Contacts of the strand formed by residues 833 - 840 (chain B) in PDB entry 3H44
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 VAL 833 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819B ALA* 4.4 2.7 - - + +
820B PHE* 4.0 38.9 - - + +
823B LEU* 4.0 35.0 - - + +
824B ARG* 4.2 16.6 - - + +
829B LEU* 4.8 0.7 - - + -
830B GLY 3.9 16.8 - - - +
831B TYR 3.6 3.8 + - - +
832B ILE* 1.3 81.0 - - - +
834B PHE* 1.3 66.2 + - - +
848B PHE* 6.5 0.4 - - + -
849B ILE 3.4 4.5 - - - -
850B ILE* 3.9 22.0 - - + -
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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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819B ALA* 5.9 0.4 - - - -
832B ILE* 5.4 5.6 - - + -
833B VAL* 1.3 80.7 - - - +
835B SER* 1.3 90.9 + - - +
836B GLY* 4.6 2.7 - - - -
837B PRO* 5.6 1.8 - - + -
847B ARG* 3.9 33.0 - - + -
848B PHE* 3.3 7.0 - - - -
849B ILE* 2.8 56.9 + - + +
850B ILE* 5.4 0.5 - - - +
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Residues in contact with SER 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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815B ILE* 4.0 11.6 - - - +
816B SER* 4.1 16.2 + - - -
819B ALA* 3.7 20.0 - - - +
834B PHE* 1.3 100.7 - - - +
836B GLY* 1.3 62.8 + - - +
847B ARG 3.4 8.7 - - - -
848B PHE* 3.6 28.5 - - - -
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Residues in contact with GLY 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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812B ALA* 4.1 9.9 - - - -
815B ILE* 5.2 0.4 - - - +
816B SER* 6.2 0.2 - - - -
834B PHE* 4.7 2.0 - - - -
835B SER* 1.3 83.4 + - - +
837B PRO* 1.4 73.7 - - - +
846B LEU* 3.7 16.6 - - - +
847B ARG* 3.0 32.6 + - - +
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Residues in contact with PRO 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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808B LEU* 3.9 24.7 - - + -
809B GLU* 4.7 14.6 - - + -
812B ALA* 3.7 21.9 - - + -
834B PHE* 5.4 2.1 - - + -
836B GLY* 1.4 84.1 - - - +
838B ARG* 1.3 57.3 + - - +
839B ARG* 4.2 17.7 + - - +
845B GLY 3.5 7.6 - - - +
847B ARG* 3.3 15.2 + - - -
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Residues in contact with ARG 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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683B MET 5.1 1.0 + - - -
686B LEU* 3.4 41.1 + - - +
687B ARG* 4.3 18.2 - - - +
690B MET* 4.0 15.7 - - - +
691B THR* 5.3 1.2 + - - -
768B GLU* 3.5 13.1 + - - -
792B GLU* 4.3 1.7 + - - -
794B TYR* 3.7 39.3 + - + -
837B PRO* 1.3 71.5 - - - +
839B ARG* 1.3 66.7 - - - +
840B ALA* 3.3 29.7 - - - +
841B ASN* 5.0 1.6 - - - +
844B GLN* 3.0 29.9 - - - +
845B GLY 2.7 13.2 + - - +
847B ARG* 3.5 35.6 - - + +
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Residues in contact with ARG 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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800B GLN* 3.6 22.9 - - - +
805B ASN* 3.5 20.9 + - - +
808B LEU* 3.9 7.5 - - - +
809B GLU* 3.0 41.8 + - - +
837B PRO* 4.2 15.0 + - - +
838B ARG* 1.3 89.2 - - - +
840B ALA* 1.3 65.3 + - - +
843B ILE 3.6 2.2 - - - -
844B GLN* 2.7 28.4 + - + +
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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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687B ARG* 6.6 0.2 - - + -
768B GLU* 3.7 11.6 - - - +
800B GLN* 4.1 1.6 - - - +
838B ARG* 3.3 31.6 - - - +
839B ARG* 1.3 76.7 - - - +
841B ASN* 1.3 67.1 + - - +
842B GLY 2.6 17.2 + - - -
843B ILE* 2.7 24.1 + - - +
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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