Contacts of the strand formed by residues 857 - 863 (chain F) in PDB entry 4OQB
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 857 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848F TYR* 3.4 25.7 + - - +
851F PHE 3.7 11.7 - - - +
852F LYS* 3.3 45.0 + - - +
853F GLN 5.3 0.2 + - - -
854F LEU* 3.3 26.2 + - + +
855F HIS* 4.1 4.2 - - - +
856F ASN* 1.3 75.2 + - - +
858F ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 858 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856F ASN* 3.5 29.2 + - - +
857F ARG* 1.3 78.8 - - - +
859F LEU* 1.3 61.6 + - - +
860F LEU* 3.5 38.5 + - + +
899F ASP* 5.6 5.7 + - - +
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Residues in contact with LEU 859 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814F ILE* 6.2 0.7 - - + -
817F TYR* 3.0 26.7 + - + -
858F ARG* 1.3 69.5 - - - +
860F LEU* 1.3 62.3 + - - +
921F LEU* 3.5 44.4 - - + +
922F GLY 4.2 15.5 - - - +
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Residues in contact with LEU 860 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817F TYR* 3.9 2.5 - - - +
858F ARG* 3.5 39.4 + - + +
859F LEU* 1.3 81.5 - - - +
861F TRP* 1.3 63.2 + - - +
862F HIS 3.9 0.2 + - - -
897F PHE* 3.9 32.6 - - + -
898F ALA 3.7 4.5 - - - +
899F ASP* 3.5 37.2 - - + +
921F LEU* 3.5 7.7 - - - -
922F GLY 3.1 23.8 + - - +
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Residues in contact with TRP 861 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814F ILE* 4.5 4.9 - - + -
817F TYR* 3.2 46.4 - + + -
818F VAL* 3.4 29.4 - - + -
821F THR* 3.7 1.6 + - - -
860F LEU* 1.3 72.5 - - - +
862F HIS* 1.3 63.0 + - - +
897F PHE* 3.4 7.6 - - - -
898F ALA 2.8 32.8 + - - +
899F ASP 3.5 11.7 - - - -
900F MET 3.4 6.1 - - - +
901F VAL* 3.3 46.8 - - + +
904F SER* 3.2 21.8 + - - +
919F ILE* 3.6 27.6 - - + -
920F LEU 3.4 15.5 - - - -
921F LEU* 3.2 34.5 - - + -
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Residues in contact with HIS 862 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F TRP* 1.3 77.4 - - - +
863F GLY* 1.3 73.1 + - - +
864F SER* 4.6 8.5 - - - -
869F PHE* 4.8 0.2 - - - -
872F ILE* 5.5 0.2 - - - +
877F LEU* 3.4 41.0 - - + +
895F ILE* 4.5 8.3 - - + -
896F TYR* 2.7 29.0 + - + -
897F PHE* 3.7 17.7 - - + -
904F SER* 3.9 2.9 - - - -
919F ILE* 3.9 1.5 - - - +
920F LEU* 2.8 54.7 + - + +
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Residues in contact with GLY 863 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862F HIS* 1.3 86.4 + - - +
864F SER* 1.3 63.7 + - - -
904F SER* 3.4 26.8 + - - +
907F TYR* 3.3 21.0 - - - +
908F CYS* 4.5 1.6 - - - -
918F LEU 4.5 1.1 - - - -
919F ILE* 3.6 15.7 - - - -
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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