Contacts of the strand formed by residues 916 - 919 (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 LYS 916 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A VAL* 6.0 1.6 - - + -
629A ASP 3.0 21.4 + - - -
630A GLY* 3.6 21.7 - - - +
721B MET* 5.9 0.2 - - + -
914B GLY 4.2 6.5 - - - +
915B ASP* 1.3 82.2 - - - +
917B PHE* 1.3 66.0 + - - +
924B LYS* 3.3 30.3 - - - +
925B GLY 3.3 8.7 - - - +
926B VAL* 4.8 6.3 - - + -
1035B ARG* 5.0 0.9 - - - +
1036B LEU* 3.3 31.5 + - + +
1038B HIS* 3.1 53.6 + - + +
1039B MET 4.8 1.5 + - - +
9R U 4.2 6.7 + - - -
10R C 4.0 6.3 + - - -
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Residues in contact with PHE 917 (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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721B MET* 5.5 0.2 - - - +
769B PHE* 5.0 5.2 - + - -
787B MET* 5.1 19.1 - - + -
789B ILE* 5.5 7.4 - - + -
798B PHE* 4.0 33.0 - + - -
799B GLY* 5.6 0.9 - - - -
911B PRO* 4.9 6.3 - - + -
912B GLN 5.5 0.2 - - - -
915B ASP* 3.1 36.3 - - - -
916B LYS* 1.3 78.2 - - - +
918B SER* 1.3 63.0 + - - +
923B GLN* 5.2 0.4 - - - +
924B LYS* 3.4 2.4 - - - +
925B GLY* 2.8 36.8 + - - +
927B CYS* 4.5 14.6 - - + -
947B ILE* 5.3 8.7 - - + -
1033B TYR* 5.7 8.7 - + + -
1034B GLN 3.8 16.2 - - - +
1035B ARG* 4.0 27.1 - - + -
1036B LEU* 3.9 1.1 - - - -
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Residues in contact with SER 918 (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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721B MET* 3.7 34.9 - - - +
917B PHE* 1.3 78.1 - - - +
919B SER* 1.3 67.7 + - - +
922B GLY 4.2 1.6 + - - -
923B GLN* 2.6 26.7 + - - +
924B LYS* 3.5 10.3 - - - +
1033B TYR* 4.5 5.7 - - - -
1034B GLN* 2.9 36.8 + - - +
1036B LEU* 3.7 4.2 - - - +
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Residues in contact with SER 919 (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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718B GLN* 3.6 10.9 + - - +
721B MET* 4.7 0.7 - - - +
918B SER* 1.3 87.5 + - - +
920B ARG* 1.3 63.0 + - - +
921B HIS* 3.2 15.7 + - - +
922B GLY 3.9 1.4 + - - -
923B GLN* 2.9 37.2 + - - +
962B MET* 5.0 0.5 - - - -
1031B VAL* 3.8 10.5 - - - +
1032B TYR 3.7 12.6 - - - -
1033B TYR* 3.5 17.7 - - - +
1034B GLN* 4.2 8.5 - - - +
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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