Contacts of the helix formed by residues 493 - 501 (chain A) in PDB entry 4HXG
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 TYR 493 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A ILE* 3.6 4.6 - - - -
492A SER* 1.3 81.0 + - - +
494A TRP* 1.3 75.6 + - - +
495A LEU* 3.4 43.7 - - + +
496A THR* 3.3 20.5 + - + +
497A SER* 3.3 4.0 + - - -
522A TYR* 3.7 11.8 - - + +
523A ARG* 3.8 22.5 + - + +
526A SER* 3.4 11.7 - - - -
528A LEU* 4.1 21.5 - - + -
529A PHE* 3.6 24.9 - + - -
553A GLN* 3.0 26.9 + - - +
556A MET* 4.2 20.0 - - + -
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Residues in contact with TRP 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A THR* 3.7 20.9 - - + +
467A TYR* 4.3 17.3 - + - -
470A TYR* 3.6 19.0 - + - -
491A ILE* 3.7 33.7 - - + -
493A TYR* 1.3 71.7 - - - +
495A LEU* 1.3 60.5 + - - +
497A SER* 3.2 7.5 + - - -
498A TYR* 2.9 26.5 + - - +
507A PHE* 5.0 13.0 - + - -
508A ASP* 3.1 29.8 - - - +
511A VAL* 5.3 3.6 - - + -
512A ILE* 3.3 38.1 - - + +
521A ASN 4.8 0.2 - - - -
522A TYR* 3.6 21.9 - - + +
525A LEU* 3.3 31.6 + - + +
526A SER* 2.8 29.3 + - - +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A TYR* 3.4 38.4 - - + +
494A TRP* 1.3 79.7 - - - +
496A THR* 1.3 59.8 + - + +
498A TYR* 3.2 11.3 + - + +
499A ALA* 2.9 27.0 + - + +
516A PRO* 3.6 42.4 - - + +
517A LEU* 4.6 17.5 - - + +
522A TYR* 3.6 12.0 - - + -
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Residues in contact with THR 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A TYR* 3.3 27.8 + - + -
495A LEU* 1.3 75.7 - - + +
497A SER* 1.3 60.1 + - - +
498A TYR 3.2 0.2 - - - -
499A ALA* 4.1 7.0 - - - +
500A PHE* 2.8 40.2 + - - +
552A ASP* 2.8 18.7 + - - +
553A GLN* 2.7 29.8 + - - -
556A MET* 3.9 12.2 - - + +
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Residues in contact with SER 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 4.5 9.4 - - - +
493A TYR 3.3 9.3 + - - -
494A TRP* 3.2 25.9 + - - -
496A THR* 1.3 84.3 + - - +
498A TYR* 1.3 61.9 + - - +
500A PHE* 5.2 0.2 - - - -
501A SER* 2.6 38.1 + - - -
504A GLY* 3.4 0.7 - - - -
507A PHE* 5.7 0.2 - - - -
508A ASP* 2.7 20.2 + - - -
548A ARG 5.4 1.1 + - - -
550A PRO* 5.4 1.6 - - - -
553A GLN* 3.3 12.9 - - - +
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Residues in contact with TYR 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A TRP 2.9 12.5 + - - +
495A LEU* 3.3 17.9 - - + +
497A SER* 1.3 79.1 + - - +
499A ALA* 1.3 71.2 + - + +
500A PHE 3.7 0.2 + - - -
501A SER 4.7 1.4 + - - +
504A GLY* 3.4 30.9 - - - -
505A LEU* 3.4 46.7 + - + +
508A ASP* 3.5 21.0 + - + -
509A LYS* 4.4 13.9 + - + -
516A PRO* 3.7 40.9 - - + +
517A LEU* 5.3 11.4 - - + +
522A TYR* 4.1 5.8 - - + -
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A LEU* 2.9 18.0 + - + +
496A THR* 3.4 5.1 + - - +
498A TYR* 1.3 90.2 - - + +
500A PHE* 1.3 60.2 + - + +
501A SER 5.0 0.6 - - - +
505A LEU* 5.1 6.7 - - - +
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Residues in contact with PHE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TRP* 3.1 44.8 + + - -
496A THR* 2.8 26.4 + - - +
499A ALA* 1.3 74.6 - - - +
501A SER* 1.3 67.7 + - - +
550A PRO* 3.5 19.3 - - + -
551A LEU 5.5 0.4 - - - -
552A ASP* 3.5 33.2 - - + -
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Residues in contact with SER 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PRO* 4.9 3.3 - - - +
140A TRP* 4.0 0.8 + - - +
497A SER* 2.6 30.7 + - - -
498A TYR 4.7 1.7 - - - +
499A ALA 5.0 0.7 - - - +
500A PHE* 1.3 84.5 - - - +
502A ASP* 1.3 65.8 + - - +
503A ILE* 3.9 3.3 + - - +
504A GLY* 3.0 21.0 + - - -
505A LEU* 5.0 1.7 + - - +
508A ASP* 4.5 0.2 + - - -
547A TYR 3.4 6.1 - - - -
548A ARG 3.1 28.4 + - - -
550A PRO* 3.8 13.5 - - - -
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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