Contacts of the strand formed by residues 908 - 914 (chain A) in PDB entry 6N8P
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 GLN 908 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A HIS* 5.7 0.8 + - - -
434A GLN* 5.8 0.6 - - - +
436A ASP* 4.2 17.2 + - - -
453A SER 5.2 2.0 + - - -
454A GLY 4.0 4.7 - - - +
903A PHE* 3.5 7.1 - - - +
904A THR* 2.8 50.5 + - + +
906A TYR* 4.9 3.1 + - - +
907A GLY* 1.3 73.4 - - - +
909A GLY* 1.3 60.2 + - - +
910A PHE* 5.0 3.1 - - + -
920A ARG* 2.9 42.1 + - + +
921A PHE* 3.2 25.1 - - - +
922A SER* 4.3 11.0 - - - +
923A LEU* 5.0 0.9 - - - -
927A TRP* 4.5 25.7 + - + +
929A VAL* 5.1 3.8 - - - +
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Residues in contact with GLY 909 (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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902A VAL 3.2 11.7 - - - -
903A PHE* 4.4 0.9 - - - -
904A THR* 4.2 0.4 - - - +
908A GLN* 1.3 77.6 - - - +
910A PHE* 1.3 72.7 + - - -
920A ARG* 3.4 4.9 - - - +
921A PHE* 2.9 52.8 + - - +
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Residues in contact with PHE 910 (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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29A HIS* 3.9 13.9 - + - -
392A HIS* 3.3 33.9 - + - -
438A LEU* 4.5 16.8 - - + -
452A ALA* 3.9 12.3 - - + -
457A LEU* 4.9 0.4 - - + -
900A SER 4.2 0.5 - - - +
901A CYS* 3.3 1.9 - - - -
902A VAL* 2.9 49.0 + - + +
904A THR* 4.4 6.3 - - + -
908A GLN* 5.0 2.0 - - + -
909A GLY* 1.3 82.1 - - - -
911A TYR* 1.3 63.0 + - - +
918A PHE* 3.9 24.0 - - + -
919A GLU 3.5 3.8 - - - -
920A ARG* 3.3 60.6 - - + -
921A PHE* 3.7 2.8 - - - -
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Residues in contact with TYR 911 (chain A).
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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25A LYS* 3.6 16.0 + - - -
889A CYS* 4.1 7.1 + - + -
890A ILE* 3.6 42.9 - - + +
894A ASP* 4.6 4.0 - - - -
897A GLY 4.0 5.2 - - - +
900A SER 3.6 6.5 - - - -
901A CYS* 3.8 21.8 - - + -
910A PHE* 1.3 76.4 - - - +
912A LEU* 1.3 69.5 + - - +
913A ILE* 3.6 16.5 + - + +
918A PHE* 3.5 7.2 - - - -
919A GLU* 2.6 77.8 + - + -
921A PHE* 3.9 21.1 - + + -
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Residues in contact with LEU 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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387A ILE* 4.4 26.5 - - + +
894A ASP* 4.4 3.6 - - - +
896A SER 5.5 2.0 - - - +
897A GLY* 3.4 26.0 + - - -
900A SER* 3.7 27.6 + - - +
911A TYR* 1.3 80.5 - - - +
913A ILE* 1.3 61.5 + - - +
914A SER 3.4 17.0 - - - +
915A PRO* 4.8 5.8 - - + +
917A GLU 3.4 18.4 - - - +
918A PHE* 3.5 37.9 - - + -
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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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28A GLU* 3.6 40.2 - - + +
894A ASP* 5.1 5.8 - - - +
911A TYR* 3.6 16.0 + - + +
912A LEU* 1.3 73.2 - - - +
914A SER* 1.3 63.6 + - - +
917A GLU* 3.2 33.7 + - + +
919A GLU* 3.3 36.6 - - + +
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Residues in contact with SER 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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33A HIS* 3.6 26.7 - - - +
912A LEU* 3.4 15.5 - - - +
913A ILE* 1.3 79.0 - - - +
915A PRO* 1.3 76.0 - - - +
916A SER 2.9 5.2 + - - -
917A GLU* 3.2 44.9 + - - +
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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