Contacts of the helix formed by residues 480 - 486 (chain B) in PDB entry 5C16
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 ARG 480 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B THR* 4.0 15.6 - - - +
442B TRP* 3.6 50.1 + - + +
443B ASP* 5.5 0.4 + - - -
478B GLY 3.7 10.1 - - - +
479B HIS* 1.3 75.9 + - - +
481B PHE* 1.3 55.4 + - - +
483B LEU* 3.9 26.3 - - + +
484B ARG* 2.9 38.3 + - + +
544B ASN* 3.0 55.4 + - - +
545B CYS* 5.3 1.6 - - - +
548B GLN* 5.1 4.4 - - - +
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Residues in contact with PHE 481 (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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474B TRP* 3.3 50.9 - + + -
475B ILE* 3.7 16.8 - - + -
479B HIS* 3.0 45.6 + + + -
480B ARG* 1.3 70.6 - - - +
482B ALA* 1.3 62.8 + - - +
484B ARG* 4.5 2.9 - - - +
485B VAL* 2.9 32.6 + - + +
487B HIS* 4.2 0.8 + - - +
501B PHE* 3.8 23.3 - + + -
533B LEU* 4.0 13.0 - - + -
541B PHE* 3.3 53.4 - + + +
543B CYS 3.6 8.0 + - - +
544B ASN* 3.5 1.0 + - - -
549B ARG* 5.1 4.7 - - - -
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 6.5 0.7 - - + -
481B PHE* 1.3 77.2 - - - +
483B LEU* 1.3 57.5 + - - +
486B GLY* 2.8 30.3 + - - -
487B HIS* 3.5 24.3 + - + -
543B CYS* 3.2 27.6 + - - +
544B ASN* 3.1 15.4 + - - +
548B GLN* 5.0 0.9 - - - +
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ARG* 3.8 26.2 - - + +
482B ALA* 1.3 77.9 - - - +
484B ARG* 1.3 86.0 + - - +
485B VAL 3.3 0.3 + - - -
486B GLY* 3.8 1.8 + - - -
494B ASP* 3.9 12.9 - - - +
496B ASP* 3.7 36.0 - - + +
497B ARG* 3.6 16.5 + - - +
544B ASN* 3.1 23.3 + - - +
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Residues in contact with ARG 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 4.0 15.8 - - - +
442B TRP* 3.8 15.6 - - - +
443B ASP* 2.8 40.3 + - - -
479B HIS* 3.8 22.9 - - + +
480B ARG* 2.9 32.6 + - + +
481B PHE* 4.1 2.5 - - - +
483B LEU* 1.3 93.9 - - - +
485B VAL* 1.3 62.6 + - + +
496B ASP* 2.9 36.8 + - - -
497B ARG* 3.2 7.8 - - - +
498B SER* 3.2 49.0 + - - +
500B ILE* 4.5 2.5 - - - -
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Residues in contact with VAL 485 (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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177B LYS* 3.3 21.7 + - - +
479B HIS* 6.3 0.2 - - - +
481B PHE* 2.9 21.9 + - + +
484B ARG* 1.3 83.2 - - + +
486B GLY* 1.3 58.9 + - - +
487B HIS* 3.4 27.1 - - + +
497B ARG* 4.0 10.3 - - - -
498B SER 5.7 1.1 - - - +
501B PHE* 6.5 0.4 - - + -
533B LEU* 3.8 33.2 - - + +
534B TYR* 3.4 33.8 - - + -
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Residues in contact with GLY 486 (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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177B LYS* 3.9 9.0 + - - -
482B ALA 2.8 17.4 + - - -
483B LEU 3.8 3.1 + - - -
484B ARG 3.7 0.8 - - - -
485B VAL* 1.3 78.4 - - - +
487B HIS* 1.3 64.9 - - - +
488B GLY 3.4 0.7 + - - -
489B ASN* 3.3 16.4 + - - +
497B ARG* 3.4 31.0 + - - -
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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
------------------------------------------------------------
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