Contacts of the helix formed by residues 499 - 504 (chain B) in PDB entry 4Y5U
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 TRP 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381B GLU* 4.0 24.6 + - + -
421B ASN* 5.2 0.7 - - - -
424B ALA* 3.5 43.5 - - + -
425B THR* 3.7 16.6 - - + -
428B TRP* 3.5 44.3 - + + -
444B GLU* 3.1 34.3 + - + +
498B SER* 1.3 73.4 - - - +
500B SER* 1.3 65.5 + - - +
502B PHE* 3.7 18.8 - + - -
503B ASN* 3.1 33.4 + - + -
504B LYS* 3.6 26.1 + - + +
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B SER* 3.2 8.4 - - - -
499B TRP* 1.3 78.1 - - - +
501B GLN* 1.3 64.4 + - - +
504B LYS* 3.0 25.0 + - - +
505B GLU* 2.7 50.6 + - - +
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Residues in contact with GLN 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B ILE* 3.7 32.7 + - + +
482B PHE* 3.6 29.1 - - - +
495B ARG* 5.4 2.2 - - - +
496B SER 3.5 4.9 + - - +
497B VAL* 3.2 13.0 - - + -
498B SER* 2.8 39.7 + - - +
499B TRP 3.4 0.2 - - - -
500B SER* 1.3 78.4 - - - +
502B PHE* 1.3 60.0 + - - +
505B GLU* 4.1 28.6 - - - +
507B LEU* 5.4 1.9 - - - +
514B PHE* 3.8 7.3 - - - +
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Residues in contact with PHE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ALA* 4.1 13.5 - - + -
427B LEU* 4.0 17.0 - - + -
428B TRP* 3.8 16.6 - + + -
451B MET* 3.6 25.6 - - + -
455B LEU* 4.5 4.5 - - + -
481B ILE* 4.2 8.9 - - + +
497B VAL* 5.2 0.9 - - + -
498B SER 3.2 15.3 + - - +
499B TRP* 3.7 33.2 - + - +
501B GLN* 1.3 80.5 - - - +
503B ASN* 1.3 56.9 + - + +
504B LYS 3.8 0.2 - - - -
513B THR* 4.8 0.4 - - - -
514B PHE* 3.6 28.8 + + - +
515B TRP* 3.1 66.5 + + + +
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Residues in contact with ASN 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B ASN* 4.4 3.7 + - - +
421B ASN* 3.3 30.7 + - - +
424B ALA* 3.1 27.5 - - - +
499B TRP* 3.1 31.6 + - + -
502B PHE* 1.3 81.1 - - + +
504B LYS* 1.3 69.3 + - - +
513B THR* 3.1 32.7 + - - +
515B TRP* 3.2 18.0 - - - +
516B GLN* 5.0 0.5 - - - +
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Residues in contact with LYS 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLU* 3.2 21.8 + - - +
421B ASN* 4.4 11.6 + - - +
499B TRP* 3.6 40.2 - - + +
500B SER* 3.0 26.8 + - - +
502B PHE 3.8 0.4 - - - -
503B ASN* 1.3 88.8 + - + +
505B GLU* 1.3 59.9 + - - +
506B ILE* 3.7 5.6 + - - +
513B THR* 4.1 4.7 - - - +
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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