Contacts of the helix formed by residues 838 - 844 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832K PHE* 6.1 0.2 - - + -
833K LEU* 2.9 45.5 + - + +
836K THR* 3.2 9.2 - - - +
837K ASN* 1.3 76.5 - - - +
839K PRO* 1.3 68.0 - - + +
840K GLN* 4.2 4.9 - - + +
841K ALA* 2.7 25.4 + - - +
842K VAL* 2.9 9.7 + - - +
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Residues in contact with PRO 839 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837K ASN 3.5 3.2 - - - +
838K ALA* 1.3 84.4 - - + +
840K GLN* 1.3 60.5 + - + +
842K VAL* 3.1 9.9 + - + +
843K LEU* 2.7 31.1 + - - +
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Residues in contact with GLN 840 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732K ARG* 5.6 3.2 - - - +
824K ASP* 4.8 1.2 + - - -
826K PRO* 4.8 7.4 - - - +
833K LEU* 4.1 18.0 - - + +
838K ALA* 3.1 6.5 - - + -
839K PRO* 1.3 83.8 - - + +
841K ALA* 1.3 60.4 + - - +
843K LEU* 3.6 8.4 + - + +
844K TYR* 3.2 34.7 + - + -
849K VAL* 3.5 13.7 - - + +
850K LEU* 4.2 8.4 - - - +
853K HIS* 3.2 53.6 + - + +
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Residues in contact with ALA 841 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833K LEU* 3.5 33.7 - - + +
834K VAL* 3.8 3.6 - - - +
837K ASN* 4.8 1.8 - - - -
838K ALA* 2.7 17.7 + - - +
840K GLN* 1.3 73.7 - - - +
842K VAL* 1.3 62.1 + - - +
843K LEU 3.2 0.2 - - - -
844K TYR 3.4 0.5 + - - -
845K ASN 3.1 3.5 + - - -
846K ASP* 2.9 42.6 + - - +
849K VAL* 3.6 17.9 - - + +
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Residues in contact with VAL 842 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837K ASN* 3.8 22.9 - - + +
838K ALA 2.9 13.1 + - - +
839K PRO* 3.6 9.6 - - + +
841K ALA* 1.3 74.7 - - - +
843K LEU* 1.3 65.8 + - - +
845K ASN* 3.3 10.4 + - - +
856L ALA* 3.5 16.8 - - - +
859L TRP* 4.2 6.1 - - + -
860L ASN* 3.9 35.9 - - + +
863L LEU* 3.8 21.1 - - + -
883L ARG* 3.5 19.3 + - - +
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Residues in contact with LEU 843 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839K PRO 2.7 18.1 + - - +
840K GLN* 3.6 11.2 - - + +
842K VAL* 1.3 77.4 - - - +
844K TYR* 1.3 83.0 + - + +
843L LEU* 4.2 25.8 - - + -
844L TYR* 3.1 39.3 + - + +
856L ALA* 3.1 15.9 - - + +
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Residues in contact with TYR 844 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840K GLN* 3.2 28.5 + - + +
841K ALA 3.4 1.7 + - - +
842K VAL 3.3 0.2 - - - -
843K LEU* 1.3 94.3 - - + +
845K ASN* 1.3 76.0 + - - +
846K ASP 3.2 1.6 - - - -
847K ARG* 3.1 28.2 + - - +
849K VAL* 3.9 18.8 - - + -
852K ASN* 3.4 32.3 + - + -
853K HIS* 4.0 25.4 + - + -
856K ALA* 3.6 11.8 - - - +
843L LEU* 3.1 43.8 + - + +
844L TYR* 4.1 22.0 - + - -
852L ASN* 4.6 3.4 - - - +
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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