Contacts of the helix formed by residues 1757 - 1761 (chain A) in PDB entry 5MV9
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 LEU1757 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1717A PHE* 4.0 28.5 - - + -
1721A TYR* 3.5 14.4 - - + +
1722A PHE* 4.6 2.2 - - + -
1723A ARG* 4.1 2.2 - - - +
1755A ALA* 3.4 4.9 - - - +
1756A LEU* 1.3 75.6 - - - +
1758A LYS* 1.4 64.8 + - - +
1759A LYS* 4.2 11.2 - - + +
1760A LEU* 3.0 35.7 + - + +
1761A LEU* 3.9 3.3 + - - +
1808A PRO 4.2 4.7 - - - +
1811A ASP* 3.6 16.8 - - + +
1812A GLU* 3.0 42.8 + - - +
1815A VAL* 4.0 16.6 - - + -
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Residues in contact with LYS1758 (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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1719A TYR 5.3 5.5 + - - -
1720A ASP* 4.1 15.6 + - - +
1721A TYR* 2.8 21.2 + - - +
1722A PHE 3.7 15.8 + - - +
1723A ARG* 3.5 7.4 - - - +
1724A PRO* 3.6 26.2 - - - +
1757A LEU* 1.4 69.9 - - - +
1759A LYS* 1.3 56.2 + - - +
1761A LEU* 3.1 48.0 - - + +
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Residues in contact with LYS1759 (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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1721A TYR 4.7 0.4 + - - -
1757A LEU* 3.1 13.1 - - + +
1758A LYS* 1.3 77.5 - - - +
1760A LEU* 1.3 73.3 + - + +
1761A LEU 3.5 0.7 + - - -
1762A GLY* 4.5 3.5 + - - -
1763A SER* 3.8 19.5 + - - -
1766A LEU* 4.7 1.4 - - - +
1807A GLU* 5.7 1.1 - - - -
1808A PRO* 3.7 33.4 - - + +
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Residues in contact with LEU1760 (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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1755A ALA* 3.8 19.3 - - + -
1757A LEU* 3.0 35.5 + - + +
1759A LYS* 1.3 86.4 - - + +
1761A LEU* 1.4 61.8 - - - +
1762A GLY 3.3 1.8 - - - -
1763A SER* 3.1 17.1 + - - +
1766A LEU* 4.1 21.3 - - + -
1767A SER* 2.9 24.0 + - - +
1808A PRO* 3.7 43.5 - - + +
1809A LEU* 4.4 9.6 - - + -
1812A GLU* 3.8 20.2 - - + +
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Residues in contact with LEU1761 (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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1723A ARG* 3.6 36.3 - - + -
1724A PRO* 4.1 8.3 - - + -
1754A GLN* 3.8 27.4 + - + +
1755A ALA 5.8 0.7 - - - +
1757A LEU 3.9 3.4 + - - +
1758A LYS* 3.1 36.5 + - + +
1759A LYS 3.3 0.4 - - - -
1760A LEU* 1.4 75.9 - - - +
1762A GLY* 1.3 61.3 + - - +
1763A SER 4.8 1.0 - - - -
1764A GLU* 5.7 0.3 - - - -
1767A SER* 4.7 3.9 + - - -
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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