Contacts of the helix formed by residues 458 - 463 (chain x) in PDB entry 5GJQ
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 458 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444x ASP 4.5 2.7 - - - +
445x GLU* 6.3 1.3 - - + -
446x TRP* 4.4 0.7 - - - -
457x VAL* 1.3 79.4 - - - +
459x PRO* 1.3 67.1 - - + +
460x GLU* 3.9 16.1 - - - +
461x ASP* 2.6 60.1 + - - +
462x ILE* 3.0 7.8 + - - +
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Residues in contact with PRO 459 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350x LEU* 4.7 12.6 - - + -
444x ASP* 2.9 34.3 - - - +
446x TRP* 4.2 21.0 - - + -
458x THR* 1.3 85.2 - - - +
460x GLU* 1.3 65.4 + - - +
462x ILE* 2.5 43.2 + - + +
463x LEU* 3.0 17.9 + - + +
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Residues in contact with GLU 460 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458x THR* 3.2 15.5 + - - +
459x PRO* 1.3 88.8 - - - +
461x ASP* 1.3 61.1 - - - +
463x LEU* 3.6 15.1 + - - +
464x ARG* 3.2 34.9 + - - +
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Residues in contact with ASP 461 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438x TRP* 6.0 3.6 - - + -
457x VAL* 3.9 18.2 - - + +
458x THR* 2.6 50.0 + - - +
460x GLU* 1.3 72.4 - - - +
462x ILE* 1.3 62.6 + - - +
464x ARG* 3.2 47.1 + - - +
465x LEU* 4.4 3.1 + - - +
471x TRP* 4.8 4.3 + - - -
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Residues in contact with ILE 462 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348x PHE* 4.2 10.9 - - + -
350x LEU* 5.0 2.2 - - + -
419x LEU* 4.7 5.4 - - + -
422x VAL* 4.4 11.0 - - + -
438x TRP* 4.0 20.4 - - + -
446x TRP* 2.9 54.7 - - + +
457x VAL* 3.8 17.5 - - + -
458x THR 3.0 6.0 + - - +
459x PRO* 2.5 23.3 + - + +
461x ASP* 1.3 67.7 - - - +
463x LEU* 1.3 57.5 + - + +
464x ARG 2.6 17.4 + - - -
465x LEU* 2.9 39.9 + - + +
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Residues in contact with LEU 463 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347x LYS* 5.1 16.4 - - + +
348x PHE* 4.1 27.1 - - + +
350x LEU* 3.4 49.1 - - + -
459x PRO 3.0 31.5 + - - +
460x GLU* 3.6 10.7 + - - +
461x ASP 3.3 0.8 - - - -
462x ILE* 1.3 77.8 - - + +
464x ARG* 1.3 58.1 + - - +
466x SER* 2.7 24.2 + - - +
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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