Contacts of the helix formed by residues 835 - 840 (chain B) 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 GLY 835 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740B HIS* 2.9 27.2 + - - -
744B ILE* 3.6 14.8 - - - -
811B MET* 3.9 13.7 - - - -
812B VAL 4.1 7.5 + - - -
813B HIS 3.5 12.7 + - - -
834B PHE* 1.3 70.9 - - - +
836B VAL* 1.3 63.5 + - - +
837B ALA 3.3 2.7 - - - -
838B ASP* 3.2 9.4 + - - -
839B LEU* 3.3 4.3 - - - +
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Residues in contact with VAL 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B PHE* 3.7 33.7 - - + -
723B LYS* 4.8 5.8 - - + +
725B ILE* 3.8 25.8 - - + -
744B ILE* 4.1 0.4 - - + +
766B LEU* 4.3 17.7 - - + -
813B HIS 4.9 0.2 + - - -
833B ASP* 3.5 42.9 + - + +
834B PHE 3.1 4.4 + - - +
835B GLY* 1.3 77.4 - - - +
837B ALA* 1.3 62.6 + - - +
839B LEU* 3.0 28.7 + - - +
840B LEU* 4.3 5.2 + - + +
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Residues in contact with ALA 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B PHE* 3.5 38.3 - - + -
813B HIS 5.0 1.7 + - - +
814B ARG* 3.7 51.5 + - + +
815B ASN* 5.6 0.8 - - + +
833B ASP 5.4 0.2 + - - -
835B GLY 3.3 0.8 + - - -
836B VAL* 1.3 78.1 - - - +
838B ASP* 1.3 61.1 + - - +
839B LEU 3.2 0.7 + - - -
840B LEU* 3.4 20.8 + - - +
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Residues in contact with ASP 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B HIS* 3.4 35.7 - - + +
812B VAL* 4.4 12.8 - - - +
813B HIS 5.7 0.2 - - - +
814B ARG* 2.9 43.8 + - - +
835B GLY* 3.2 4.9 + - - +
837B ALA* 1.3 73.5 - - - +
839B LEU* 1.3 58.2 + - - +
840B LEU 3.1 10.8 + - - +
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Residues in contact with LEU 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B ILE* 5.3 4.9 - - + -
734B PHE* 4.0 16.6 - - + -
738B THR* 4.6 4.3 - - + +
740B HIS* 4.1 11.4 - - + -
741B MET* 3.7 38.1 - - + +
744B ILE* 3.5 20.2 - - + -
764B LEU* 4.5 14.6 - - + -
766B LEU* 5.2 8.3 - - + -
835B GLY 3.3 25.4 - - - +
836B VAL* 3.0 21.7 + - + +
838B ASP* 1.3 76.8 - - - +
840B LEU* 1.3 68.1 - - + +
841B PRO* 4.5 1.6 - - - +
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Residues in contact with LEU 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B PHE* 3.9 36.8 - - + +
725B ILE* 3.9 17.9 - - + -
726B GLU 3.8 17.9 - - - +
727B ASP* 4.5 7.0 - - + -
728B LYS* 6.3 2.2 - - + -
734B PHE* 3.4 32.5 - - + -
814B ARG* 5.4 1.7 + - - -
836B VAL 4.5 5.6 - - - +
837B ALA 3.4 14.4 + - - +
838B ASP* 3.1 5.5 - - - +
839B LEU* 1.3 85.8 - - + +
841B PRO* 1.4 81.1 - - + +
842B PRO* 3.8 1.7 - - - +
845B LYS* 5.2 7.6 - - - +
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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
------------------------------------------------------------
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