Contacts of the helix formed by residues 970 - 976 (chain B) in PDB entry 3LJ1
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 970 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903B ILE* 4.1 2.9 - - - -
968B ARG 5.1 2.2 - - - +
969B PRO* 1.3 77.2 - - - +
971B ALA* 1.3 66.5 + - - +
972B MET* 3.6 8.0 + - - +
973B LYS* 3.2 24.7 + - + +
974B VAL* 3.1 21.2 + - - +
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Residues in contact with ALA 971 (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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782B ALA* 4.6 4.3 - - - +
785B VAL* 4.3 4.5 - - + -
786B ALA* 3.6 34.7 - - + +
789B HIS* 4.0 16.7 + - + +
903B ILE* 3.7 24.0 - - + +
906B MET* 4.7 3.1 - - + -
970B THR* 1.3 73.2 - - - +
972B MET* 1.3 61.8 + - - +
974B VAL* 3.3 20.4 - - - +
975B LEU* 3.4 12.6 + - - +
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Residues in contact with MET 972 (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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786B ALA* 4.0 25.7 - - + +
790B SER* 5.3 7.2 - - - -
970B THR* 3.2 7.2 + - - +
971B ALA* 1.3 78.0 - - - +
973B LYS* 1.3 64.4 + - - +
975B LEU* 3.1 33.5 + - + +
976B ARG* 3.3 41.0 + - - +
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Residues in contact with LYS 973 (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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959B GLN* 4.3 13.4 + - - +
969B PRO* 3.7 25.0 - - + +
970B THR* 3.2 23.1 + - + +
972B MET* 1.3 75.3 - - - +
974B VAL* 1.3 66.2 + - - +
976B ARG* 3.2 26.2 + - + +
977B HIS* 3.4 10.7 + - - +
1100B LYS* 3.3 38.2 - - - +
1114B TYR* 6.4 0.4 - - + -
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Residues in contact with VAL 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B ALA* 4.3 11.9 - - + -
903B ILE* 4.6 4.5 - - + -
906B MET* 5.2 2.0 - - - -
910B PHE* 4.1 19.3 - - + -
956B LEU* 4.2 13.0 - - + -
960B MET* 4.2 20.4 - - + -
969B PRO* 4.0 21.8 - - + +
970B THR 3.1 17.3 + - - +
971B ALA* 3.3 13.2 - - - +
972B MET 3.2 0.4 - - - -
973B LYS* 1.3 77.0 - - - +
975B LEU* 1.3 62.4 + - - +
977B HIS* 3.0 19.9 + - - +
980B PHE* 3.2 19.8 - - + -
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Residues in contact with LEU 975 (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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779B ARG* 3.5 30.6 - - + +
782B ALA* 3.3 25.4 - - + -
783B SER* 3.6 22.2 - - - +
786B ALA* 4.0 19.7 - - + -
971B ALA 3.4 9.4 + - - +
972B MET* 3.1 22.7 + - - +
974B VAL* 1.3 79.0 - - - +
976B ARG* 1.3 61.2 + - + +
977B HIS 3.5 0.5 + - - +
980B PHE* 3.7 22.3 - - + +
981B TRP* 5.5 1.0 - - - -
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Residues in contact with ARG 976 (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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972B MET* 3.3 43.4 + - + +
973B LYS* 3.2 17.1 + - + +
974B VAL 3.2 0.8 - - - -
975B LEU* 1.3 75.5 - - + +
977B HIS* 1.3 67.2 + - - +
978B PRO* 3.5 1.9 - - - +
981B TRP* 3.0 23.5 + - - +
1096B TYR* 4.6 4.7 + - - +
1112B PHE 5.0 0.3 - - - +
1113B LEU 3.8 15.9 - - - +
1114B TYR* 3.3 41.4 + - - +
1115B SER* 4.1 11.2 + - - +
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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