Contacts of the helix formed by residues 904 - 917 (chain B) in PDB entry 1LD7
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 904 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609B HIS* 4.3 1.0 - - - -
612B GLU* 2.8 29.7 + - - -
896B PRO 3.8 8.7 - - - -
903B ILE* 1.3 75.0 - - - +
905B PRO* 1.3 70.7 - - - +
906B ASP* 3.1 10.8 - - - -
907B LYS* 2.9 17.4 + - - +
908B VAL* 3.1 10.7 + - - +
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Residues in contact with PRO 905 (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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896B PRO* 3.3 35.4 - - + +
897B THR 4.0 5.6 - - - +
898B HIS* 3.9 33.6 - - + +
899B PRO* 6.0 0.2 - - + -
904B GLY* 1.3 83.3 - - - +
906B ASP* 1.3 64.7 + - - +
908B VAL* 3.2 5.4 + - + +
909B ILE* 3.0 34.3 + - + +
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Residues in contact with ASP 906 (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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612B GLU* 4.5 1.2 - - - +
904B GLY* 3.3 16.8 - - - -
905B PRO* 1.3 78.3 - - - +
907B LYS* 1.3 86.4 + - - +
909B ILE* 3.5 9.4 + - - +
910B GLN* 3.0 28.0 + - - +
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Residues in contact with LYS 907 (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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612B GLU* 3.2 29.2 - - - +
661B CYS 3.6 18.6 - - - +
662B ILE* 3.0 33.4 + - + +
663B ILE 4.2 8.7 + - - -
664B GLY* 4.8 4.0 - - - +
669B TYR* 4.6 0.5 + - - -
903B ILE* 3.8 15.4 - - + +
904B GLY 2.9 8.6 + - - +
906B ASP* 1.3 93.4 + - - +
908B VAL* 1.3 58.4 + - - +
910B GLN* 3.5 14.2 + - - +
911B ALA* 3.0 31.9 + - - +
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Residues in contact with VAL 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B LEU* 4.4 5.4 - - + -
898B HIS* 3.8 26.2 - - + +
901B TYR* 3.7 37.0 - - + -
903B ILE* 3.6 22.9 - - + -
904B GLY 3.1 13.1 + - - +
905B PRO 3.2 6.9 + - - +
907B LYS* 1.3 77.0 - - - +
909B ILE* 1.3 60.3 + - + +
911B ALA* 3.3 1.2 + - - +
912B THR* 2.9 47.0 + - + +
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Residues in contact with ILE 909 (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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898B HIS* 6.5 0.2 - - + -
905B PRO* 3.0 21.6 + - + +
906B ASP* 3.9 6.7 - - - +
908B VAL* 1.3 77.9 - - + +
910B GLN* 1.3 57.3 + - - +
912B THR* 3.1 6.7 + - - +
913B THR* 2.7 45.5 + - - +
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Residues in contact with GLN 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B GLY* 2.6 34.1 + - - -
669B TYR* 3.0 19.3 + - + +
906B ASP* 3.0 18.7 + - - +
907B LYS* 3.9 13.8 + - - +
909B ILE* 1.3 78.7 - - - +
911B ALA* 1.3 62.0 + - - +
913B THR* 3.8 4.4 - - - -
914B TYR* 3.1 23.6 + - - +
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Residues in contact with ALA 911 (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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661B CYS* 3.6 29.6 - - + -
669B TYR* 3.4 20.1 + - + -
713B LEU* 4.2 7.9 - - + +
907B LYS 3.0 18.8 + - - +
908B VAL* 3.8 3.8 - - - +
910B GLN* 1.3 74.3 - - - +
912B THR* 1.3 67.2 + - - +
914B TYR* 3.2 2.1 + - - +
915B PHE* 3.0 35.5 + - + -
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Residues in contact with THR 912 (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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712B SER 4.6 5.8 - - - +
713B LEU* 4.0 29.6 - - + +
715B ASN* 5.5 0.2 - - - +
901B TYR* 5.5 3.1 - - - +
908B VAL* 2.9 37.1 + - + +
909B ILE* 3.1 10.9 + - - +
911B ALA* 1.3 75.1 - - - +
913B THR* 1.3 61.6 + - - +
915B PHE* 4.4 0.2 - - - +
916B LEU* 2.9 45.7 + - - +
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Residues in contact with THR 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909B ILE* 2.7 34.7 + - - +
910B GLN* 3.8 5.8 - - - -
912B THR* 1.3 82.0 + - - +
914B TYR* 1.3 65.3 + - - +
916B LEU* 3.4 14.8 + - - +
917B GLN* 3.6 21.6 + - + +
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Residues in contact with TYR 914 (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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666B GLU* 3.7 31.6 - - + +
669B TYR* 3.5 49.1 - + + -
670B ASP* 2.7 29.5 + - - -
910B GLN 3.1 18.0 + - - +
911B ALA 3.5 4.3 - - - +
913B THR* 1.3 79.1 - - - +
915B PHE* 1.3 74.1 + + - +
917B GLN* 3.2 31.4 + - - +
918B LYS* 3.5 34.9 + - - +
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Residues in contact with PHE 915 (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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661B CYS* 4.8 5.2 - - - -
669B TYR* 3.5 53.6 - + + -
672B ILE* 4.1 14.6 - - + -
674B ARG* 3.7 33.5 + - + -
713B LEU 3.1 23.3 - - - +
714B THR* 3.5 31.6 - - + +
715B ASN* 3.1 15.4 + - + +
911B ALA* 3.0 24.8 + - + +
912B THR 4.4 0.7 - - - +
914B TYR* 1.3 86.3 - + - +
916B LEU* 1.3 56.9 + - - +
917B GLN 3.0 5.6 - - - -
918B LYS* 2.9 31.1 + - + +
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Residues in contact with LEU 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B ASN* 3.6 28.5 + - + +
912B THR* 2.9 37.2 + - - +
913B THR* 3.8 9.6 - - - +
914B TYR 3.3 0.6 - - - -
915B PHE* 1.3 77.0 - - - +
917B GLN* 1.3 59.4 + - + +
918B LYS 3.1 7.6 + - - +
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Residues in contact with GLN 917 (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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913B THR* 3.6 22.0 - - + +
914B TYR* 3.4 21.3 - - - +
915B PHE 3.0 1.0 - - - -
916B LEU* 1.3 79.8 - - + +
918B LYS* 1.3 61.8 + - + +
919B PRO* 4.6 1.7 - - - +
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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