Contacts of the helix formed by residues 838 - 844 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832I PHE* 6.1 0.2 - - + -
833I LEU* 2.9 45.9 + - + +
836I THR* 3.2 9.2 - - - +
837I ASN* 1.3 74.9 - - - +
839I PRO* 1.3 66.9 - - + +
840I GLN* 4.2 5.2 - - + +
841I ALA* 2.7 24.9 + - - +
842I VAL* 3.0 9.7 + - - +
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Residues in contact with PRO 839 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837I ASN 3.5 3.4 - - - +
838I ALA* 1.3 84.9 - - + +
840I GLN* 1.3 59.3 + - + +
842I VAL* 3.1 9.7 + - + +
843I LEU* 2.8 31.1 + - - +
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Residues in contact with GLN 840 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732I ARG* 5.6 3.0 - - - +
824I ASP* 4.8 1.4 + - - -
826I PRO* 4.8 6.9 - - - +
833I LEU* 4.1 20.6 - - + +
838I ALA* 3.1 4.0 - - + -
839I PRO* 1.3 84.9 - - + +
841I ALA* 1.3 60.0 + - - +
843I LEU* 3.6 8.9 + - + -
844I TYR* 3.2 35.4 + - + -
849I VAL* 3.5 14.2 - - + +
850I LEU* 4.2 7.7 - - - +
853I HIS* 3.2 53.5 + - + +
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Residues in contact with ALA 841 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833I LEU* 3.5 33.4 - - + +
834I VAL* 3.9 3.6 - - - +
837I ASN* 4.8 1.8 - - - -
838I ALA* 2.7 17.9 + - - +
840I GLN* 1.3 72.5 - - - +
842I VAL* 1.3 63.4 + - + +
844I TYR 3.4 0.5 + - - -
845I ASN 3.1 3.3 + - - -
846I ASP* 2.9 42.8 + - - +
849I VAL* 3.6 19.0 - - + +
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Residues in contact with VAL 842 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837I ASN* 3.8 22.2 - - + +
838I ALA 3.0 13.4 + - - +
839I PRO* 3.6 9.2 - - + +
841I ALA* 1.3 76.8 - - - +
843I LEU* 1.3 64.4 + - - +
845I ASN* 3.3 9.4 + - - +
856J ALA* 3.4 29.7 - - - +
859J TRP* 4.2 6.3 - - + -
860J ASN* 4.0 23.8 - - + +
863J LEU* 4.0 19.7 - - + -
883J ARG* 3.5 21.0 + - - +
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Residues in contact with LEU 843 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839I PRO 2.8 16.6 + - - +
840I GLN* 3.6 12.6 - - + +
841I ALA 3.2 0.2 - - - -
842I VAL* 1.3 78.4 - - - +
844I TYR* 1.3 77.1 + - + +
845I ASN* 3.4 0.4 + - - -
843J LEU* 4.0 31.2 - - + -
844J TYR* 3.0 48.6 + - + +
856J ALA* 3.2 14.8 - - + +
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Residues in contact with TYR 844 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840I GLN* 3.2 28.9 + - + +
841I ALA 3.4 1.5 + - - +
842I VAL 3.3 0.2 - - - -
843I LEU* 1.3 94.1 - - + +
845I ASN* 1.3 76.4 + - - +
846I ASP 3.2 0.7 - - - -
847I ARG* 3.2 27.4 + - - +
849I VAL* 3.9 18.2 - - + -
852I ASN* 3.4 32.7 + - + -
853I HIS* 3.9 24.5 + - + +
856I ALA* 3.6 13.0 - - - +
843J LEU* 2.7 41.6 + - - +
844J TYR* 3.8 23.1 - + - -
852J ASN* 4.4 4.9 - - - +
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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