - - +
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Residues in contact with VAL 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C PHE* 4.3 25.4 - - + -
438C LEU* 5.3 2.7 - - + -
446C LEU* 5.0 2.2 - - + -
457C ILE* 4.4 17.3 - - + -
472C ALA 2.9 14.3 + - - +
473C PHE* 3.9 7.2 - - - +
475C LYS* 1.3 74.7 - - - +
477C SER* 1.3 60.7 + - - +
479C VAL* 3.0 28.4 - - - +
490C VAL* 3.7 27.5 - - + +
493C ALA* 3.7 31.2 - - + -
494C VAL* 3.9 11.7 - - + +
497C LEU* 5.6 4.3 - - + -
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Residues in contact with SER 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C PHE* 2.5 28.2 + - - -
474C LEU* 3.0 5.9 + - - -
476C VAL* 1.3 72.2 - - - +
478C SER* 1.3 53.7 + - - +
479C VAL 2.5 19.3 + - - -
480C PHE* 2.8 13.2 + - - +
490C VAL* 4.2 11.7 - - - -
494C VAL* 4.1 2.4 - - - +
537C GLY* 3.2 15.7 - - - -
538C PRO* 3.7 20.4 - - - -
541C ALA* 3.0 30.7 - - - +
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Residues in contact with SER 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C PRO* 3.6 18.5 - - - +
474C LEU 2.7 15.2 + - - -
475C LYS* 2.4 27.8 + - - -
477C SER* 1.3 70.4 - - - +
479C VAL* 1.3 60.9 + - - +
480C PHE 3.7 0.4 - - - -
481C LYS* 3.8 8.8 + - - -
534C ASN 6.1 0.4 - - - -
537C GLY* 4.9 4.5 - - - -
538C PRO* 4.8 5.1 - - - +
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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
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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