Contacts of the helix formed by residues 837 - 845 (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 HIS 837 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812B GLU* 3.3 26.2 - - - -
815B ALA* 4.1 10.0 + - + +
816B LEU* 3.6 38.0 + - + -
819B ARG* 5.2 4.9 - - + +
829B LEU* 4.3 11.9 - - + -
833B GLU 3.2 6.2 + - - +
834B ALA* 2.9 19.4 + - - +
836B ALA* 1.3 78.4 - - - +
838B SER* 1.3 79.4 + - - +
839B PHE* 2.9 25.8 + - - +
840B PHE* 3.1 12.4 + - + +
844B ARG* 2.9 19.8 + - - -
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Residues in contact with SER 838 (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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812B GLU* 3.8 19.9 - - - +
836B ALA 3.7 1.2 + - - -
837B HIS* 1.3 83.1 + - - +
839B PHE* 1.3 64.8 + - - +
840B PHE 3.0 2.7 - - - -
841B ASP* 3.0 38.7 + - - +
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Residues in contact with PHE 839 (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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655B VAL* 3.9 12.6 - - + -
658B VAL* 4.0 17.7 - - + -
659B LYS* 3.2 68.2 + - + +
662B MET* 5.1 0.4 - - + -
747B LEU* 4.2 17.9 - - + -
751B LEU* 5.1 0.9 - - + -
810B PRO* 4.7 5.4 - - + -
812B GLU* 3.8 18.8 - - + +
813B ALA* 3.5 37.7 - - + -
816B LEU* 3.6 23.3 - - + -
837B HIS* 2.9 18.4 + - + +
838B SER* 1.3 78.0 + - - +
840B PHE* 1.3 71.4 + + + +
841B ASP 3.6 0.2 + - - -
842B GLU 4.6 0.2 + - - -
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Residues in contact with PHE 840 (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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659B LYS* 3.2 33.2 - - - -
662B MET* 4.0 10.8 - - + -
663B TYR* 3.4 34.5 - + + -
666B PHE* 4.0 9.9 - + - -
816B LEU* 3.8 26.0 - - + -
834B ALA 3.1 33.0 - - - -
835B CYS* 3.6 18.6 - - - +
837B HIS* 3.1 11.0 + - + +
838B SER 3.0 0.8 - - - -
839B PHE* 1.3 90.6 - + - +
841B ASP* 1.3 63.8 + - - +
842B GLU 3.2 3.1 - - - -
843B LEU* 3.0 28.3 + - + +
844B ARG* 3.5 11.2 + - - +
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Residues in contact with ASP 841 (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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836B ALA 4.9 0.7 - - - +
838B SER* 3.0 36.4 + - - +
839B PHE 3.4 0.4 - - - -
840B PHE* 1.3 77.2 - - - +
842B GLU* 1.3 63.0 + - - +
844B ARG* 2.8 45.3 + - - +
845B ASP* 3.5 5.4 + - - +
876B ILE* 5.7 0.7 - - - +
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Residues in contact with GLU 842 (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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656B ILE* 3.8 24.4 + - + +
659B LYS* 2.8 39.1 + - + +
839B PHE 4.6 1.2 + - - -
840B PHE 3.2 0.6 + - - -
841B ASP* 1.3 78.4 - - - +
843B LEU* 1.3 62.3 + - - +
845B ASP* 3.2 23.7 + - + +
848B VAL* 3.4 20.6 - - + +
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Residues in contact with LEU 843 (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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656B ILE* 4.0 20.2 - - + -
659B LYS* 3.6 24.7 - - + +
660B LEU* 3.9 33.2 - - + -
663B TYR* 3.5 45.3 - - + -
840B PHE* 3.0 21.1 + - + +
842B GLU* 1.3 76.9 - - - +
844B ARG* 1.3 62.1 + - + +
845B ASP 3.3 1.1 + - - +
848B VAL* 3.7 19.5 - - + +
856B THR* 5.5 0.9 - - + -
859B LEU* 4.1 12.7 - - + +
860B PHE* 3.4 17.4 - - + -
881B HIS* 5.3 0.2 + - - -
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Residues in contact with ARG 844 (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* 4.3 8.7 - - - -
835B CYS 3.0 22.8 + - - -
836B ALA* 3.7 10.5 + - - +
837B HIS 2.9 22.8 + - - -
840B PHE* 3.5 12.1 + - - +
841B ASP* 2.8 42.9 + - - +
843B LEU* 1.3 77.1 - - + +
845B ASP* 1.3 63.0 + - - +
846B PRO* 3.5 3.1 - - - +
860B PHE* 3.8 25.8 - - + -
876B ILE* 3.3 33.5 + - - +
877B LEU* 4.3 10.9 + - - +
879B PRO* 3.8 15.3 - - + +
881B HIS* 3.4 19.0 + - - -
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Residues in contact with ASP 845 (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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841B ASP 3.5 4.6 + - - +
842B GLU* 3.2 22.2 + - + +
843B LEU 4.1 0.7 - - - +
844B ARG* 1.3 78.5 - - - +
846B PRO* 1.3 76.8 - - - +
847B ASN* 2.7 36.7 + - - +
848B VAL* 3.2 25.4 + - + +
881B HIS* 4.1 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