Contacts of the helix formed by residues 775 - 784 (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 SER 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ANP 2.8 29.3 + - - -
773A LEU 3.9 2.5 + - - +
774A GLY* 1.3 75.0 - - - +
776A LEU* 1.3 63.1 + - - +
777A LEU* 4.0 10.8 - - - -
778A ASP* 3.7 27.2 + - - +
779A HIS* 3.2 22.5 + - - +
818A ALA 4.5 0.9 - - - -
819A ARG* 3.6 18.3 + - - +
821A VAL 3.7 5.6 - - - -
822A LEU* 3.7 2.4 - - - +
823A LEU* 4.1 0.6 - - - +
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Residues in contact with LEU 776 (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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774A GLY 3.9 0.8 + - - -
775A SER* 1.3 71.0 - - - +
777A LEU* 1.3 59.4 + - - +
779A HIS* 3.4 2.3 - - + +
780A VAL* 3.0 32.6 + - + +
795A TRP* 3.5 38.4 - - + -
799A ILE* 4.0 8.1 - - + -
818A ALA* 3.9 4.7 - - + +
821A VAL* 2.9 45.1 + - + +
823A LEU* 3.7 12.3 - - + +
829A VAL* 3.7 20.4 - - + -
885A LEU* 3.3 38.8 - - + -
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Residues in contact with LEU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A SER* 3.3 2.9 - - - -
776A LEU* 1.3 78.0 - - - +
778A ASP* 1.3 70.7 + - - +
780A VAL* 3.1 21.6 - - - +
781A ARG* 3.2 48.0 - - - +
818A ALA* 3.4 24.5 + - + -
819A ARG* 3.8 26.9 - - + +
884A GLU* 3.8 20.6 - - + +
889A GLY* 4.2 15.5 - - - +
890A ALA 5.4 1.1 - - - +
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Residues in contact with ASP 778 (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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301A ANP 5.2 4.5 + - - -
775A SER* 3.7 24.2 + - - +
776A LEU 3.5 0.2 - - - -
777A LEU* 1.3 84.7 - - - +
779A HIS* 1.3 59.8 + - - +
781A ARG* 3.9 23.0 + - - +
782A GLN* 3.4 22.9 + - - +
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Residues in contact with HIS 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 4.9 15.2 + - + +
775A SER 3.2 19.1 + - - +
776A LEU* 3.4 9.6 - - - +
777A LEU 3.1 0.6 - - - -
778A ASP* 1.3 77.0 - - - +
780A VAL* 1.3 66.1 + - - +
782A GLN* 3.2 2.8 + - - -
783A HIS* 3.1 55.5 + + - +
787A LEU* 3.9 18.4 - - + +
795A TRP* 3.7 30.4 - + - -
823A LEU* 4.4 18.0 - - + +
826A PRO* 5.1 5.5 + - + -
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Residues in contact with VAL 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A LEU* 3.0 15.7 + - + +
777A LEU* 3.1 22.9 - - - +
779A HIS* 1.3 75.8 - - - +
781A ARG* 1.3 56.4 + - - +
784A ARG* 2.6 35.0 + - - +
787A LEU* 3.8 24.9 - - + -
792A LEU* 5.0 4.3 - - + -
795A TRP* 4.6 11.9 - - + -
885A LEU* 3.9 33.2 - - + +
888A PHE* 3.8 13.5 - - + +
889A GLY* 3.6 22.7 - - - +
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Residues in contact with ARG 781 (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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777A LEU* 3.2 44.7 + - - +
778A ASP* 3.9 19.0 + - - +
779A HIS 3.2 0.2 - - - -
780A VAL* 1.3 78.7 - - - +
782A GLN* 1.3 58.2 + - + +
784A ARG* 3.0 24.1 + - - +
888A PHE 3.6 15.5 - - - +
889A GLY* 2.7 30.9 + - - +
890A ALA* 4.9 1.4 - - - +
891A GLU* 5.0 12.9 - - - +
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Residues in contact with GLN 782 (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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778A ASP 3.4 15.4 + - - +
779A HIS* 3.2 5.8 + - - +
781A ARG* 1.3 80.7 - - - +
783A HIS* 1.3 73.4 + - + +
784A ARG* 5.0 0.5 - - - +
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Residues in contact with HIS 783 (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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779A HIS* 3.1 52.7 + + - +
782A GLN* 1.3 89.0 + - + +
784A ARG* 1.3 71.7 + - - +
786A ALA* 3.2 27.0 + - + +
787A LEU* 4.1 19.5 - - + -
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Residues in contact with ARG 784 (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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780A VAL* 2.6 25.4 + - - +
781A ARG* 3.0 26.4 + - - +
782A GLN 4.7 0.9 - - - +
783A HIS* 1.3 74.5 - - - +
785A GLY* 1.3 63.3 + - - +
786A ALA 3.3 1.0 + - - -
787A LEU* 3.4 24.9 + - - +
887A THR 4.1 16.2 + - - -
888A PHE* 3.4 41.0 + - + +
890A ALA* 6.2 0.4 - - - +
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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