Contacts of the helix formed by residues 2060 - 2071 (chain B) in PDB entry 1WUF
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 THR2060 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067A ILE* 3.7 14.8 - - + +
1071A GLN* 4.8 2.5 - - - +
2050B ALA* 3.5 5.6 - - - -
2051B PHE 3.1 9.4 - - - -
2052B PRO 3.8 10.5 - - - +
2053B LEU 3.7 4.3 - - - -
2054B PRO* 3.4 38.8 - - + -
2058B GLU 4.1 2.0 - - - +
2059B GLU* 1.3 80.9 - - - +
2061B LEU* 1.3 54.6 + - - +
2062B SER* 3.7 7.0 + - - -
2063B SER* 2.8 33.4 + - - -
2064B ALA* 2.7 34.3 + - - +
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Residues in contact with LEU2061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2010B HIS* 3.8 3.1 - - + +
2030B ASP* 3.5 45.5 - - + +
2031B PHE* 3.7 20.9 - - - +
2032B TYR* 3.7 22.2 - - + -
2048B LEU* 3.4 29.4 - - + +
2050B ALA* 3.5 25.6 - - - +
2051B PHE 3.1 12.2 + - - +
2052B PRO* 4.6 6.9 - - + +
2060B THR* 1.3 71.5 - - - +
2062B SER* 1.3 57.8 + - - +
2065B ILE* 3.0 35.1 + - - +
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Residues in contact with SER2062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A LEU* 4.0 8.9 - - - +
1067A ILE* 5.7 0.2 - - - +
1070A GLU* 2.7 36.9 + - - -
2032B TYR* 5.7 1.6 - - - -
2052B PRO* 5.0 3.5 + - - +
2060B THR* 3.7 10.7 + - - -
2061B LEU* 1.3 78.4 - - - +
2063B SER* 1.3 62.0 + - - +
2065B ILE* 3.3 20.7 - - - +
2066B LEU* 3.4 10.4 - - - +
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Residues in contact with SER2063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A SER* 4.6 15.0 - - - -
1066A LEU* 4.4 6.7 - - - +
1067A ILE* 3.9 22.0 - - - +
2058B GLU 5.0 0.7 + - - -
2059B GLU* 4.3 5.2 - - - +
2060B THR* 2.8 32.0 + - - -
2062B SER* 1.3 78.3 + - - +
2064B ALA* 1.3 68.4 + - - +
2066B LEU* 3.2 8.8 - - - +
2067B ILE* 3.0 26.6 + - - +
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Residues in contact with ALA2064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2048B LEU* 3.8 24.7 - - + -
2050B ALA* 4.2 4.5 - - + -
2059B GLU* 4.1 20.0 - - + +
2060B THR 2.7 24.0 + - - +
2061B LEU 3.9 1.8 - - - +
2063B SER* 1.3 71.5 + - - +
2065B ILE* 1.3 60.6 + - - +
2066B LEU 3.0 2.0 - - - -
2067B ILE* 3.0 11.3 + - - +
2068B ILE* 2.8 31.9 + - - +
2100B ALA* 3.8 4.4 - - + +
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Residues in contact with ILE2065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008B LEU* 4.2 16.6 - - + -
2032B TYR* 3.5 58.8 - - + +
2034B ILE* 4.3 4.5 - - + -
2048B LEU* 3.8 7.5 - - + +
2061B LEU 3.0 16.3 + - - +
2062B SER* 3.3 18.8 - - - +
2064B ALA* 1.3 77.9 - - - +
2066B LEU* 1.3 63.8 + - - +
2068B ILE* 3.5 24.4 + - + +
2069B LYS* 3.1 40.1 + - - +
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Residues in contact with LEU2066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062A SER* 3.9 21.1 - - - +
1063A SER* 4.3 12.6 - - - +
1066A LEU* 5.2 10.1 - - + -
2062B SER 3.4 12.1 - - - +
2063B SER* 3.2 13.4 + - - +
2064B ALA 3.0 0.8 - - - -
2065B ILE* 1.3 81.6 - - + +
2067B ILE* 1.3 62.6 + - + +
2069B LYS* 3.3 19.0 + - - +
2070B GLU* 2.9 65.6 + - + +
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Residues in contact with ILE2067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A PRO* 5.5 0.9 - - + -
1058A GLU 5.1 0.4 - - - +
1060A THR* 3.6 33.9 - - + +
1062A SER* 5.7 0.2 - - - +
1063A SER* 3.9 13.7 - - - +
2063B SER 3.0 15.9 + - - +
2064B ALA* 3.0 9.7 + - - +
2066B LEU* 1.3 77.1 - - + +
2068B ILE* 1.3 57.8 + - - +
2070B GLU* 4.9 1.8 - - + +
2071B GLN* 2.6 59.8 + - + +
2072B LEU* 3.2 7.9 + - + -
2094B ILE* 5.4 2.7 - - + -
2097B ASN* 3.5 39.5 - - + +
2100B ALA* 4.4 9.6 - - + -
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Residues in contact with ILE2068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008B LEU* 4.5 11.9 - - + -
2034B ILE* 3.9 18.4 - - + -
2048B LEU* 4.3 7.9 - - + -
2064B ALA 2.8 16.9 + - - +
2065B ILE* 3.5 29.6 - - + +
2066B LEU 3.2 0.2 - - - -
2067B ILE* 1.3 79.5 - - - +
2069B LYS* 1.3 60.9 + - - +
2072B LEU* 4.1 7.6 - - + -
2073B LEU* 3.0 52.8 + - + +
2100B ALA* 3.9 27.6 - - + +
2103B ALA* 4.0 8.7 - - + -
2104B VAL* 3.8 13.5 - - + -
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Residues in contact with LYS2069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008B LEU* 3.5 22.0 - - + -
2032B TYR* 6.0 0.2 + - - -
2065B ILE* 3.1 33.8 + - - +
2066B LEU* 3.8 19.1 - - + +
2067B ILE 3.3 0.2 - - - -
2068B ILE* 1.3 81.3 - - - +
2070B GLU* 1.3 63.9 + - + +
2073B LEU* 4.5 6.8 - - - +
2074B PRO* 3.5 18.4 - - - +
2365B GLU* 3.4 31.1 + - - +
2367B ILE* 4.2 9.6 - - + +
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Residues in contact with GLU2070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A PRO 5.5 1.0 - - - +
1062A SER* 2.6 32.2 + - - -
2066B LEU* 2.9 45.5 + - + +
2067B ILE* 4.5 2.1 - - + +
2069B LYS* 1.3 78.0 - - + +
2071B GLN* 1.3 78.8 + - - +
2074B PRO* 3.8 11.3 - - - +
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Residues in contact with GLN2071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A PRO 4.0 9.2 - - - +
1053A LEU* 3.1 31.7 - - - +
1054A PRO* 3.4 35.5 - - + +
1060A THR* 4.6 4.7 - - - +
1062A SER* 5.7 0.2 + - - -
2067B ILE* 2.6 38.2 + - + +
2069B LYS 3.5 0.4 - - - -
2070B GLU* 1.3 95.0 + - - +
2072B LEU* 1.3 61.5 + - - +
2074B PRO* 3.6 8.4 - - - +
2075B LEU* 3.2 25.1 - - - +
2093B TRP* 3.9 9.7 - - + -
2094B ILE* 4.0 12.1 - - + -
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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