Contacts of the helix formed by residues 836 - 840 (chain A) in PDB entry 3LMG
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 836 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A PHE* 3.9 29.4 - - + -
723A LYS* 4.8 7.2 - - + +
725A ILE* 3.8 26.2 - - + -
744A ILE* 4.8 0.7 - - + -
766A LEU* 4.3 18.6 - - + -
813A HIS 4.6 0.2 + - - -
815A ASN* 6.3 0.2 - - - +
833A ASP* 3.6 41.6 + - - +
834A PHE 3.2 4.0 + - - +
835A GLY* 1.3 77.9 - - - +
837A ALA* 1.3 63.2 + - - +
839A LEU* 2.9 27.6 + - + +
840A LEU* 4.0 5.6 - - + +
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Residues in contact with ALA 837 (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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701A PHE* 3.7 35.4 - - + -
813A HIS 5.1 0.9 + - - +
814A ARG* 3.7 50.3 + - + +
815A ASN* 5.5 1.5 - - + +
835A GLY* 3.2 0.8 - - - -
836A VAL* 1.3 79.1 - - - +
838A ASP* 1.3 56.8 + - - +
839A LEU 3.1 4.4 + - - -
840A LEU* 3.4 22.8 + - - +
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Residues in contact with ASP 838 (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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740A HIS* 3.6 38.2 - - + +
812A VAL* 4.8 14.0 - - - +
814A ARG* 2.7 35.4 + - - +
835A GLY* 3.3 3.6 + - - +
836A VAL 3.2 1.2 - - - -
837A ALA* 1.3 75.7 - - - +
839A LEU* 1.3 60.2 + - - +
840A LEU 3.3 4.7 - - - +
869A TYR* 5.9 0.5 - - - +
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Residues in contact with LEU 839 (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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725A ILE* 4.0 20.6 - - + -
734A PHE* 4.1 20.1 - - + -
738A THR* 4.6 4.7 - - + +
740A HIS* 4.0 14.6 - - + -
741A MET* 3.5 33.4 - - + -
744A ILE* 4.4 9.4 - - + -
764A LEU* 3.8 22.9 - - + -
766A LEU* 4.3 9.6 - - + -
835A GLY 4.1 7.0 - - - +
836A VAL* 2.9 25.5 + - - +
838A ASP* 1.3 78.8 - - - +
840A LEU* 1.3 63.5 + - + +
841A PRO* 4.4 3.3 - - - +
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Residues in contact with LEU 840 (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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701A PHE* 3.5 46.9 - - + +
725A ILE* 3.8 20.2 - - + -
726A GLU 3.5 25.4 - - - +
727A ASP* 4.6 9.4 - - - +
728A LYS* 6.2 1.3 - - + -
734A PHE* 4.1 9.6 - - + -
814A ARG* 5.6 1.0 + - - -
836A VAL 4.0 11.2 - - - +
837A ALA 3.4 15.3 + - - +
838A ASP* 4.5 3.6 - - - -
839A LEU* 1.3 83.3 - - + +
841A PRO* 1.4 77.1 - - + +
842A PRO* 3.7 2.6 - - - +
843A ASP* 6.3 0.7 - - + -
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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