Contacts of the helix formed by residues 468 - 484 (chain B) in PDB entry 5FZT
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 GLU 468 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492A LEU* 4.3 11.0 - - - +
467B PRO* 1.3 83.7 - - + +
469B LEU* 1.3 66.9 + - - +
470B ASP* 3.3 7.2 - - + +
471B ASP* 3.1 23.1 + - - +
472B ILE* 3.1 25.1 + - - +
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491A VAL* 5.6 1.1 - - + -
1492A LEU* 4.0 22.2 - - + +
1495A ALA* 4.2 17.5 - - + -
1540A VAL* 4.6 11.9 - - + -
1543A ILE* 3.9 23.3 - - + +
1544A LYS* 3.7 34.3 - - + +
1547A ASP* 3.7 34.5 - - + +
468B GLU* 1.3 75.0 + - - +
470B ASP* 1.3 63.6 + - - +
472B ILE* 3.2 6.3 + - + +
473B LEU* 3.0 21.7 + - - +
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Residues in contact with ASP 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A LYS* 3.1 28.3 + - - +
468B GLU* 3.3 5.3 - - + +
469B LEU* 1.3 77.4 - - - +
471B ASP* 1.3 67.9 + - - +
473B LEU* 3.3 8.6 + - - +
474B TYR* 3.1 36.3 + - + -
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Residues in contact with ASP 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B PRO* 5.1 6.4 - - + +
468B GLU* 3.1 29.4 + - - +
470B ASP* 1.3 78.3 - - - +
472B ILE* 1.3 65.2 + - - +
474B TYR* 3.4 14.6 + - - +
475B HIS* 3.0 23.7 + - - +
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Residues in contact with ILE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1492A LEU* 3.9 15.3 - - + -
1495A ALA* 3.9 13.0 - - + +
1496A THR* 3.3 37.7 - - - +
1499A ALA* 3.6 27.8 - - + -
1540A VAL* 4.4 14.4 - - + -
467B PRO* 4.0 18.8 - - + -
468B GLU 3.1 15.7 + - - +
469B LEU* 3.2 8.5 + - + +
471B ASP* 1.3 75.6 - - - +
473B LEU* 1.3 61.8 + - - +
475B HIS* 3.2 6.3 + - - +
476B VAL* 3.1 25.7 + - + +
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537A ALA 4.6 0.2 - - - +
1540A VAL* 3.6 28.7 - - + +
1541A LYS* 4.2 17.9 - - + +
1544A LYS* 3.7 37.9 - - + -
469B LEU 3.0 12.9 + - - +
470B ASP* 3.6 9.6 - - - +
472B ILE* 1.3 74.7 - - - +
474B TYR* 1.3 68.3 + - + +
475B HIS 3.2 0.2 + - - -
476B VAL* 3.4 4.1 + - + +
477B LYS* 3.0 51.2 + - + +
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Residues in contact with TYR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B ASP* 3.1 34.8 + - + -
471B ASP* 3.4 15.5 + - - +
473B LEU* 1.3 76.3 - - + +
475B HIS* 1.3 57.0 + - - +
477B LYS* 3.3 21.9 + - + +
478B GLY* 2.9 26.9 + - - -
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Residues in contact with HIS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A ALA* 4.6 9.6 + - + -
1503A SER* 2.7 29.6 + - - -
471B ASP 3.0 17.7 + - - +
472B ILE* 3.6 6.7 - - - +
473B LEU 3.2 0.2 - - - -
474B TYR* 1.3 77.6 - - - +
476B VAL* 1.3 72.4 + - + +
478B GLY* 3.2 2.6 + - - -
479B MET* 2.9 49.9 + - + +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A ALA* 3.8 28.9 - - + +
1502A THR* 5.2 0.7 - - - +
1503A SER* 5.6 0.9 - - - +
1533A ALA* 4.9 1.6 - - - +
1536A THR* 3.9 23.1 - - + -
