Contacts of the strand formed by residues 805 - 809 (chain D) in PDB entry 5DFV
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 THR 805 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D GLN* 3.1 22.3 + - - +
507D SER 4.1 0.7 + - - -
508D PRO* 3.0 33.4 + - + +
509D ALA 3.3 4.7 - - - +
511D LEU* 4.6 4.7 - - + -
521D ILE* 3.3 40.5 - - + +
730D ALA 3.8 0.5 - - - +
731D THR* 3.4 5.6 - - - +
732D TYR* 3.0 32.8 + - - -
804D GLY* 1.3 72.1 + - - -
806D LYS* 1.3 71.6 + - - +
807D LEU 3.7 0.7 + - - -
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Residues in contact with LYS 806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D ALA 3.1 9.5 + - - +
510D SER* 3.5 12.2 - - - -
511D LEU* 2.8 35.3 + - - +
730D ALA 3.7 5.8 - - - +
731D THR* 4.1 20.3 - - + +
804D GLY 4.3 0.2 - - - -
805D THR* 1.3 72.2 - - - +
807D LEU* 1.3 61.7 + - - +
808D GLU* 3.4 33.5 + - - +
2034D LYS* 5.1 10.1 - - - +
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Residues in contact with LEU 807 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LEU* 3.6 13.0 - - + +
513D VAL* 3.8 22.4 - - + -
519D ALA* 4.5 9.2 - - + -
521D ILE* 5.4 3.6 - - + -
721D ILE* 3.4 33.7 - - + -
724D VAL* 4.8 8.3 - - + -
728D ASP* 3.6 23.6 - - + +
729D ALA* 3.5 10.9 - - - +
730D ALA 2.7 34.0 + - - +
732D TYR* 3.7 10.3 - - + -
805D THR 3.7 0.2 + - - -
806D LYS* 1.3 75.9 - - - +
808D GLU* 1.3 91.4 + - - +
809D ILE* 5.5 0.4 - - + -
2058D GLN* 4.9 0.2 + - - -
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Residues in contact with GLU 808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D SER* 4.5 8.1 - - - -
511D LEU 2.7 20.7 + - - +
512D SER* 3.5 15.7 - - - -
513D VAL 3.6 9.0 + - - +
806D LYS* 3.4 40.2 + - - +
807D LEU* 1.3 93.8 - - - +
809D ILE* 1.3 66.7 + - - +
2032D TYR* 5.8 1.8 - - + +
2034D LYS* 5.1 5.2 + - - +
2058D GLN* 3.8 13.3 - - + +
2065D TYR* 2.7 36.4 + - - +
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Residues in contact with ILE 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D SER* 4.8 0.2 - - - -
513D VAL 3.5 7.6 - - - +
515D LEU* 3.9 27.8 - - + +
724D VAL* 5.1 5.4 - - + -
725D GLU 4.1 3.4 - - - +
726D GLU* 3.2 44.4 - - + +
729D ALA* 4.2 9.6 - - + -
807D LEU* 5.5 0.7 - - + -
808D GLU* 1.3 81.8 - - - +
810D LYS* 1.3 74.2 + - - +
2000D ARG* 3.5 5.4 + - + +
2032D TYR* 3.8 9.4 - - - -
2058D GLN* 3.1 30.7 - - - +
2059D ASP 6.1 0.9 - - - +
2060D SER 6.1 0.7 - - - +
2063D SER* 4.2 19.2 - - - +
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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