Contacts of the helix formed by residues 831 - 840 (chain B) in PDB entry 5J3V
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 ASP 831 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791B GLN 4.4 8.5 - - - +
794B ILE* 3.8 28.9 - - + +
795B ARG* 3.0 43.9 + - - +
798B CYS* 5.7 0.5 - - - -
827B GLY 5.2 0.3 - - - +
828B VAL 3.1 7.5 + - - +
830B GLN* 1.3 92.3 - - - +
832B PHE* 1.3 58.2 + - - +
833B ILE* 3.1 8.5 - - - +
834B PHE* 3.2 26.4 + - + +
835B PHE* 3.6 8.7 + - - +
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Residues in contact with PHE 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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828B VAL* 2.8 31.8 + - + +
829B ILE* 3.5 18.7 + - + +
830B GLN 3.6 0.6 + - - -
831B ASP* 1.3 75.0 - - - +
833B ILE* 1.3 64.7 + - - +
834B PHE 3.2 0.4 + - - -
835B PHE* 3.5 19.4 + + - +
836B CYS* 3.3 37.3 + - - -
856B ILE* 3.8 18.2 - - + -
857B LEU* 3.6 22.0 - - + -
860B PHE* 3.5 62.8 - + + -
869B TRP* 4.7 2.0 - + - -
872B PHE* 3.8 9.9 - + + -
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Residues in contact with ILE 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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830B GLN 5.5 3.6 - - - +
831B ASP* 3.1 3.3 - - - -
832B PHE* 1.3 81.4 - - - +
834B PHE* 1.3 73.7 + - + +
836B CYS* 3.7 4.2 + - - +
837B ASP* 3.4 26.2 + - - +
872B PHE* 3.5 24.0 - - + -
875B GLN* 3.3 31.4 - - + +
876B PHE* 4.1 18.5 - - + -
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Residues in contact with PHE 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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794B ILE 4.5 5.2 - - - +
795B ARG* 3.2 55.6 - - + -
798B CYS* 3.2 28.7 - - + +
799B THR* 3.5 33.0 - - + -
802B ARG* 5.6 1.8 - - - -
831B ASP* 3.2 24.0 + - + +
833B ILE* 1.3 90.6 - - + +
835B PHE* 1.3 63.8 + - - +
836B CYS 3.1 1.8 - - - -
837B ASP* 3.1 24.3 + - + +
838B ALA 3.2 4.2 + - - -
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Residues in contact with PHE 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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794B ILE* 6.4 1.1 - - + -
797B TRP* 5.6 2.0 - + - -
798B CYS* 3.7 17.2 - - - -
814B PHE* 5.3 2.2 - + - -
817B ILE* 4.4 24.5 - - + -
818B CYS* 5.4 0.2 - - - -
821B ILE* 3.9 23.8 - - + -
828B VAL* 3.7 28.3 - - + -
831B ASP 3.6 4.1 + - - +
832B PHE* 3.5 25.3 + + - +
833B ILE 3.5 0.4 - - - -
834B PHE* 1.3 79.5 - - - +
836B CYS* 1.3 61.2 + - - +
838B ALA* 3.4 3.4 + - + +
839B VAL* 3.2 44.1 + - + +
853B PHE* 4.4 9.9 - + - -
856B ILE* 3.7 29.8 - - + -
857B LEU* 4.3 13.9 - - + -
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Residues in contact with CYS 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 PHE* 3.3 40.8 + - - -
833B ILE 3.9 4.7 - - - +
834B PHE 3.1 0.8 - - - -
835B PHE* 1.3 76.6 - - - +
837B ASP* 1.3 65.2 + - - +
839B VAL* 4.7 1.3 - - - -
840B ALA* 3.1 4.3 + - - +
857B LEU* 3.9 13.7 - - - -
869B TRP* 5.0 1.6 - - - -
872B PHE* 4.3 2.5 - - - -
876B PHE* 3.9 29.8 - - + -
883B ARG* 2.3 51.4 + - - +
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Residues in contact with ASP 837 (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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798B CYS* 5.6 1.8 - - + +
802B ARG* 3.3 58.4 + - + +
833B ILE* 3.4 20.4 + - - +
834B PHE* 3.1 20.6 + - + +
836B CYS* 1.3 78.1 - - - +
838B ALA* 1.3 60.3 + - - +
840B ALA* 3.7 11.7 + - - +
841B SER 3.8 4.0 + - - -
876B PHE* 4.8 11.3 - - - -
877B PRO* 5.9 2.1 - - - +
879B PRO* 4.8 11.0 - - - +
883B ARG* 5.4 0.2 - - - +
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Residues in contact with ALA 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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797B TRP* 4.7 1.3 - - + -
798B CYS* 3.8 39.9 + - + +
801B LEU 5.3 0.2 - - - -
802B ARG* 4.4 4.9 - - + +
814B PHE* 3.6 25.5 - - + -
834B PHE 3.2 4.6 + - - -
835B PHE* 3.7 9.0 - - + +
836B CYS 3.2 0.6 - - - -
837B ASP* 1.3 76.1 - - - +
839B VAL* 1.3 61.0 + - - +
841B SER* 2.5 28.2 + - - -
842B TRP* 3.6 6.6 - - - -
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Residues in contact with VAL 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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814B PHE* 4.4 3.4 - - + -
835B PHE* 3.2 45.2 + - + +
836B CYS* 3.4 0.6 + - - -
838B ALA* 1.3 74.8 - - - +
840B ALA* 1.3 62.3 + - - +
842B TRP* 3.1 27.4 + - + +
853B PHE* 3.6 40.4 - - + -
857B LEU* 4.9 4.3 - - + -
883B ARG* 3.4 13.7 - - - +
888B TYR* 3.8 24.2 + - + +
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Residues in contact with ALA 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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836B CYS 3.1 7.3 + - - +
837B ASP 3.9 7.6 - - - +
838B ALA 3.2 0.4 - - - -
839B VAL* 1.3 76.3 - - - +
841B SER* 1.3 60.5 + - - +
842B TRP 3.1 3.6 + - - +
879B PRO* 3.6 24.0 - - + -
882B GLU* 3.6 32.0 - - - +
883B ARG* 3.0 29.7 - - - +
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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