Contacts of the helix formed by residues 450 - 455 (chain J) in PDB entry 6GYS
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 450 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397J ARG* 3.4 25.4 - - - -
444J ASN 4.0 1.4 + - - -
445J ASN* 2.9 27.6 - - - +
447J HIS* 2.9 37.6 + - - +
448J ALA 3.2 3.9 - - - -
449J LYS* 1.3 78.9 - - - +
451J GLU* 1.3 65.2 + - - +
452J PHE* 3.2 4.9 - - - -
453J PHE* 3.2 23.6 + - - +
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Residues in contact with GLU 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J PRO* 5.3 10.3 - - + +
445J ASN 3.3 7.2 - - - -
446J PHE* 3.3 36.3 - - + +
447J HIS 3.4 5.3 + - - +
450J SER* 1.3 79.0 - - - +
452J PHE* 1.3 57.7 + - - +
454J ASN* 2.9 25.1 + - - +
455J ARG* 2.8 44.2 + - - +
497J PRO* 3.0 36.3 - - + +
499J ILE* 4.5 0.7 - - - +
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Residues in contact with PHE 452 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J PHE* 3.5 20.9 - + - -
121J ASN* 3.3 25.4 - - + -
122J LEU* 3.6 21.3 - - + -
173J TYR* 3.2 45.1 - + + +
175J PRO* 5.6 4.3 - - + +
394J ASN* 3.2 42.6 - - - -
398J PHE* 4.1 3.5 - + - -
449J LYS* 3.5 22.2 - - - -
450J SER* 4.3 1.8 - - - -
451J GLU* 1.3 76.2 + - - +
453J PHE* 1.3 77.2 + + - +
454J ASN 3.1 0.9 - - - -
455J ARG* 2.9 29.5 + - - +
456J HIS* 4.0 1.4 + - - +
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Residues in contact with PHE 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394J ASN* 3.3 22.0 - - - -
397J ARG* 3.3 47.1 - - + -
398J PHE* 3.5 33.2 - + + -
401J PHE* 3.2 44.1 - + + -
445J ASN* 3.4 29.8 - - + -
450J SER* 3.2 15.0 + - - +
451J GLU 3.2 0.2 - - - -
452J PHE* 1.3 100.3 - + - +
454J ASN* 1.3 58.5 + - - +
455J ARG 3.5 2.1 + - - -
456J HIS* 4.1 8.1 + - - +
459J VAL* 4.3 7.6 - - - +
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Residues in contact with ASN 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401J PHE* 5.0 0.5 - - - -
441J LEU 4.0 3.3 - - - +
442J ILE* 2.7 52.2 + - - +
445J ASN* 2.4 25.8 + - - +
446J PHE* 3.3 21.1 - - + -
451J GLU* 2.9 18.6 + - - +
453J PHE* 1.3 79.7 - - - +
455J ARG* 1.3 58.8 + - - +
456J HIS 3.7 1.3 - - - -
459J VAL* 4.4 8.0 - - - +
496J LEU* 3.9 14.4 - - + +
497J PRO* 5.1 0.3 - - - +
500J PHE* 3.3 22.8 - - - -
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Residues in contact with ARG 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J TYR* 2.4 61.7 + - + -
173J TYR* 2.8 34.4 + - + +
174J MET 2.6 19.4 + - - -
175J PRO* 3.5 18.8 - - - +
176J VAL* 4.1 6.7 - - - +
201J GLU* 5.5 3.4 - - - +
205J GLN* 3.7 4.8 + - - +
243J THR* 5.4 0.2 - - - -
244J THR* 5.4 0.2 - - - +
451J GLU* 2.8 30.9 + - - +
452J PHE* 2.9 16.7 + - - +
454J ASN* 1.3 83.7 - - - +
456J HIS* 1.3 60.8 + - - +
457J PRO* 4.2 1.9 - - - +
497J PRO* 6.0 1.4 - - - +
499J ILE* 3.5 37.8 - - + +
500J PHE* 3.6 10.5 - - - -
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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