Contacts of the strand formed by residues 2006 - 2010 (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 THR2006 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023C THR* 5.0 12.3 - - + -
1068C THR* 6.2 0.9 - - + -
2004D ALA 3.9 1.9 + - - -
2005D PRO* 1.3 69.2 - - - +
2007D VAL* 1.3 63.2 + - - +
2008D SER* 4.0 12.1 + - - +
2027D PHE* 3.4 4.9 - - - +
2029D ASN* 3.0 40.7 + - - +
2030D ASN* 5.4 5.2 + - - +
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Residues in contact with VAL2007 (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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2005D PRO* 3.6 17.8 + - + +
2006D THR* 1.3 74.4 - - - +
2008D SER* 1.3 70.3 + - - +
2026D CYS* 3.5 26.0 - - - -
2027D PHE 3.2 5.6 - - - +
2028D LEU* 4.3 7.0 - - + -
2086D CYS* 4.0 15.7 - - - +
2088D ALA* 3.9 22.9 - - + -
2097D ILE* 4.1 20.5 - - + +
2099D LYS* 3.5 41.2 - - + +
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Residues in contact with SER2008 (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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1023C THR* 3.2 33.5 + - - +
2006D THR* 4.2 9.2 + - - +
2007D VAL* 1.3 79.4 + - - +
2009D ILE* 1.3 62.4 + - - +
2010D PHE* 3.1 24.0 - - - -
2026D CYS* 3.5 2.0 - - - -
2027D PHE* 3.2 30.4 + - - -
2099D LYS* 4.7 3.4 - - - -
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Residues in contact with ILE2009 (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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1012C PRO* 4.9 3.3 - - - +
1013C VAL* 4.9 9.9 - - + +
2008D SER* 1.3 69.5 - - - +
2010D PHE* 1.3 78.3 + - - +
2011D PRO* 4.2 4.5 - - - +
2024D VAL* 4.0 5.6 - - + -
2025D VAL 3.6 8.5 - - - +
2026D CYS* 3.7 5.2 - - + +
2040D TRP* 4.6 3.8 - - + -
2084D TYR 4.3 2.5 - - - +
2085D THR* 3.7 7.6 - - - +
2086D CYS* 3.2 35.9 - - + +
2099D LYS* 2.9 43.7 - - + +
2100D SER* 3.9 8.7 - - - +
2101D PHE* 3.4 34.3 - - + -
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Residues in contact with PHE2010 (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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1010C LEU* 3.3 49.2 - - + +
1011C VAL 3.5 12.6 - - - +
1012C PRO* 4.0 14.6 - - + -
1023C THR* 3.2 38.6 - - - -
1024C LEU* 4.2 6.5 - - - -
2008D SER* 3.1 33.7 - - - -
2009D ILE* 1.3 81.5 - - - +
2011D PRO* 1.3 70.5 - - + +
2023D SER 4.2 0.5 - - - +
2024D VAL* 3.7 4.7 - - - +
2025D VAL* 2.9 34.5 + - + +
2027D PHE* 3.6 25.4 - + - -
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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