Contacts of the helix formed by residues 727 - 739 (chain A) in PDB entry 1LDJ
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 HIS 727 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A LEU 3.8 1.2 + - - -
726A LYS* 1.3 67.5 - - - +
728A GLN* 1.3 58.4 + - + +
730A LEU* 2.7 27.2 + - - +
731A LEU* 2.9 38.5 + - + +
746A VAL* 5.3 3.4 - - - +
750A LYS* 3.4 30.3 - - + +
753A ILE* 4.0 16.6 - - + +
770A ASP* 2.7 40.2 + - + +
772A TYR* 2.5 39.3 + - - +
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Residues in contact with GLN 728 (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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726A LYS* 3.4 2.3 - - + +
727A HIS* 1.3 83.1 - - + +
729A GLN* 1.3 60.0 + - + +
731A LEU* 3.3 17.5 + - - +
732A GLY* 2.7 31.7 + - - -
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Residues in contact with GLN 729 (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 LEU* 3.0 29.5 - - + +
726A LYS* 2.9 43.6 + - - +
728A GLN* 1.3 79.1 - - + +
730A LEU* 1.3 66.4 + - - +
732A GLY* 3.7 1.5 - - - +
733A GLU* 2.9 32.8 + - + +
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Residues in contact with LEU 730 (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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715A ILE* 3.8 31.4 - - + -
718A ILE* 4.0 22.2 - - + -
719A MET* 3.7 28.9 - - + -
725A LEU* 3.8 12.4 - - + +
726A LYS 2.9 10.0 + - - +
727A HIS* 2.7 18.4 + - - +
729A GLN* 1.3 73.2 - - - +
731A LEU* 1.3 67.3 + - - +
733A GLU* 3.2 1.8 + - - +
734A VAL* 3.1 21.3 + - + +
753A ILE* 4.2 24.5 - - + -
762A LEU* 5.1 0.9 - - + -
772A TYR* 4.3 17.9 - - + -
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Residues in contact with LEU 731 (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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727A HIS* 2.9 42.2 + - + +
728A GLN* 3.5 16.2 - - - +
730A LEU* 1.3 75.2 - - - +
732A GLY* 1.3 67.4 + - - +
734A VAL* 2.8 25.3 + - - +
735A LEU* 3.3 9.7 + - + +
746A VAL* 3.9 32.3 - - + +
749A ILE* 3.7 39.9 - - + -
750A LYS 4.7 2.7 - - - +
753A ILE* 4.1 15.3 - - + -
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Residues in contact with GLY 732 (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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728A GLN* 2.7 25.7 + - - -
729A GLN* 3.7 2.0 - - - -
731A LEU* 1.3 72.3 - - - +
733A GLU* 1.3 63.8 + - - +
735A LEU* 3.0 15.5 + - - +
736A THR* 2.9 22.8 + - - -
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Residues in contact with GLU 733 (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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718A ILE* 3.4 30.9 - - + +
722A ARG* 2.7 47.6 + - - -
725A LEU* 4.3 2.5 - - + +
729A GLN* 2.9 32.4 + - + +
730A LEU 3.3 6.5 - - - +
732A GLY* 1.3 69.2 - - - +
734A VAL* 1.3 56.9 + - - +
736A THR* 2.3 39.0 + - - +
737A GLN* 2.8 17.6 + - - +
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Residues in contact with VAL 734 (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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711A ILE* 4.6 3.8 - - + -
714A ALA* 4.9 3.4 - - + -
715A ILE* 3.3 33.7 - - + +
718A ILE* 3.5 15.2 - - + +
730A LEU* 3.5 12.8 - - + +
731A LEU 2.8 14.5 + - - +
733A GLU* 1.3 75.1 - - - +
735A LEU* 1.3 63.0 + - - +
737A GLN* 3.2 6.4 - - - +
738A LEU* 3.0 41.5 + - + +
744A PRO* 3.7 5.2 - - + -
749A ILE* 3.4 33.2 - - + -
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Residues in contact with LEU 735 (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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731A LEU* 3.8 6.1 - - + +
732A GLY* 3.0 16.3 + - - +
734A VAL* 1.3 73.6 - - - +
736A THR* 1.3 72.4 + - - +
738A LEU 2.5 15.2 + - - +
739A SER* 2.8 15.3 + - - +
743A LYS* 4.2 26.9 - - + +
744A PRO* 3.5 42.4 - - + +
746A VAL* 5.9 6.1 - - + +
749A ILE* 4.0 13.5 - - + -
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Residues in contact with THR 736 (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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732A GLY 2.9 16.2 + - - -
733A GLU* 2.3 37.6 + - - +
735A LEU* 1.3 73.2 - - - +
737A GLN* 1.3 68.5 + - + +
739A SER* 3.4 15.3 + - - -
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Residues in contact with GLN 737 (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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714A ALA* 4.9 2.2 - - + +
717A ARG* 2.9 41.6 - - - +
718A ILE* 4.3 19.8 - - + +
733A GLU* 2.8 22.1 + - + +
734A VAL* 3.2 9.0 - - - +
736A THR* 1.3 91.1 - - - +
738A LEU* 1.3 74.6 + - + +
739A SER* 3.6 0.3 + - - -
740A SER* 3.7 13.2 + - - -
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Residues in contact with LEU 738 (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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710A LEU* 4.4 10.1 - - + +
711A ILE* 3.7 28.0 - - + -
714A ALA* 4.3 12.1 - - + -
717A ARG* 5.2 5.2 - - - +
734A VAL* 3.0 37.5 + - + +
735A LEU 2.5 12.1 + - - -
737A GLN* 1.3 85.1 - - + +
739A SER* 1.3 64.3 + - - +
740A SER* 3.1 4.5 - - - -
741A ARG* 2.7 19.3 + - + +
742A PHE* 3.0 40.0 + - + +
744A PRO* 3.9 8.7 - - + -
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Residues in contact with SER 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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457A GLU* 4.6 4.0 - - - +
459A LYS* 5.9 0.3 + - - -
735A LEU* 2.8 16.5 + - - +
736A THR* 3.4 13.6 + - - -
737A GLN 4.5 0.2 + - - -
738A LEU* 1.3 76.0 - - - +
740A SER* 1.3 67.2 + - - -
741A ARG 2.9 8.0 + - - -
742A PHE* 3.5 15.7 + - - -
743A LYS* 5.1 5.2 - - - +
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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