Contacts of the helix formed by residues 482 - 487 (chain C) in PDB entry 5VOT
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 482 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751B LEU* 5.5 2.9 - - - -
755B GLU* 3.2 15.5 - - + +
480C THR* 3.8 21.4 + - + +
481C ILE* 1.3 79.7 - - - +
483C LEU* 1.3 59.7 + - - +
484C VAL* 3.3 15.8 - - - +
485C ARG* 3.1 27.1 + - - +
486C GLU* 2.9 31.7 + - - +
654C SER* 4.2 16.8 - - - +
657C GLU* 5.7 4.9 - - + +
730C LYS* 5.3 8.5 - - - +
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Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B LEU* 3.7 26.5 - - + +
751B LEU* 3.6 35.0 - - + +
752B LYS* 3.8 39.5 - - + -
755B GLU* 2.6 30.5 + - - +
482C THR* 1.3 71.4 - - - +
484C VAL* 1.3 58.1 + - + +
486C GLU* 2.9 9.2 + - + +
487C GLU* 2.8 47.6 + - + +
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Residues in contact with VAL 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B GLU* 5.0 6.5 - - - +
460C TRP* 4.2 19.9 - - + -
482C THR* 3.3 16.8 - - - +
483C LEU* 1.3 80.1 - - + +
485C ARG* 1.3 68.6 + - + +
487C GLU* 3.2 37.2 + - - +
488C VAL* 3.8 11.4 + - - +
657C GLU* 4.7 27.4 - - + +
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Residues in contact with ARG 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C TYR* 3.6 22.4 - - - +
451C GLY 3.7 16.9 + - - -
460C TRP* 5.0 11.4 - - + -
464C VAL* 4.9 11.0 - - + +
479C LEU* 3.3 18.6 - - - +
480C THR* 2.2 61.6 + - - +
482C THR* 3.1 21.2 + - - +
483C LEU 3.1 0.8 - - - -
484C VAL* 1.3 80.9 - - + +
486C GLU* 1.3 62.8 + - - +
488C VAL* 3.2 22.4 - - + +
489C ILE* 3.3 4.7 + - + +
491C PHE* 3.3 30.1 - - + -
654C SER* 3.3 34.6 + - - +
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Residues in contact with GLU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LYS* 4.1 14.6 + - - +
747B ASN* 5.5 1.6 + - - -
748B LEU* 5.1 8.8 - - + +
751B LEU* 3.5 31.7 - - + +
481C ILE* 3.2 14.4 - - + +
482C THR 2.9 18.0 + - - +
483C LEU* 3.2 10.8 - - + +
485C ARG* 1.3 77.5 - - - +
487C GLU* 1.3 56.5 + - - +
488C VAL 2.9 3.5 + - - -
489C ILE 2.7 24.8 + - - +
490C ASP* 4.5 2.1 - - - +
491C PHE* 3.0 42.9 + - + +
738C LYS* 3.8 6.6 + - - -
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Residues in contact with GLU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748B LEU* 5.7 6.3 - - + -
453C ARG* 5.6 3.6 + - - -
483C LEU* 2.8 40.6 + - + +
484C VAL* 3.4 32.5 - - - +
485C ARG 3.2 0.6 - - - -
486C GLU* 1.3 75.2 - - - +
488C VAL* 1.3 59.2 + - + +
738C LYS* 2.6 22.8 + - - +
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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