Contacts of the strand formed by residues 1027 - 1035 (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 TYR1027 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A THR* 3.4 6.3 + - - -
828A CYS 3.4 18.6 + - - +
829A GLY* 3.6 2.5 - - - -
830A MET* 3.5 33.0 - - + +
775B VAL* 3.0 51.6 + - + +
963B PHE* 2.3 53.0 + + + -
966B SER* 3.2 28.0 - - - -
967B LEU* 3.3 27.7 - - + +
1008B HIS 4.6 1.1 - - - -
1009B GLY 5.1 0.4 - - - -
1010B ASN* 4.2 12.8 - - + -
1026B ILE* 1.3 83.9 - - - +
1028B VAL* 1.3 68.4 + - - +
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Residues in contact with VAL1028 (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* 3.8 20.9 - - + -
773B VAL 3.3 14.4 - - - +
774B ALA* 4.2 5.8 - - + -
943B ILE* 5.8 2.9 - - + -
945B PRO* 5.6 0.2 - - + -
966B SER* 4.5 2.3 - - - +
967B LEU* 5.3 0.7 - - - +
970B LYS* 2.9 32.2 + - - +
1009B GLY 3.9 6.4 - - - +
1010B ASN* 4.8 1.4 - - - +
1011B GLU* 3.7 39.9 - - + +
1013B MET* 4.4 15.3 - - + -
1026B ILE* 3.9 8.0 + - + -
1027B TYR* 1.3 90.9 - - - +
1029B GLY* 1.3 62.0 + - - +
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Residues in contact with GLY1029 (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* 3.2 9.0 - - - +
773B VAL* 2.4 47.1 + - - +
966B SER* 3.7 18.5 + - - -
970B LYS* 3.8 14.4 - - - -
1027B TYR* 4.9 0.4 - - - -
1028B VAL* 1.3 76.3 - - - +
1030B VAL* 1.3 58.9 + - - +
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Residues in contact with VAL1030 (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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751B ILE* 5.7 8.3 - - + -
770B ASN* 5.6 4.5 - - + -
771B ALA 3.5 8.3 - - - +
772B VAL* 3.7 8.5 - - + -
773B VAL 4.0 0.4 - - - +
965B GLU 3.4 15.4 - - - +
966B SER* 3.8 3.5 + - - +
969B GLY* 3.4 23.3 - - - +
973B ALA* 4.9 3.8 - - + -
1029B GLY* 1.3 78.3 - - - +
1031B VAL* 1.3 69.3 + - - +
44J TYR* 3.2 38.1 - - + +
48J ARG* 3.4 28.3 - - + +
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Residues in contact with VAL1031 (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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770B ASN* 4.4 2.7 - - - -
771B ALA 3.5 13.8 + - - +
773B VAL* 3.5 17.0 - - + +
919B SER* 3.8 20.2 - - - +
920B ARG* 4.8 2.9 - - - -
921B HIS* 4.3 17.9 - - + +
962B MET* 3.6 25.6 - - + +
965B GLU* 4.7 2.5 - - + -
966B SER* 3.5 22.9 - - - +
1030B VAL* 1.3 80.1 - - - +
1032B TYR* 1.3 76.4 + - - +
1033B TYR* 3.1 19.8 + - + -
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Residues in contact with TYR1032 (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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703B LEU* 5.9 1.3 - - + -
748B GLN 3.3 22.9 + - - -
750B PRO* 3.5 24.0 - - + +
752B VAL* 5.8 3.3 - - + +
757B TYR* 6.4 0.2 - + - -
767B ASN* 2.5 32.3 + - - -
768B GLY* 2.6 20.3 + - - -
769B PHE 3.2 16.8 - - - -
770B ASN* 3.2 28.7 + - - +
919B SER* 3.7 12.3 - - - -
920B ARG* 3.2 61.5 - - - +
1031B VAL* 1.3 71.2 - - - +
1033B TYR* 1.3 66.1 + - - +
1034B GLN* 3.8 22.2 - - + -
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Residues in contact with TYR1033 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768B GLY* 3.9 0.9 - - - -
769B PHE* 3.2 45.4 + - + +
771B ALA* 4.7 11.4 - - + +
773B VAL* 3.3 34.9 - - + +
787B MET* 3.8 15.8 - - + +
798B PHE* 5.1 4.7 - + + -
917B PHE* 5.7 8.1 - + + -
918B SER 4.0 4.7 - - - +
919B SER* 3.5 20.6 - - - -
923B GLN* 3.4 26.5 + - - -
947B ILE* 3.6 43.3 - - + -
949B ILE* 4.7 0.2 - - - +
962B MET* 4.0 4.0 - - - -
1031B VAL* 3.1 20.3 + - + -
1032B TYR* 1.3 77.1 - - - +
1034B GLN* 1.3 71.3 + - - +
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Residues in contact with GLN1034 (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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494B TYR* 5.1 4.4 - - - -
700B LEU* 5.9 0.6 - - - +
703B LEU* 5.7 4.4 - - - +
718B GLN* 4.3 5.6 + - - +
721B MET* 4.2 3.8 - - - +
722B GLY* 4.0 14.7 + - - -
725B THR* 3.3 32.2 - - + +
767B ASN* 4.2 12.3 - - - +
768B GLY* 5.0 5.2 - - - -
769B PHE* 5.8 2.5 - - - -
917B PHE* 3.8 11.0 - - - +
918B SER* 2.9 33.6 + - - +
919B SER 4.2 15.2 - - - +
920B ARG* 4.4 14.7 - - - +
1032B TYR* 3.8 26.5 - - + +
1033B TYR* 1.3 80.9 - - - +
1035B ARG* 1.3 62.8 + - - +
1036B LEU* 3.8 5.2 - - + +
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Residues in contact with ARG1035 (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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725B THR* 3.4 6.1 - - - -
726B MET* 3.1 62.6 + - + +
744B LEU* 4.5 13.4 - - + +
767B ASN 5.2 5.5 + - - +
769B PHE* 5.2 8.8 - - + -
799B GLY* 3.2 33.7 + - - -
801B GLY 5.1 1.8 - - - +
909B ARG* 3.4 31.9 + - - +
910B THR 4.1 0.8 + - - -
911B PRO* 3.5 32.9 - - - +
915B ASP* 4.0 12.1 + - + +
916B LYS 5.0 1.3 - - - +
917B PHE* 4.0 20.7 - - + -
1034B GLN* 1.3 74.6 - - - +
1036B LEU* 1.3 67.5 + - - +
1040B VAL* 3.9 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