Contacts of the strand formed by residues 863 - 866 (chain A) in PDB entry 3P8C
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 ARG 863 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856A CYS 3.9 0.3 - - - +
857A TYR* 3.9 2.4 - - - -
858A ASN* 2.8 32.0 + - - +
861A THR* 3.3 10.7 + - - +
862A ASN* 1.3 82.1 - - - +
864A PHE* 1.3 65.5 + - - +
908A PHE* 3.5 47.4 - - + -
909A VAL 3.6 6.3 - - - +
910A GLY* 4.5 2.2 - - - -
911A PRO* 4.9 3.3 - - + +
912A PRO* 6.0 1.0 - - - +
621B GLN* 5.3 2.0 + - - -
624B LEU* 3.7 44.6 + - - +
625B SER* 4.7 0.6 - - - +
628B LEU* 3.9 10.7 - - - +
660B PRO* 4.2 7.7 - - - +
661B GLY 3.6 10.7 - - - +
663B GLU* 2.9 38.0 + - - -
664B SER* 3.4 18.2 - - - +
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Residues in contact with PHE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A PHE* 3.5 38.4 - + + -
855A TYR* 3.8 22.3 - - + -
856A CYS 3.4 6.5 - - - -
857A TYR* 3.5 44.2 - + + -
862A ASN 5.6 0.2 - - - -
863A ARG* 1.3 73.5 - - - +
865A VAL* 1.3 64.7 + - - +
908A PHE* 3.2 9.5 - - - +
909A VAL* 2.8 41.5 + - + +
914A PHE* 3.9 11.9 - + - -
1002A ASN* 3.7 16.6 - - - -
1005A LEU* 4.0 17.3 - - + -
1009A LEU* 3.5 30.7 - - + -
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Residues in contact with VAL 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TYR* 3.4 9.6 - - - -
856A CYS* 2.6 53.7 + - + +
863A ARG 5.5 0.2 - - - +
864A PHE* 1.3 80.4 - - - +
866A ARG* 1.3 66.5 + - - +
907A ASN 3.8 17.0 - - - +
908A PHE* 4.3 3.1 - - + -
661B GLY 3.5 24.5 - - - +
664B SER* 3.8 29.8 - - - +
665B MET* 3.9 21.1 - - + -
666B ARG 5.2 0.9 - - - +
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Residues in contact with ARG 866 (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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791A ASP* 3.2 25.5 + - - +
850A ASP* 2.7 43.0 + - - -
854A ASN* 3.5 17.5 - - + +
855A TYR* 3.3 31.9 + - + +
856A CYS* 4.2 2.7 - - - -
865A VAL* 1.3 81.9 - - - +
867A THR* 1.3 70.1 + - + +
872A SER* 5.1 7.2 + - - -
874A GLU* 5.0 9.1 + - - -
877A ARG* 5.0 0.8 - - - +
906A ARG 5.7 1.6 + - - -
907A ASN 5.1 3.7 + - - +
1151A GLN 4.8 2.3 - - - +
665B MET* 5.7 4.7 - - + +
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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