Contacts of the strand formed by residues 769 - 775 (chain B) in PDB entry 5M64
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 PHE 769 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744B LEU* 5.1 4.7 - - + -
746B THR* 3.4 28.9 - - - +
748B GLN* 3.6 17.3 - - + -
768B GLY* 1.3 82.4 - - - +
770B ASN* 1.3 75.1 + - - +
771B ALA* 4.6 3.1 - - + -
796B ARG* 5.6 5.8 - - - +
798B PHE* 3.4 48.5 - + - -
799B GLY* 3.5 28.7 - - - -
917B PHE* 5.0 6.5 - + - -
1032B TYR* 3.2 16.9 - - - -
1033B TYR* 3.2 33.4 + - + +
1034B GLN 5.9 0.4 - - - -
1035B ARG* 5.2 10.8 - - + -
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Residues in contact with ASN 770 (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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748B GLN* 4.3 3.4 - - - +
749B THR 3.1 27.7 + - - -
750B PRO* 3.5 6.4 - - - +
751B ILE* 3.3 22.8 + - + +
769B PHE* 1.3 83.8 - - - +
771B ALA* 1.3 61.6 + - - +
1030B VAL* 5.6 4.5 - - + -
1031B VAL 4.4 3.1 - - - +
1032B TYR* 3.2 33.7 + - - +
8J PHE* 4.6 6.9 - - - -
48J ARG* 3.7 22.5 + - - +
49J MET* 5.9 1.0 - - - +
52J THR* 3.3 18.9 - - + +
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Residues in contact with ALA 771 (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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769B PHE* 4.4 4.9 + - + -
770B ASN* 1.3 75.0 - - - +
772B VAL* 1.3 64.2 + - - +
773B VAL* 3.4 5.4 + - - +
798B PHE* 3.9 18.6 - - + -
946B ASP* 3.3 25.8 - - - +
947B ILE* 4.7 5.8 - - + -
1030B VAL* 3.5 16.3 - - - +
1031B VAL 3.5 12.5 + - - +
1033B TYR* 4.7 8.0 - - + +
8J PHE* 4.5 2.5 - - + -
48J ARG* 3.4 11.2 - - - +
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Residues in contact with VAL 772 (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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771B ALA* 1.3 70.6 - - - +
773B VAL* 1.3 63.5 + - - +
943B ILE* 5.3 13.9 - - + -
944B GLN 4.2 9.4 - - - +
945B PRO* 4.2 8.4 - - + +
946B ASP* 2.9 42.2 + - - +
947B ILE* 3.3 11.6 + - - +
970B LYS* 6.2 0.4 - - - -
1028B VAL* 3.8 22.4 - - + -
1029B GLY 3.3 12.6 - - - +
1030B VAL* 3.7 9.4 - - + -
8J PHE* 4.6 2.2 - - + -
9J SER* 5.0 3.1 - - - +
44J TYR* 5.4 7.0 - - + -
45J CYS* 5.8 1.6 - - + -
48J ARG* 3.3 20.9 - - - +
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Residues in contact with VAL 773 (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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771B ALA 3.8 5.6 - - - +
772B VAL* 1.3 68.2 - - - +
774B ALA* 1.3 61.7 + - - +
775B VAL* 4.0 10.3 + - + +
947B ILE* 4.2 4.9 - - + -
949B ILE* 4.0 22.2 - - + +
962B MET* 4.4 9.6 - - + -
966B SER* 4.9 2.0 - - - +
1028B VAL* 3.3 4.8 - - - +
1029B GLY* 2.4 55.6 + - - +
1031B VAL* 3.5 32.3 - - + +
1033B TYR* 3.3 41.7 - - + +
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Residues in contact with ALA 774 (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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772B VAL 3.9 0.2 + - - -
773B VAL* 1.3 74.1 - - - +
775B VAL* 1.3 60.9 + - - +
776B ILE* 3.0 21.0 + - + +
937B PRO* 6.4 0.4 - - + -
945B PRO* 3.6 33.9 - - + -
947B ILE 3.5 12.1 + - - +
948B ILE* 3.5 7.6 - - + -
949B ILE 3.4 16.8 + - - -
1026B ILE* 4.8 6.1 - - + -
1027B TYR 3.8 6.7 - - - +
1028B VAL* 4.2 8.1 - - + -
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Residues in contact with VAL 775 (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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827A THR* 2.9 21.7 + - - -
828A CYS 4.7 4.0 - - - +
773B VAL* 3.9 10.7 - - + +
774B ALA* 1.3 68.0 - - - +
776B ILE* 1.3 60.0 + - - +
949B ILE* 3.5 21.5 - - + +
951B PRO* 3.6 20.9 - - + -
954B PHE* 3.6 34.5 - - + -
962B MET* 5.1 5.2 - - + -
963B PHE* 4.5 8.1 - - + -
966B SER* 5.6 0.9 - - - +
1027B TYR* 3.0 46.0 + - + +
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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