Contacts of the helix formed by residues 838 - 844 (chain J) in PDB entry 1SOJ
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 ALA 838 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833J LEU* 2.9 46.7 + - + +
836J THR* 3.2 9.9 - - - +
837J ASN* 1.3 79.8 - - - +
839J PRO* 1.3 77.0 - - + +
840J GLN* 4.1 5.8 - - + +
841J ALA* 2.9 13.1 + - - +
842J VAL* 3.2 9.9 + - - +
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Residues in contact with PRO 839 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860I ASN* 6.0 1.8 - - - +
837J ASN 3.6 2.6 - - - +
838J ALA* 1.3 87.0 - - + +
840J GLN* 1.3 64.1 + - + +
842J VAL* 3.4 9.2 + - + +
843J LEU* 3.1 23.0 + - - +
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Residues in contact with GLN 840 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732J ARG* 5.7 3.8 - - - +
824J ASP* 4.8 2.8 + - - -
826J PRO* 5.3 3.5 - - - +
833J LEU* 4.3 17.8 - - + +
838J ALA* 3.0 6.8 - - + -
839J PRO* 1.3 84.1 - - + +
841J ALA* 1.3 63.7 + - - +
843J LEU* 3.4 9.3 + - + -
844J TYR* 3.2 36.9 + - + -
849J VAL* 3.4 11.0 - - + +
850J LEU* 4.3 6.4 - - - +
853J HIS* 3.7 47.7 + - + +
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Residues in contact with ALA 841 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833J LEU* 3.5 33.2 - - + +
834J VAL* 3.9 5.4 - - - +
837J ASN* 4.9 1.8 - - - -
838J ALA* 2.9 8.9 + - - +
840J GLN* 1.3 76.3 - - - +
842J VAL* 1.3 65.9 + - + +
844J TYR 3.6 0.3 + - - -
845J ASN* 3.2 2.6 + - - -
846J ASP* 2.9 44.4 + - - +
849J VAL* 3.5 19.6 - - + +
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Residues in contact with VAL 842 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856I ALA* 3.3 21.2 - - - +
859I TRP* 4.4 4.3 - - + -
860I ASN* 3.9 39.7 - - + +
863I LEU* 3.9 22.9 - - + -
883I ARG* 3.8 17.4 + - - +
837J ASN* 4.5 15.9 - - - +
838J ALA 3.2 12.1 + - - +
839J PRO* 3.8 9.4 - - + +
841J ALA* 1.3 77.2 - - + +
843J LEU* 1.3 64.6 + - - +
845J ASN* 3.0 12.0 + - - +
846J ASP* 5.6 0.2 - - - +
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Residues in contact with LEU 843 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843I LEU* 4.0 28.5 - - + -
844I TYR* 2.7 44.0 + - + +
856I ALA* 3.2 13.2 - - + +
839J PRO 3.1 17.5 + - - +
840J GLN* 3.5 12.8 - - + +
842J VAL* 1.3 78.2 - - - +
844J TYR* 1.3 86.7 + - + +
845J ASN* 4.0 0.2 + - - -
853J HIS* 6.2 0.4 - - - +
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Residues in contact with TYR 844 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843I LEU* 3.0 44.1 + - + +
844I TYR* 3.8 23.1 - + - -
852I ASN* 4.7 3.4 - - - +
840J GLN* 3.2 28.0 + - + +
841J ALA 4.7 0.4 - - - +
842J VAL 3.2 0.4 - - - -
843J LEU* 1.3 95.5 - - + +
845J ASN* 1.3 74.2 + - - +
846J ASP 3.1 2.2 - - - +
847J ARG* 2.9 31.0 + - - +
849J VAL* 3.8 18.4 - - + -
852J ASN* 3.5 31.1 + - + +
853J HIS* 4.0 27.9 + - + -
856J ALA* 3.5 10.9 - - - +
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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