Contacts of the helix formed by residues 830 - 836 (chain B) in PDB entry 1J1B
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 830 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740B VAL* 4.7 1.1 - - - -
828B ARG 4.9 3.4 - - - +
829B LEU* 1.3 77.3 - - - +
831B PRO* 1.3 70.3 - - - +
832B LEU* 3.7 6.6 + - - +
833B GLU* 3.1 41.3 + - - +
834B ALA* 2.9 26.1 + - - +
869B SER* 4.8 9.1 + - - +
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Residues in contact with PRO 831 (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 PHE* 3.4 38.8 - - + +
669B LEU* 3.8 14.1 - - + -
670B ALA* 3.5 13.5 - - - +
673B HIS* 3.5 31.9 - - + +
740B VAL* 4.0 14.1 - - + -
830B THR* 1.3 87.6 - - - +
832B LEU* 1.3 62.8 + - - +
834B ALA* 3.1 3.8 + - - +
835B CYS* 3.0 26.2 + - - -
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Residues in contact with LEU 832 (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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670B ALA* 4.1 15.0 - - + +
830B THR* 3.3 3.9 + - - +
831B PRO* 1.3 79.0 - - - +
833B GLU* 1.3 63.0 + - - +
835B CYS* 3.2 16.7 + - + +
836B ALA* 3.3 12.8 + - - +
862B PHE* 4.1 17.3 - - + -
866B GLU 3.8 16.2 - - - +
867B LEU* 3.8 29.4 - - + +
869B SER* 3.5 26.5 - - - +
870B ASN 3.9 15.9 - - - +
873B LEU* 3.9 13.4 - - + +
877B LEU* 3.6 26.3 - - + +
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Residues in contact with GLU 833 (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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828B ARG 4.7 0.5 - - - +
829B LEU* 3.5 27.4 - - + +
830B THR* 3.1 41.9 + - - +
832B LEU* 1.3 74.1 - - - +
834B ALA* 1.3 66.0 + - - +
836B ALA* 3.1 13.5 + - - +
837B HIS* 3.2 11.4 + - - +
870B ASN* 4.5 11.7 + - + +
873B LEU* 3.9 21.8 - - + -
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Residues in contact with ALA 834 (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 PHE* 3.7 37.2 - - + -
816B LEU* 4.5 2.2 - - + -
820B LEU* 4.4 11.9 - - + -
829B LEU* 4.3 11.4 - - + +
830B THR 2.9 12.4 + - - +
831B PRO 3.4 9.4 - - - +
833B GLU* 1.3 77.5 - - - +
835B CYS* 1.3 63.3 + - - +
837B HIS* 2.9 15.8 + - - +
840B PHE* 3.1 18.5 - - - -
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Residues in contact with CYS 835 (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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663B TYR* 3.6 21.6 - - + -
666B PHE* 3.6 20.0 - - - -
667B ARG* 3.7 27.4 - - - -
831B PRO 3.0 18.7 + - - -
832B LEU* 3.2 14.1 + - - +
834B ALA* 1.3 75.9 - - - +
836B ALA* 1.3 57.6 + - - +
837B HIS 3.2 0.9 + - - -
840B PHE* 3.6 17.4 - - - -
844B ARG* 3.0 20.6 + - - -
862B PHE* 4.9 4.7 - - + -
877B LEU* 3.6 15.7 - - + -
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Residues in contact with ALA 836 (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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832B LEU 3.3 8.0 + - - +
833B GLU* 3.1 11.1 + - - +
834B ALA 3.1 0.8 - - - -
835B CYS* 1.3 76.0 - - - +
837B HIS* 1.3 66.5 + - - +
838B SER* 3.7 1.0 + - - -
841B ASP* 4.9 0.7 - - - +
844B ARG* 3.7 10.0 + - - +
873B LEU* 4.5 16.2 - - + -
876B ILE* 3.9 29.4 - - + +
877B LEU* 3.7 16.4 - - + +
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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