Contacts of the helix formed by residues 738 - 747 (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 THR 738 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A ALA* 4.5 5.4 - - + +
737A VAL* 1.3 90.6 - - - +
739A ASP* 1.3 63.4 + - - +
740A HIS* 3.5 9.7 + - - +
741A MET* 3.2 42.5 + - - +
742A LEU* 3.6 4.2 + - - +
839A LEU* 4.6 3.4 - - + +
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Residues in contact with ASP 739 (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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680A VAL* 5.8 3.5 - - - +
738A THR* 1.3 75.4 - - - +
740A HIS* 1.3 61.5 + - - +
742A LEU* 3.4 17.4 + - - +
743A ALA* 3.2 19.2 + - - +
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Residues in contact with HIS 740 (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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738A THR* 3.2 8.8 + - - +
739A ASP* 1.3 77.6 - - - +
741A MET* 1.3 63.3 + - - +
743A ALA* 3.2 11.8 + - - +
744A ILE* 3.1 31.2 + - + +
811A MET* 4.0 28.7 - - + -
812A VAL 5.5 0.7 - - - -
835A GLY* 2.8 29.4 + - - -
838A ASP* 3.6 37.6 - - + +
839A LEU* 4.0 9.0 - - + -
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Residues in contact with MET 741 (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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682A ALA* 4.4 4.1 - - - +
734A PHE* 4.8 6.7 - - - +
736A ALA 4.0 8.5 - - - +
737A VAL* 3.7 16.4 - - + -
738A THR* 3.2 43.3 + - - +
740A HIS* 1.3 77.0 - - - +
742A LEU* 1.3 58.7 + - - +
744A ILE* 3.6 7.8 + - - +
745A GLY* 3.1 21.7 + - - -
755A LEU* 4.7 4.3 - - - +
758A LEU* 3.0 41.3 - - + +
760A PRO* 5.3 1.1 - - + -
764A LEU* 3.0 34.5 - - + -
766A LEU* 6.0 0.7 - - + -
839A LEU* 3.5 23.6 - - + -
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Residues in contact with LEU 742 (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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680A VAL* 4.7 19.5 - - + +
681A LEU* 4.8 3.4 - - - -
682A ALA* 3.7 35.6 - - + +
684A ILE* 6.0 1.8 - - + -
737A VAL* 3.8 19.7 - - + -
738A THR 3.6 10.5 + - - +
739A ASP* 3.4 18.3 + - - +
740A HIS 3.2 0.6 - - - -
741A MET* 1.3 74.8 - - - +
743A ALA* 1.3 57.2 + - - +
745A GLY* 3.0 1.7 + - - +
746A SER* 2.8 40.8 + - - +
758A LEU* 5.9 0.4 - - + -
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Residues in contact with ALA 743 (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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680A VAL* 6.0 2.5 - - - -
739A ASP 3.2 10.2 + - - +
740A HIS* 3.2 23.5 + - + +
742A LEU* 1.3 80.4 - - - +
744A ILE* 1.3 61.6 + - - +
746A SER* 3.6 9.4 + - - -
747A LEU* 3.6 21.7 + - - +
811A MET* 5.3 6.5 - - + -
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Residues in contact with ILE 744 (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* 3.1 37.1 + - + +
741A MET* 3.8 8.1 - - - +
743A ALA* 1.3 78.6 - - - +
745A GLY* 1.3 62.0 + - - +
746A SER 3.3 0.7 + - - -
747A LEU* 3.6 11.0 + - - +
755A LEU* 3.8 30.5 - - + +
766A LEU* 5.5 7.6 - - + -
811A MET* 3.5 20.4 - - + -
834A PHE* 3.9 33.0 - - + +
835A GLY 3.6 16.8 - - - +
836A VAL* 4.4 2.0 - - + +
839A LEU* 4.4 18.4 - - + -
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Residues in contact with GLY 745 (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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681A LEU 3.8 10.0 - - - +
682A ALA* 3.8 19.9 - - - +
741A MET 3.1 8.6 + - - -
742A LEU 3.0 8.8 + - - -
744A ILE* 1.3 78.5 - - - +
746A SER* 1.3 61.3 + - - +
747A LEU 3.5 4.5 + - - +
754A ARG* 5.2 1.7 + - - +
755A LEU* 3.9 28.8 - - - +
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Residues in contact with SER 746 (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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680A VAL* 3.2 38.4 - - - +
681A LEU* 3.3 11.2 + - - +
742A LEU 2.8 20.7 + - - -
743A ALA* 4.0 7.2 - - - -
744A ILE 3.3 0.4 - - - -
745A GLY* 1.3 77.6 - - - +
747A LEU* 1.3 67.1 + - - +
748A ASP* 3.6 5.4 + - - +
754A ARG* 5.9 0.2 - - - -
805A TYR* 4.7 1.6 + - - -
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Residues in contact with LEU 747 (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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743A ALA 3.6 18.6 - - - +
744A ILE* 4.0 6.1 - - - +
745A GLY 3.3 4.4 - - - +
746A SER* 1.3 80.7 - - - +
748A ASP* 1.3 60.6 + - - +
752A ILE* 3.7 18.2 - - + +
754A ARG* 3.5 21.1 - - - +
755A LEU 4.9 0.7 + - - -
805A TYR* 3.6 19.1 - - + +
806A LEU* 3.5 26.0 - - + -
809A HIS* 3.6 34.3 - - + +
811A MET* 3.7 22.0 - - + -
834A PHE* 3.7 15.2 - - + -
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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