1537A ALA* 4.0 23.6 - - - +
1540A VAL* 4.0 20.2 - - + -
472B ILE* 3.1 17.3 + - + +
473B LEU* 3.5 13.2 - - + +
475B HIS* 1.3 83.6 - - + +
477B LYS* 1.3 59.4 - - - +
479B MET* 3.7 6.1 - - - +
480B GLN* 3.0 28.9 + - - +
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537A ALA* 4.8 2.2 - - + -
1541A LYS* 4.4 25.1 - - - +
473B LEU* 3.0 48.7 + - + +
474B TYR* 3.8 24.6 - - + +
476B VAL* 1.3 79.9 - - + +
478B GLY* 1.3 60.5 + - - +
480B GLN* 3.4 16.1 + - - +
481B ARG* 3.1 42.2 + - - +
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Residues in contact with GLY 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B TYR 2.9 14.5 + - - -
475B HIS 3.2 2.9 + - - -
477B LYS* 1.3 74.7 - - - +
479B MET* 1.3 64.9 + - - +
481B ARG* 3.4 12.6 + - - +
482B ILE* 3.1 28.0 + - - +
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503A SER* 3.1 43.1 - - - +
1506A CYS* 5.2 7.4 - - - -
1533A ALA* 4.9 4.0 - - + -
475B HIS* 2.9 39.7 + - + +
476B VAL* 3.7 9.4 - - - +
478B GLY* 1.3 77.2 - - - +
480B GLN* 1.3 51.7 + - - +
482B ILE* 3.1 10.9 + - - +
483B VAL* 2.8 55.3 + - + +
486B TRP* 6.1 2.5 - - - -
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Residues in contact with GLN 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1533A ALA* 4.1 21.0 - - - +
1534A ASN* 3.2 27.1 + - - +
1537A ALA* 3.4 25.8 - - + +
1538A ASN* 5.0 5.3 + - - +
1541A LYS* 5.1 6.2 + - - +
476B VAL 3.0 17.6 + - - +
477B LYS* 3.5 15.6 - - - +
478B GLY 3.3 0.2 - - - -
479B MET* 1.3 76.8 - - - +
481B ARG* 1.3 65.3 + - + +
484B ASN* 3.1 46.1 + - - +
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Residues in contact with ARG 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B LYS* 3.1 32.8 + - - +
478B GLY* 3.7 13.0 - - - +
479B MET 3.3 0.4 - - - -
480B GLN* 1.3 80.4 - - + +
482B ILE* 1.3 67.3 + - + +
484B ASN* 3.8 6.7 + - - +
485B GLN* 3.7 19.8 + - - +
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Residues in contact with ILE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B GLY 3.1 14.2 + - - +
479B MET* 3.1 15.3 + - - +
481B ARG* 1.3 77.3 - - + +
483B VAL* 1.3 66.2 + - + +
485B GLN* 3.1 17.6 + - + +
486B TRP* 3.5 32.6 - - + +
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1506A CYS* 4.2 15.0 - - + -
1529A ALA* 3.7 32.8 - - + +
1530A LYS* 3.4 18.6 - - + +
1533A ALA* 4.1 9.4 - - + -
479B MET* 2.8 37.9 + - + +
480B GLN 4.3 0.2 - - - +
482B ILE* 1.3 74.4 - - + +
484B ASN* 1.3 61.3 + - - +
485B GLN 3.1 1.2 + - - -
486B TRP* 3.2 53.2 + - + +
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Residues in contact with ASN 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530A LYS* 3.8 30.8 + - - +
1533A ALA* 6.0 0.7 - - - -
1534A ASN* 3.0 39.6 + - - -
480B GLN* 3.1 31.9 + - - +
481B ARG* 4.3 5.7 - - - +
482B ILE 3.2 0.6 - - - -
483B VAL* 1.3 76.2 - - - +
485B GLN* 1.3 71.5 + - - +
486B TRP 3.4 0.4 - - - -
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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