Contacts of the strand formed by residues 831 - 838 (chain B) in PDB entry 5MQF
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 TYR 831 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B GLU 3.9 0.2 + - - -
830B PRO* 1.3 72.2 - - - +
832B TYR* 1.3 62.5 + - - +
833B PHE* 4.7 0.2 - - - +
874B PHE* 5.4 7.0 - - + -
875B ILE 3.2 19.7 - - - +
876B PRO* 4.7 1.8 - - + -
877B ALA 4.6 0.2 - - - +
901B PHE* 4.7 0.2 - - - -
902B HIS* 2.8 48.6 + - + +
903B HIS* 4.1 1.3 + - + -
904B TRP* 4.3 10.7 - - - +
905B GLN* 5.2 5.4 - - + +
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Residues in contact with TYR 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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830B PRO 4.0 2.8 + - - -
831B TYR* 1.3 70.7 - - - +
833B PHE* 1.3 58.9 + - - +
834B VAL* 4.1 1.1 + - - +
873B ALA 3.4 1.4 - - - +
874B PHE* 4.8 0.2 - - - -
875B ILE* 2.9 36.7 + - - +
877B ALA* 4.4 9.2 - - + +
880B SER* 4.4 20.6 - - - -
899B SER* 4.3 15.5 - - - -
900B VAL 2.8 19.7 - - - +
901B PHE* 4.4 2.0 - - - +
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Residues in contact with PHE 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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831B TYR 3.4 2.0 + - - +
832B TYR* 1.3 71.0 - - - +
834B VAL* 1.3 58.3 + - - +
835B GLU 4.2 0.6 + - - -
858B THR* 5.5 4.0 - - - -
872B LYS* 5.6 3.8 - - + -
873B ALA 2.7 18.8 - - - +
874B PHE* 4.5 4.3 - - + +
898B LEU 3.5 1.0 - - - +
899B SER* 3.0 2.6 - - - -
900B VAL* 2.9 30.7 + - + +
902B HIS* 4.3 15.9 - - + -
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Residues in contact with VAL 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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832B TYR 5.4 0.9 - - - +
833B PHE* 1.3 71.7 - - - +
835B GLU* 1.3 60.7 + - - +
836B VAL* 4.7 1.7 - - - +
871B ILE 3.2 6.8 - - - +
872B LYS* 4.0 1.1 - - - -
873B ALA* 2.9 40.6 + - + +
883B PHE* 6.3 2.9 - - + -
897B SER* 4.7 8.3 - - - -
898B LEU 2.7 18.8 - - - +
899B SER* 3.7 15.3 - - - -
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Residues in contact with GLU 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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237B LEU* 4.8 19.3 - - + +
833B PHE 4.2 0.8 - - - -
834B VAL* 1.3 71.4 - - - +
836B VAL* 1.3 59.1 + - - +
870B THR* 6.1 3.1 - - - -
871B ILE 3.6 5.2 - - - -
872B LYS* 3.8 12.9 - - + +
896B PHE 3.9 0.7 - - - +
897B SER* 2.9 3.3 - - - -
898B LEU* 2.9 32.0 + - + +
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Residues in contact with VAL 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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834B VAL* 4.7 2.0 - - + +
835B GLU* 1.3 74.7 - - - +
837B GLN* 1.3 61.4 + - - +
838B ALA* 5.3 2.5 - - + -
846B VAL* 5.4 11.0 - - + -
869B TYR 3.3 1.1 - - - +
870B THR* 2.9 29.1 - - - -
871B ILE* 2.9 23.4 + - + +
895B ALA* 5.3 8.1 - - + -
896B PHE 3.5 4.7 - - - -
897B SER* 3.7 15.0 - - - -
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Residues in contact with GLN 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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336A ASN* 5.9 4.5 - - + -
836B VAL* 1.3 72.7 - - - +
838B ALA* 1.3 55.8 + - - +
868B LEU* 5.6 7.9 - - + -
869B TYR 3.3 5.4 - - - +
870B THR* 4.6 4.7 - - - +
895B ALA* 2.8 30.7 + - - -
896B PHE* 2.9 24.7 + - + +
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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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836B VAL* 5.3 3.1 - - + -
837B GLN* 1.3 76.5 - - - +
839B PRO* 1.3 74.8 - - + +
842B CYS* 3.6 23.6 - - + +
843B VAL* 4.3 3.4 - - + +
846B VAL* 6.1 0.9 - - + -
868B LEU* 5.3 2.6 - - - +
869B TYR* 2.8 38.4 + - - +
895B ALA* 3.6 17.3 - - + +
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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