Contacts of the strand formed by residues 912 - 918 (chain A) in PDB entry 2G30
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 912 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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853A GLN* 3.6 5.2 + - - -
854A ILE* 2.9 38.0 + - + +
857A CYS* 3.4 47.1 - - + -
858A HIS* 3.2 6.7 - - - -
859A LEU 2.2 40.2 + - - -
864A VAL* 4.0 6.7 - - + -
903A LEU* 4.0 22.0 - - + -
904A ARG 3.4 9.0 - - - +
905A ILE* 3.6 46.8 - - + +
906A GLN 4.9 6.5 - - - -
909A ASN 5.4 3.1 - - - -
910A PRO 4.8 1.8 - - - -
911A ASN* 1.3 80.3 - - - +
913A THR* 1.3 61.8 + - - +
914A LEU 4.0 0.2 - - - -
935A LEU* 4.8 4.9 - - + -
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Residues in contact with THR 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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851A GLN* 4.1 33.0 - - + +
852A PHE 3.6 5.2 - - - +
853A GLN* 2.8 25.4 + - - +
902A GLU* 3.5 3.9 - - - +
903A LEU* 3.5 4.7 - - - -
904A ARG* 2.8 59.1 + - - +
906A GLN* 5.5 2.4 + - - -
909A ASN* 5.7 0.3 + - - -
911A ASN 4.0 2.1 + - - -
912A TYR* 1.3 72.1 - - - +
914A LEU* 1.3 61.8 + - - +
915A SER* 4.4 4.2 + - - +
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Residues in contact with LEU 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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851A GLN* 3.3 3.0 - - - -
852A PHE* 2.8 44.9 + - + +
854A ILE* 3.6 20.2 - - + -
901A ALA* 3.9 6.5 - - + -
902A GLU 3.5 9.4 - - - +
903A LEU* 4.0 6.7 - - + -
912A TYR 4.0 0.8 + - - -
913A THR* 1.3 72.5 - - - +
915A SER* 1.3 62.4 + - - +
916A LEU* 3.9 36.8 - - + -
928A TYR* 4.3 13.2 - - + -
931A TYR* 3.7 55.0 - - + -
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Residues in contact with SER 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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841A TRP* 4.1 4.7 - - - -
849A GLU* 3.6 21.3 - - - -
850A LEU 3.4 4.5 - - - -
851A GLN* 3.0 31.2 + - - +
900A LEU 3.9 0.2 - - - +
901A ALA* 3.2 5.5 - - - +
902A GLU* 2.8 45.1 + - - -
913A THR* 4.0 3.0 + - - +
914A LEU* 1.3 74.4 - - - +
916A LEU* 1.3 63.2 + - - +
15P ARG* 3.4 14.6 + - - -
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Residues in contact with LEU 916 (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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848A ASN 3.7 2.4 - - - +
849A GLU* 3.4 4.2 - - - -
850A LEU* 2.8 36.8 + - - +
852A PHE* 3.7 15.7 - - + -
899A ILE* 4.0 14.6 - - + -
900A LEU 3.4 3.6 - - - +
901A ALA* 3.5 28.7 - - + -
914A LEU* 3.9 21.5 - - + -
915A SER* 1.3 76.2 - - - +
917A LYS* 1.3 62.0 + - - +
918A CYS 4.4 0.2 + - - -
924A SER* 3.4 43.6 + - - +
927A ILE* 3.9 21.5 - - + -
928A TYR 4.1 4.9 - - - +
931A TYR* 4.8 1.6 - - + -
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Residues in contact with LYS 917 (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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841A TRP* 2.7 71.3 + - + +
844A ILE* 3.2 47.3 + - + +
845A PRO 3.8 7.4 - - - -
846A ASN* 3.4 24.1 + - - +
848A ASN 4.6 2.2 - - - -
849A GLU* 4.0 22.5 + - + +
898A TRP 4.3 0.2 - - - +
899A ILE* 3.7 1.7 - - - -
900A LEU* 2.8 39.9 + - + +
915A SER 4.3 0.2 + - - -
916A LEU* 1.3 77.8 - - - +
918A CYS* 1.3 63.5 + - - +
15P ARG* 5.8 0.2 - - - +
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Residues in contact with CYS 918 (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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844A ILE* 4.3 8.0 - - - +
848A ASN* 3.1 24.2 + - - +
897A ILE* 3.6 19.1 - - - -
898A TRP 3.5 19.3 - - - +
899A ILE* 3.9 7.9 - - + -
916A LEU 4.2 0.8 + - - -
917A LYS* 1.3 77.5 - - - +
919A ARG* 1.3 64.3 + - - +
920A ALA 3.2 34.9 + - - +
921A PRO* 3.7 6.3 - - + +
923A VAL* 3.8 9.6 - - - -
924A SER* 4.0 16.3 + - - +
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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