Contacts of the strand formed by residues 748 - 751 (chain A) in PDB entry 2DFS
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 LYS 748 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A GLU* 2.7 43.6 + - - -
479A LYS* 6.0 0.2 - - - -
480A GLU* 2.9 29.2 + - - +
701A ARG* 4.2 17.7 - - + +
702A TRP 3.4 13.0 - - - +
703A THR* 4.6 11.7 - - + -
704A TYR* 2.8 27.0 + - - -
745A GLY* 3.0 16.6 + - - -
747A THR* 1.3 86.4 - - - +
749A ILE* 1.4 58.7 + - - +
750A PHE* 3.9 12.3 - - + -
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Residues in contact with ILE 749 (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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700A SER 3.7 1.0 - - - +
701A ARG* 3.4 6.4 - - - -
702A TRP* 2.8 32.0 + - + +
703A THR 4.8 0.4 - - - +
704A TYR* 3.5 34.1 - - + +
707A PHE* 3.7 46.7 - - + -
728A CYS* 4.6 2.0 - - + -
732A LEU* 4.0 6.1 - - + -
742A TYR* 4.5 2.9 - - + -
743A GLN 3.7 11.2 - - - +
744A PHE* 3.7 22.4 - - + -
748A LYS* 1.4 73.4 - - - +
750A PHE* 1.3 68.1 + - - +
751A PHE* 3.6 26.8 - - + -
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Residues in contact with PHE 750 (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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476A GLU* 3.2 29.4 - - + -
477A TYR* 4.0 20.9 - + - -
480A GLU* 3.7 22.2 - - + -
482A ILE* 3.4 35.0 - - + -
698A PHE* 3.5 22.4 - + + -
700A SER 3.7 3.6 - - - -
701A ARG* 3.5 34.5 - - + -
742A TYR* 3.2 6.4 - - - +
743A GLN* 2.9 40.6 + - + +
748A LYS* 3.9 19.5 - - + -
749A ILE* 1.3 77.6 - - - +
751A PHE* 1.3 59.2 + - - +
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Residues in contact with PHE 751 (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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698A PHE* 3.3 24.1 - - - +
700A SER* 2.8 36.0 + - - +
702A TRP* 4.5 15.5 - + + -
707A PHE* 3.7 28.9 - + - -
732A LEU* 3.5 23.8 - - + -
736A ILE* 4.6 3.1 - - + -
741A LYS 3.8 1.8 - - - -
742A TYR* 4.0 11.0 - + + -
749A ILE* 3.6 35.4 - - + -
750A PHE* 1.3 74.2 - - - +
752A ARG* 1.4 70.2 + - - +
755A GLN* 4.2 15.9 - - + -
756A VAL* 4.2 14.6 - - + -
759A LEU* 3.9 17.5 - - + -
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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