Contacts of the helix formed by residues 494 - 500 (chain A) in PDB entry 5E3A
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 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLN* 5.3 0.5 + - - -
396A ASP* 5.8 4.5 - - + -
460A LEU* 5.5 1.8 - - - -
489A TYR* 3.9 7.3 - - - -
492A GLY 4.6 6.7 + - - +
493A GLU* 1.3 78.8 - - - +
495A TRP* 1.3 65.3 + - - +
496A ASP* 3.8 7.2 + - - +
497A SER* 2.5 42.0 + - - -
498A LYS* 3.1 15.1 + - - +
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Residues in contact with TRP 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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396A ASP* 3.9 22.1 + - - +
460A LEU* 4.9 6.0 - - + +
489A TYR* 3.3 22.9 - - - -
494A THR* 1.3 74.2 - - - +
496A ASP* 1.3 76.2 + - - +
499A PHE* 3.2 60.8 + + - +
503A ALA* 2.9 40.0 + - + +
506A TYR* 3.4 38.4 - + + -
507A GLU* 3.8 14.7 - - + +
629A LYS* 3.5 35.2 - - + -
1B TYR* 3.8 21.3 - + - +
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Residues in contact with ASP 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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196A TYR* 3.7 20.6 + - - -
317A SER* 2.9 19.6 + - - -
322A PHE* 4.7 3.6 - - - -
323A GLY 3.4 20.1 - - - +
324A SER* 4.1 12.4 - - - +
494A THR* 3.2 6.8 + - - +
495A TRP* 1.3 85.2 - - - +
497A SER* 1.3 61.2 + - - +
500A SER* 2.9 29.6 + - - -
503A ALA* 3.5 12.5 - - - +
804A K 2.9 15.2 - - - -
1B TYR* 5.9 2.1 - - - -
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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
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182A LYS* 4.8 9.0 + - - -
185A GLN* 3.6 33.8 - - - +
189A ASP* 3.6 25.7 + - - +
322A PHE* 4.5 7.3 - - - -
324A SER* 5.1 0.2 - - - -
493A GLU* 3.5 5.7 - - - -
494A THR* 2.5 47.5 + - - -
496A ASP* 1.3 79.1 - - - +
498A LYS* 1.3 62.8 + - - +
500A SER* 4.4 2.4 + - - -
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Residues in contact with LYS 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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182A LYS* 5.4 5.2 + - - +
488A TRP 4.7 6.3 + - - -
489A TYR* 3.5 24.0 - - + -
493A GLU* 3.4 38.6 + - + +
494A THR 3.1 13.0 + - - +
497A SER* 1.3 88.8 + - - +
499A PHE* 1.3 71.3 + - + +
500A SER* 3.7 2.8 + - - -
632A GLY* 3.2 28.9 + - - -
634A VAL* 3.4 31.1 - - + +
638A ARG* 5.2 0.3 + - - -
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Residues in contact with PHE 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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489A TYR* 3.7 11.0 - - - -
495A TRP* 3.2 54.0 + + + +
498A LYS* 1.3 87.2 - - + +
500A SER* 1.3 73.2 + - - +
501A THR 3.0 3.5 + - - -
502A ILE* 3.1 33.5 + - + +
503A ALA* 3.9 15.3 - - + +
506A TYR* 4.2 9.6 - + - -
628A LEU 3.8 13.7 - - - -
629A LYS* 4.4 1.6 - - - -
632A GLY* 4.0 15.0 - - - -
633A ASP 3.7 18.2 - - - -
634A VAL* 3.8 15.7 - - + -
637A GLY* 4.0 22.4 - - - -
638A ARG* 3.1 7.5 + - - -
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Residues in contact with SER 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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322A PHE* 3.0 49.4 - - - +
323A GLY* 3.9 8.7 - - - -
496A ASP 2.9 20.9 + - - -
497A SER 4.6 3.8 - - - -
498A LYS 4.5 2.7 + - - -
499A PHE* 1.3 73.4 - - - +
501A THR* 1.3 65.8 + - - +
503A ALA* 3.1 18.2 + - - +
504A SER 4.6 1.0 + - - -
638A ARG* 2.5 31.4 + - - -
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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