Contacts of the helix formed by residues 480 - 490 (chain H) in PDB entry 5G04
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 ASN 480 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475H ALA* 2.9 28.8 + - + +
476H LEU* 5.2 0.4 - - - -
478H SER* 3.6 10.0 + - - +
479H TYR* 2.1 40.5 + - - +
481H CYS* 1.3 64.0 + - - +
482H LYS* 4.0 4.9 - - - +
483H GLU* 3.0 55.2 - - + +
484H ALA* 3.2 23.8 + - - +
667H GLN* 5.8 1.1 - - - -
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Residues in contact with CYS 481 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476H LEU* 5.8 1.8 - - - +
479H TYR* 3.5 14.2 + - - +
480H ASN* 1.3 73.8 - - - +
482H LYS* 1.3 59.2 + - - +
484H ALA* 3.9 4.8 - - - +
485H ILE* 3.1 30.1 + - - +
508H ALA* 3.5 15.0 - - - +
511H GLU* 3.7 18.6 - - - -
512H LEU* 3.3 51.8 - - + -
665H ASN* 5.3 1.1 - - - -
667H GLN* 3.3 20.9 + - - +
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Residues in contact with LYS 482 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480H ASN* 3.4 5.2 - - - +
481H CYS* 1.3 74.8 - - - +
483H GLU* 1.3 65.7 + - + +
484H ALA 3.2 1.3 - - - -
485H ILE* 3.4 8.1 + - + +
486H ASN* 3.1 24.8 + - - +
512H LEU* 4.0 31.2 - - + +
514H GLU* 4.2 10.8 + - - -
667H GLN* 5.3 3.6 - - - +
698H ILE 4.5 7.7 + - - -
699H ASP* 3.6 22.0 + - - -
700H PRO* 5.7 3.2 - - - +
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Residues in contact with GLU 483 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475H ALA* 5.0 6.4 - - + +
480H ASN* 3.0 39.5 - - + +
482H LYS* 1.3 76.9 - - + +
484H ALA* 1.3 53.2 + - - +
486H ASN* 3.3 5.0 + - - +
487H ILE* 2.7 47.8 + - + +
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Residues in contact with ALA 484 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472H GLY* 3.7 24.9 - - - +
475H ALA* 4.1 5.3 - - + +
476H LEU* 3.9 22.2 - - + +
480H ASN 3.2 19.9 + - - +
481H CYS* 3.9 5.6 - - - +
483H GLU* 1.3 73.2 - - - +
485H ILE* 1.3 65.3 + - - +
487H ILE* 3.3 4.4 + - - +
488H LEU* 2.9 33.8 + - + +
508H ALA* 4.8 3.8 - - + -
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Residues in contact with ILE 485 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481H CYS 3.1 17.9 - - - +
482H LYS* 3.4 10.7 + - + +
484H ALA* 1.3 77.3 - - - +
486H ASN* 1.3 64.9 + - + +
488H LEU* 3.4 5.1 + - - +
489H SER* 3.2 32.3 + - - +
505H ILE* 3.4 44.7 - - + +
508H ALA* 3.7 13.2 - - + -
509H TYR* 3.5 46.2 - - + +
512H LEU* 4.8 3.6 - - + -
108X LYS* 5.3 7.6 - - - +
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Residues in contact with ASN 486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482H LYS 3.1 14.1 + - - +
483H GLU* 3.8 4.9 - - - +
485H ILE* 1.3 80.0 - - + +
487H ILE* 1.3 68.9 + - + +
489H SER* 3.3 14.5 + - - -
490H HIS* 3.2 37.9 + - - -
108X LYS* 5.3 7.1 + - - +
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Residues in contact with ILE 487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468H GLU* 3.5 27.4 - - + +
471H LYS* 4.0 17.9 - - + -
472H GLY* 3.6 21.3 - - - +
483H GLU* 2.7 30.3 + - + +
484H ALA* 3.9 2.9 - - - +
486H ASN* 1.3 76.8 - - + +
488H LEU* 1.3 62.3 + - - +
489H SER 3.4 0.5 + - - -
490H HIS* 3.4 30.1 + - + +
491H LEU* 4.3 5.9 - - - +
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Residues in contact with LEU 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469H MET* 4.6 21.8 - - + +
472H GLY* 4.7 10.8 - - - -
473H TYR 5.4 0.4 - - - +
476H LEU* 4.8 9.0 - - + -
484H ALA* 2.9 25.2 + - + +
485H ILE* 3.9 4.3 - - - +
487H ILE* 1.3 74.4 - - - +
489H SER* 1.3 64.2 + - - +
490H HIS 3.2 0.2 - - - -
491H LEU* 3.2 39.5 + - + +
496H TYR* 4.3 7.0 - - - -
500H TRP* 4.8 4.3 - - + -
501H VAL* 3.8 21.9 - - + +
504H GLN* 4.0 21.8 - - + -
505H ILE* 3.8 32.5 - - + +
508H ALA* 5.7 0.4 - - + -
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Residues in contact with SER 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485H ILE* 3.2 21.4 + - - +
486H ASN* 3.8 8.3 - - - -
487H ILE 3.3 0.6 - - - -
488H LEU* 1.3 78.7 - - - +
490H HIS* 1.3 60.4 + - - +
491H LEU 3.1 1.0 - - - +
496H TYR* 4.0 12.0 - - - -
505H ILE* 5.3 2.6 - - - +
105X GLN* 2.9 41.3 + - - +
108X LYS* 3.9 31.1 + - - -
109X ALA 4.2 8.1 + - - -
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Residues in contact with HIS 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468H GLU* 6.3 2.2 - - + -
486H ASN* 3.2 45.8 + - - -
487H ILE* 3.4 25.2 + - + +
488H LEU 3.2 1.2 - - - -
489H SER* 1.3 75.4 - - - +
491H LEU* 1.3 65.0 + - - +
492H PRO* 3.7 3.8 - - - +
108X LYS* 3.9 22.0 + - + +
109X ALA* 4.5 16.4 - - - +
110X LEU* 6.2 0.6 - - - +
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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