Contacts of the strand formed by residues 911 - 915 (chain A) in PDB entry 1Y6A
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 MET 911 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A ARG* 3.5 44.9 - - + +
832A LEU* 4.0 13.9 - - + -
834A LEU* 4.6 9.0 - - - -
865A VAL* 3.7 20.4 - - + -
866A LYS 3.3 3.8 - - - -
867A MET* 3.6 33.4 - - + +
902A ALA* 3.3 6.8 - - - +
903A CYS* 2.9 46.2 + - + +
909A PRO* 3.7 10.1 - - + +
910A LEU* 1.3 81.9 - - - +
912A VAL* 1.3 64.3 + - - +
913A ILE* 4.1 1.8 - - + -
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Residues in contact with VAL 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864A ALA 3.7 1.2 - - - +
865A VAL* 3.5 2.1 - - - -
866A LYS* 2.8 39.8 + - + +
880A LEU* 3.7 34.8 - - + +
883A GLU* 5.2 3.8 - - + -
884A LEU* 4.0 32.1 - - + +
887A LEU* 4.3 14.6 - - + -
899A LEU* 3.8 22.9 - - + -
901A GLY 4.0 2.2 - - - -
902A ALA* 4.6 0.2 - - - +
910A LEU* 5.0 3.4 - - + -
911A MET* 1.3 78.3 - - - +
913A ILE* 1.3 62.3 + - - +
914A VAL* 4.0 7.4 + - + +
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Residues in contact with ILE 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A PHE* 3.8 37.5 - - + -
832A LEU* 4.0 16.6 - - + -
854A ILE* 3.8 18.4 - - + -
863A VAL* 3.4 37.5 - - + -
864A ALA 3.4 4.7 - - - +
865A VAL* 4.4 13.5 - - + -
899A LEU* 3.5 1.7 - - - +
900A LEU* 2.7 31.0 + - + -
901A GLY 2.9 26.5 + - - +
902A ALA* 4.5 1.1 - - - +
903A CYS* 4.1 8.3 - - - -
911A MET 4.8 1.1 - - - +
912A VAL* 1.3 76.5 - - - +
914A VAL* 1.3 62.3 + - - +
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Residues in contact with VAL 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A AAZ 3.8 26.0 - - + -
863A VAL* 3.7 6.9 - - - +
864A ALA* 2.8 39.7 + - + +
866A LYS* 6.1 0.9 - - + +
887A LEU* 4.1 24.9 - - + -
897A VAL* 3.7 20.0 - - + -
898A ASN 3.2 16.6 - - - +
899A LEU* 4.2 2.2 - - - -
900A LEU* 3.7 5.8 - - - +
912A VAL* 4.4 11.4 - - + +
913A ILE* 1.3 79.3 - - - +
915A GLU* 1.3 62.8 + - - +
916A PHE 3.6 0.2 + - - -
1045A PHE* 4.5 8.5 - - + -
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Residues in contact with GLU 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A AAZ 3.3 18.9 - - - -
892A HIS* 4.8 5.0 - - - -
896A VAL 3.3 1.2 - - - +
897A VAL* 3.6 10.9 - - + +
898A ASN* 2.8 49.9 + - - +
900A LEU* 3.7 24.8 - - + +
914A VAL* 1.3 78.5 - - - +
916A PHE* 1.3 63.3 + - - +
917A CYS* 4.3 1.5 - - - -
1041A LYS* 2.9 40.1 + - + +
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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