Contacts of the helix formed by residues 499 - 509 (chain N) 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 SER 499 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497N ARG* 4.0 17.9 - - - -
498N SER* 1.3 80.6 + - - +
500N ASP* 1.3 57.5 + - - +
501N ILE 3.2 2.7 - - - -
502N ILE* 2.7 38.6 + - - -
503N SER* 2.6 34.5 + - - -
548N ARG* 5.7 1.1 - - - +
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Residues in contact with ASP 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N ILE* 4.9 5.9 - - + +
404N ILE* 3.4 28.9 - - + +
405N LYS* 3.4 20.6 - - - +
408N ARG* 2.8 52.6 + - - +
414N MET* 5.8 0.3 - - - +
455N GLU* 6.1 0.9 - - + -
498N SER 2.9 11.7 + - - +
499N SER* 1.3 69.2 - - - +
501N ILE* 1.3 71.9 + - + +
503N SER* 4.0 2.1 + - - -
504N LEU* 2.9 34.2 + - - +
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Residues in contact with ILE 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N ILE* 6.3 0.4 - - + -
442N LEU* 4.9 18.2 - - + -
452N LEU* 5.1 1.6 - - - +
455N GLU* 3.5 35.0 - - + +
456N LEU* 4.1 3.4 - - + +
499N SER 2.8 3.6 + - - -
500N ASP* 1.3 88.8 - - + +
502N ILE* 1.3 58.8 + - - +
504N LEU* 2.9 34.4 - - + +
505N LEU* 3.1 25.5 - - + +
548N ARG* 3.4 54.0 - - - +
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Residues in contact with ILE 502 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499N SER* 2.7 28.8 + - - +
501N ILE* 1.3 71.2 - - - +
503N SER* 1.3 56.4 + - - +
505N LEU* 3.4 10.1 + - + +
506N VAL* 3.0 43.8 + - + +
547N LEU 5.7 0.2 - - - +
548N ARG* 4.0 48.5 - - + +
549N PHE* 4.4 19.5 - - + -
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Residues in contact with SER 503 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400N TYR* 4.2 2.5 + - - -
404N ILE* 4.6 12.5 - - - +
414N MET* 4.7 7.4 - - - +
417N LEU* 5.9 1.6 - - - +
425N ARG* 5.3 5.6 + - - -
496N ARG 5.5 0.9 - - - -
497N ARG 4.3 9.2 - - - -
498N SER 3.7 16.3 + - - -
499N SER* 2.6 19.6 + - - -
500N ASP* 4.0 5.4 + - - -
502N ILE* 1.3 70.4 - - - +
504N LEU* 1.3 57.5 + - - +
506N VAL* 4.4 7.4 - - - -
507N SER* 2.9 34.4 + - - -
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Residues in contact with LEU 504 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397N ILE* 3.8 20.2 - - + -
400N TYR* 4.6 8.2 - - + -
401N ILE* 3.7 48.7 - - + -
404N ILE* 4.7 6.9 - - + +
438N ILE* 4.6 15.9 - - + -
442N LEU* 6.4 1.3 - - + -
452N LEU* 6.0 4.0 - - + -
455N GLU* 6.4 0.2 - - + -
500N ASP 2.9 21.3 + - - +
501N ILE* 2.9 29.8 - - + +
503N SER* 1.3 75.8 + - - +
505N LEU* 1.3 63.0 + - + +
507N SER* 2.9 20.6 + - - -
508N ILE* 3.4 13.8 + - + +
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Residues in contact with LEU 505 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438N ILE* 4.6 9.0 - - + -
442N LEU* 4.8 15.7 - - + -
501N ILE* 3.1 28.0 - - + +
502N ILE* 3.4 11.6 + - + +
504N LEU* 1.3 79.7 - - + +
506N VAL* 1.3 66.0 + - + +
508N ILE* 3.3 22.9 - - - +
510N GLY* 3.3 14.9 - - - -
515N PHE* 3.8 39.9 - - + -
545N LEU* 4.8 11.7 - - + -
548N ARG* 5.5 2.7 - - + -
549N PHE* 4.0 31.0 - - + -
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Residues in contact with VAL 506 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425N ARG* 4.9 2.7 + - - +
429N ARG* 5.2 1.7 + - - -
502N ILE* 3.0 31.7 + - + +
503N SER* 4.4 6.1 - - - -
505N LEU* 1.3 73.9 - - + +
507N SER* 1.3 64.2 + - - +
509N TYR 4.3 0.2 - - - -
510N GLY* 3.4 33.0 + - - +
511N SER 5.1 4.9 - - - +
512N LYS* 6.2 1.6 - - + -
549N PHE* 5.1 10.8 - - + -
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Residues in contact with SER 507 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400N TYR* 2.9 34.8 + - - -
425N ARG* 3.3 48.7 - - - +
428N LEU* 5.7 0.2 - - - +
429N ARG* 3.7 14.0 + - - -
503N SER 2.9 18.6 + - - -
504N LEU 2.9 11.4 + - - -
506N VAL* 1.3 79.5 - - - +
508N ILE* 1.3 65.8 + - - +
509N TYR 3.5 0.5 + - - -
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Residues in contact with ILE 508 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397N ILE* 3.8 25.8 - - + -
400N TYR* 5.6 0.4 - - + -
425N ARG* 5.3 1.6 - - - +
428N LEU* 3.6 40.6 - - + -
429N ARG* 3.6 18.9 + - - +
434N THR* 4.3 3.1 - - - +
438N ILE* 3.5 24.5 - - + -
504N LEU* 3.4 13.7 - - + +
505N LEU* 3.3 17.5 - - - +
507N SER* 1.3 82.8 + - - +
509N TYR* 1.3 78.0 + - + +
515N PHE* 3.5 27.6 - - + -
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Residues in contact with TYR 509 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428N LEU 4.0 3.0 + - - -
429N ARG* 4.1 46.0 + - + +
432N GLU* 3.5 28.8 - - + +
434N THR* 2.6 28.7 + - - -
435N VAL* 3.5 46.5 + - + +
438N ILE* 4.2 0.7 - - + -
506N VAL 4.3 2.2 - - - -
507N SER 4.7 2.5 - - - -
508N ILE* 1.3 108.5 - - + +
510N GLY* 1.3 58.1 + - - +
514N LEU* 5.5 15.0 - - + -
515N PHE* 4.1 5.8 - + + -
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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