Contacts of the helix formed by residues 752 - 757 (chain B) in PDB entry 1LDK
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 CYS 752 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B LYS* 3.4 47.1 - - + -
711B ILE* 4.9 9.9 - - - -
712B GLN* 3.2 36.4 - - - +
748B VAL 5.0 2.7 - - - -
749B ILE* 4.4 12.3 - - - -
751B LYS* 1.3 78.1 - - + +
753B ILE* 1.3 62.3 + - - +
754B ASP 3.1 2.2 - - - -
755B ILE* 3.1 29.6 + - + +
756B LEU 4.1 0.2 + - - -
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Residues in contact with ILE 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B GLN* 4.7 2.7 - - - +
715B ILE* 4.1 25.4 - - + -
730B LEU* 5.7 2.2 - - + -
749B ILE 4.8 6.5 - - - +
750B LYS* 3.8 27.1 - - + +
751B LYS 3.1 3.9 - - - +
752B CYS* 1.3 78.8 - - - +
754B ASP* 1.3 79.5 + - - +
755B ILE 2.9 6.7 + - - -
756B LEU* 4.0 14.1 + - + +
757B ILE* 4.2 13.0 - - - +
762B LEU* 5.1 3.1 - - + -
772B TYR* 4.3 27.4 - - + +
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Residues in contact with ASP 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750B LYS* 3.1 18.0 + - - -
751B LYS* 3.3 20.8 - - - +
752B CYS 3.1 0.2 - - - -
753B ILE* 1.3 94.4 - - - +
755B ILE* 1.3 75.4 + - + +
757B ILE* 4.4 18.1 + - - +
758B GLU* 4.8 2.4 + - - +
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Residues in contact with ILE 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B LEU* 6.5 0.4 - - + -
712B GLN* 5.1 2.7 - - + +
751B LYS* 3.0 44.2 - - - +
752B CYS* 3.3 18.6 - - + +
753B ILE 2.9 3.4 - - - -
754B ASP* 1.3 93.6 - - + +
756B LEU* 1.4 56.5 + - + +
757B ILE 3.1 2.1 + - - -
758B GLU* 2.5 39.8 + - - +
759B LYS* 3.4 29.4 - - + +
1063C ALA 5.5 4.0 - - - +
1067C GLU* 4.3 18.4 - - - +
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Residues in contact with LEU 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B GLN* 2.5 71.3 - - + +
715B ILE* 3.6 26.0 - - + -
752B CYS 4.3 1.6 - - - +
753B ILE* 4.0 10.4 + - + +
754B ASP 3.8 0.2 - - - -
755B ILE* 1.4 67.3 - - - +
757B ILE* 1.3 59.1 + - - +
758B GLU 3.2 0.2 - - - -
759B LYS* 2.8 46.8 + - - +
760B GLU 3.3 0.2 + - - -
761B TYR* 3.1 45.6 + - + +
762B LEU* 4.6 13.0 - - + +
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Residues in contact with ILE 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B ILE 4.2 17.2 + - - +
754B ASP* 4.5 13.2 - - - +
755B ILE 3.1 0.6 + - - -
756B LEU* 1.3 75.1 - - - +
758B GLU* 1.3 59.0 + - - +
759B LYS 3.2 3.6 + - - -
760B GLU* 3.6 11.4 + - - +
761B TYR 4.5 0.8 + - - +
762B LEU* 3.9 24.8 + - + +
763B GLU* 5.4 12.8 - - + -
764B ARG 6.0 0.9 - - - +
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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