Contacts of the helix formed by residues 443 - 446 (chain V) in PDB entry 5IY8
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 VAL 443 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337V VAL* 4.5 4.9 - - + -
410V TYR* 4.5 4.3 - - - -
440V LEU* 4.1 14.1 - - + +
441V ASP 4.2 3.6 - - - -
442V GLU* 1.3 75.4 - - - +
444V HIS* 1.3 67.1 + - - +
445V THR 2.8 1.9 + - - -
446V ILE* 3.2 15.8 + - + +
447V PRO* 3.9 2.1 - - - +
465V GLY* 3.9 15.5 - - - -
466V LEU 2.9 24.8 + - - +
467V THR* 3.6 23.2 - - + -
480V LEU* 4.1 23.4 - - + +
484V ILE* 3.8 29.2 - - + -
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Residues in contact with HIS 444 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366V ASN* 6.3 0.2 - - - -
442V GLU* 3.4 33.7 + - + -
443V VAL* 1.3 80.7 - - - +
445V THR* 1.3 58.9 + - - +
447V PRO* 2.6 31.3 - - - +
448V ALA* 6.0 0.2 - - - +
467V THR* 3.0 20.1 + - - -
469V THR* 4.0 26.6 + - + +
470V LEU* 3.2 37.5 - - - +
471V VAL* 3.9 4.9 - - - +
472V ARG* 5.8 7.4 - - + -
480V LEU* 5.2 2.9 - - - -
613V THR* 5.3 8.3 + - + +
635V GLN* 5.4 3.2 + - - -
638V GLN* 5.3 1.3 - - - -
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Residues in contact with THR 445 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366V ASN* 4.8 7.6 + - + +
410V TYR* 3.7 36.6 - - + -
442V GLU* 2.7 30.1 + - - +
443V VAL 2.8 3.8 + - - -
444V HIS* 1.3 83.9 + - - +
446V ILE* 1.3 57.5 + - + -
447V PRO* 3.9 0.5 - - - +
448V ALA* 4.1 14.4 - - - +
451V PHE* 4.4 11.8 - - + +
22Y G 5.9 2.5 - - - +
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Residues in contact with ILE 446 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364V LEU* 4.9 0.2 - - + -
410V TYR* 3.6 31.6 - - + -
440V LEU* 4.1 20.9 - - + -
443V VAL* 3.2 16.7 + - + +
445V THR* 1.3 75.4 - - - +
447V PRO* 1.4 60.7 - - + +
448V ALA 3.1 10.2 + - - -
451V PHE* 3.3 34.8 - - + +
452V ARG* 3.2 19.2 + - - -
454V VAL* 4.2 15.7 - - + -
455V LEU* 3.7 19.7 - - + -
480V LEU* 4.6 1.6 - - + -
483V LEU* 4.3 9.2 - - + -
484V ILE* 4.2 15.9 - - + -
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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