Contacts of the strand formed by residues 854 - 859 (chain A) in PDB entry 5ON2
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 LEU 854 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A VAL* 4.1 5.6 - - - +
803A VAL* 3.5 30.5 - - + +
805A GLN* 3.6 39.0 - - + +
848A ILE 4.1 0.2 - - - +
849A TYR* 3.6 3.5 - - - -
850A VAL* 2.8 41.7 + - + +
853A LYS* 1.3 81.9 - - + +
855A LEU* 1.3 69.9 + - - +
856A ASN* 4.6 1.1 - - + +
19B G 3.2 60.1 - - + +
20B U 5.5 4.5 - - - -
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Residues in contact with LEU 855 (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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802A VAL* 4.2 1.1 - - + +
803A VAL 2.9 13.3 + - - +
804A VAL* 3.5 7.5 - - + +
805A GLN* 2.7 33.1 + - - +
822A GLU* 4.9 1.1 - - + -
825A VAL* 4.2 16.4 - - + -
826A ARG* 4.1 22.7 - - + -
829A ALA* 4.0 27.1 - - + -
847A VAL* 3.7 23.1 - - + -
848A ILE 3.5 14.1 - - - +
849A TYR* 3.7 24.2 - - + -
854A LEU* 1.3 76.0 - - - +
856A ASN* 1.3 54.3 + - - +
857A LEU* 4.3 18.8 - - + -
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Residues in contact with ASN 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLN* 3.3 24.4 - - - +
807A ASN 3.5 4.0 + - - -
808A GLY* 2.8 28.1 + - - +
847A VAL* 3.9 0.9 - - - +
848A ILE* 2.8 41.6 + - + +
854A LEU* 4.3 2.4 - - + +
855A LEU* 1.3 72.8 - - - +
857A LEU* 1.3 67.4 + - - +
858A VAL* 3.8 7.6 + - - +
19B G 4.2 11.5 - - - +
56B C 3.0 45.8 + - - +
57B A 4.6 0.4 + - - -
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Residues in contact with LEU 857 (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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804A VAL* 5.1 2.2 - - + -
805A GLN 3.0 17.9 + - - +
806A VAL* 3.5 5.5 - - + -
807A ASN* 2.8 31.0 + - - +
826A ARG* 4.3 12.3 - - - +
829A ALA* 5.6 2.2 - - + -
835A VAL* 4.4 13.5 - - + -
839A LEU* 3.9 32.3 - - + -
844A VAL* 4.6 8.7 - - + -
846A LYS 4.0 2.0 - - - -
847A VAL* 3.9 34.3 - - + -
855A LEU* 4.3 21.3 - - + -
856A ASN* 1.3 73.7 + - - +
858A VAL* 1.3 60.7 + - - +
859A VAL* 3.6 12.4 - - + +
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Residues in contact with VAL 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A ASN* 3.5 7.4 - - - +
844A VAL* 3.9 2.9 - - - +
845A ARG* 3.2 33.5 + - + +
846A LYS* 2.9 40.7 + - + +
848A ILE* 4.8 6.3 - - + -
856A ASN* 4.1 5.8 - - - +
857A LEU* 1.3 72.7 - - - +
859A VAL* 1.3 66.4 + - - +
56B C 3.7 46.7 - - - +
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Residues in contact with VAL 859 (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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806A VAL* 3.8 18.2 - - + -
807A ASN* 2.7 30.2 + - - +
838A TYR 4.2 4.7 - - - +
839A LEU* 3.9 21.1 - - + -
842A VAL* 3.3 37.5 - - + -
843A THR 3.7 9.4 - - - +
844A VAL* 5.2 2.2 - - - -
845A ARG* 4.6 4.3 + - - -
857A LEU* 3.6 15.5 - - + +
858A VAL* 1.3 82.6 - - - +
860A GLY* 1.3 69.7 + - - +
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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