Contacts of the helix formed by residues 482 - 487 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A THR* 3.8 21.8 + - + +
481A ILE* 1.3 81.0 - - - +
483A LEU* 1.3 60.7 + - - +
484A VAL* 3.2 15.8 - - - +
485A ARG* 3.1 26.1 + - - +
486A GLU* 2.9 32.0 + - - +
654A SER* 4.2 16.2 - - - +
657A GLU* 5.8 5.6 - - + -
730A LYS* 5.3 8.5 - - + +
751D LEU* 5.5 2.2 - - - -
755D GLU* 3.2 15.0 - - + +
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Residues in contact with LEU 483 (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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482A THR* 1.3 71.4 - - - +
484A VAL* 1.3 58.4 + - + +
486A GLU* 2.9 9.5 + - + +
487A GLU* 2.8 49.0 + - + +
748D LEU* 3.7 27.1 - - + +
751D LEU* 3.6 33.6 - - + +
752D LYS* 3.8 40.6 - - + -
755D GLU* 2.6 31.4 + - + +
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A TRP* 4.2 21.2 - - + -
482A THR* 3.2 16.2 - - - +
483A LEU* 1.3 78.3 - - + +
485A ARG* 1.3 69.1 + - + +
487A GLU* 3.3 36.8 + - - +
488A VAL* 3.8 11.3 + - - +
657A GLU* 4.7 27.4 - - + +
755D GLU* 5.0 6.1 - - - +
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Residues in contact with ARG 485 (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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450A TYR* 3.6 21.6 - - - +
451A GLY 3.8 17.1 + - - -
460A TRP* 5.0 11.6 - - + -
464A VAL* 4.9 11.0 - - + +
479A LEU* 3.3 18.5 - - - +
480A THR* 2.2 61.3 + - - +
482A THR* 3.1 22.5 + - - +
484A VAL* 1.3 80.9 - - + +
486A GLU* 1.3 64.3 + - - +
488A VAL* 3.2 21.6 - - - +
489A ILE* 3.3 7.9 + - + +
491A PHE* 3.4 26.5 - - + -
654A SER* 3.3 35.0 - - - +
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Residues in contact with GLU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 3.2 15.0 - - + +
482A THR 2.9 18.1 + - - +
483A LEU* 2.9 11.6 + - + +
485A ARG* 1.3 78.1 - - - +
487A GLU* 1.3 57.0 + - - +
488A VAL 2.9 3.9 + - - -
489A ILE 2.7 24.5 + - - +
490A ASP* 4.5 1.9 - - - +
491A PHE* 3.0 43.0 + - + +
738A LYS* 3.8 6.2 + - - -
493D LYS* 4.1 15.4 + - - +
747D ASN* 5.5 1.4 + - - -
748D LEU* 5.1 8.7 - - + +
751D LEU* 3.5 29.1 - - + +
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Residues in contact with GLU 487 (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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453A ARG* 5.6 3.8 + - - -
483A LEU* 2.8 40.5 + - + +
484A VAL* 3.4 32.9 - - - +
485A ARG 3.2 1.0 - - - -
486A GLU* 1.3 74.6 - - - +
488A VAL* 1.3 59.7 + - + +
738A LYS* 2.6 22.2 + - - +
748D LEU* 5.7 6.3 - - + -
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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