Contacts of the strand formed by residues 2022 - 2031 (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 ALA2022 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2012D PRO* 3.8 6.7 - - + +
2016D GLN* 3.9 6.9 - - - +
2017D LEU* 3.6 17.9 - - + -
2021D GLY* 1.3 75.5 - - - +
2023D SER* 1.3 62.4 + - - +
2024D VAL* 4.1 1.9 + - - +
2071D LEU 4.0 0.7 - - - +
2072D THR* 5.6 0.6 - - - +
2073D LEU* 2.9 38.5 + - - +
2075D LYS* 3.9 5.4 - - - -
2078D TYR* 3.5 32.9 - - + +
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Residues in contact with SER2023 (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* 6.1 1.2 - - - +
1027C LEU* 4.0 16.5 - - - +
1029C LYS* 4.3 5.0 - - - -
2010D PHE 4.2 0.9 - - - +
2012D PRO* 3.4 22.6 - - - +
2016D GLN* 2.8 31.4 + - - +
2022D ALA* 1.3 71.8 - - - +
2024D VAL* 1.3 62.0 + - - +
2025D VAL* 3.9 4.3 + - - +
2070D THR* 4.4 8.1 - - - -
2071D LEU 3.5 5.2 - - - -
2072D THR* 3.3 33.2 + - - +
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Residues in contact with VAL2024 (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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2009D ILE* 4.0 5.2 - - + -
2010D PHE 3.7 8.1 - - - +
2012D PRO* 3.7 19.1 - - + -
2022D ALA 4.9 1.8 - - - +
2023D SER* 1.3 74.2 - - - +
2025D VAL* 1.3 59.9 + - - +
2040D TRP* 3.2 37.1 - - + -
2071D LEU* 2.8 43.9 + - + +
2073D LEU* 5.5 2.5 - - + -
2078D TYR* 4.3 11.4 - - + -
2084D TYR* 4.5 12.1 - - + -
2101D PHE* 3.7 31.9 - - + -
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Residues in contact with VAL2025 (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* 3.8 25.4 - - + -
1027C LEU* 4.0 19.3 - - + -
1064C SER* 4.4 4.9 - - - +
2008D SER 4.7 0.2 - - - -
2009D ILE* 3.6 3.3 - - - +
2010D PHE* 2.9 35.3 + - + +
2023D SER 3.9 4.0 - - - +
2024D VAL* 1.3 74.8 - - - +
2026D CYS* 1.3 67.4 + - - +
2027D PHE* 3.5 39.9 - - + -
2068D SER* 4.6 2.2 - - - +
2069D SER 3.7 10.5 - - - +
2070D THR* 3.8 21.3 - - + +
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Residues in contact with CYS2026 (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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2007D VAL* 3.5 21.5 - - - -
2008D SER 3.5 6.3 - - - -
2009D ILE* 3.7 8.3 - - + -
2025D VAL* 1.3 77.2 - - - +
2027D PHE* 1.3 62.6 + - - +
2028D LEU* 3.7 6.9 - - + +
2040D TRP* 3.6 16.4 - - + -
2068D SER* 3.9 0.9 - - - -
2069D SER* 3.0 32.3 + - - +
2086D CYS* 2.0 49.8 - - + -
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Residues in contact with PHE2027 (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* 4.6 4.5 - - + -
1023C THR* 5.1 2.0 - - - -
1024C LEU 4.1 1.6 - - - -
1025C GLY* 4.1 13.9 - - - -
1052C PHE* 3.7 24.2 - + - -
1064C SER* 3.9 12.6 - - - -
1065C SER 3.6 21.1 - - - -
1066C SER* 3.8 18.2 - - - -
2006D THR 3.4 1.9 - - - +
2007D VAL* 3.2 7.3 - - - +
2008D SER* 3.2 33.4 + - - +
2010D PHE* 3.6 34.5 - + - -
2025D VAL* 3.5 23.6 - - + -
2026D CYS* 1.3 70.5 - - - +
2028D LEU* 1.3 65.5 + - - +
2029D ASN* 3.4 17.9 - - - +
2067D MET 3.9 1.8 - - - -
2068D SER* 3.7 17.0 - - - -
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Residues in contact with LEU2028 (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* 3.9 15.9 - - + -
2006D THR 3.9 3.1 - - - -
2007D VAL* 4.3 6.7 - - + -
2026D CYS* 3.7 26.0 - - + +
2027D PHE* 1.3 79.5 - - - +
2029D ASN* 1.3 59.9 + - - +
2031D PHE* 3.3 7.4 - - - -
2036D ILE* 3.8 24.0 - - + -
2037D ASN 4.9 0.4 - - - +
2038D VAL* 3.3 35.0 - - + -
2067D MET* 2.7 50.3 + - + +
2069D SER* 5.2 0.2 - - - -
2086D CYS* 4.4 2.9 - - - -
2088D ALA* 3.6 24.5 - - + -
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Residues in contact with ASN2029 (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* 5.8 1.0 - - - +
1050C HIS* 3.4 18.0 - - - -
1052C PHE* 3.9 6.6 - - - -
1066C SER* 2.7 33.5 + - - -
1068C THR* 4.4 10.3 - - + +
2005D PRO* 3.5 2.5 - - - +
2006D THR* 3.0 42.2 + - + +
2027D PHE* 3.4 20.0 - - - +
2028D LEU* 1.3 80.7 + - - +
2030D ASN* 1.3 83.2 + - - +
2031D PHE* 3.6 2.0 - - - -
2065D TYR 4.0 0.2 - - - -
2066D SER* 3.5 3.8 - - - +
2067D MET 3.8 4.3 - - - +
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Residues in contact with ASN2030 (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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1048C GLY* 6.4 0.2 - - - -
1050C HIS* 3.0 34.9 + - - -
1068C THR* 5.5 6.5 + - - +
2003D ALA* 4.0 8.8 - - - +
2004D ALA 3.6 10.9 - - - +
2006D THR* 5.4 6.1 + - - +
2029D ASN* 1.3 84.1 - - - +
2031D PHE* 1.3 57.4 + - - +
2059D ASP* 4.9 0.2 - - - +
2062D ASP* 3.2 22.3 - - - +
2064D THR* 3.3 18.6 + - + +
2065D TYR 3.0 5.5 + - - -
2066D SER* 2.9 13.3 + - - -
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Residues in contact with PHE2031 (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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2003D ALA* 3.2 19.3 - - - +
2005D PRO* 3.8 26.5 - - + -
2028D LEU 3.3 26.9 - - - -
2029D ASN 4.1 0.2 - - - -
2030D ASN* 1.3 73.7 - - - +
2032D TYR* 1.3 64.3 + - - +
2033D PRO 3.3 23.1 - - - -
2034D LYS* 3.5 18.8 - - - -
2036D ILE* 3.1 38.1 - - + -
2055D TRP* 4.3 3.8 - - - -
2064D THR* 3.3 4.6 - - - -
2065D TYR* 2.8 62.7 + - + +
2066D SER* 3.6 5.6 - - - -
2067D MET* 3.6 7.6 - - + -
2090D HIS* 4.2 1.8 - + - +
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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