Contacts of the helix formed by residues 2064 - 2074 (chain B) in PDB entry 5WBY
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 THR2064 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2015B GLU* 4.9 0.9 - - - +
2018B ARG* 3.8 23.5 - - - +
2062B PRO 3.7 0.2 - - - -
2063B GLN* 1.3 81.7 + - - +
2065B LEU* 1.3 64.3 + - - +
2066B LYS* 3.8 2.9 + - - +
2067B GLU* 3.2 28.2 + - - +
2068B THR* 2.8 27.7 + - - -
2125B TYR 3.7 10.2 + - - -
2126B VAL 3.5 22.4 + - - +
2128B PRO* 3.6 23.1 - - + -
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Residues in contact with LEU2065 (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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2064B THR* 1.3 73.6 - - - +
2066B LYS* 1.3 57.3 + - - +
2068B THR* 3.3 11.3 + - + +
2069B SER* 3.0 30.3 + - - -
2124B GLN* 3.7 21.7 + - + +
2125B TYR* 3.3 34.6 + - + +
2128B PRO* 5.4 3.8 - - + +
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Residues in contact with LYS2066 (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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2022B LEU* 4.1 34.1 - - + -
2024B HIS* 4.3 13.7 - - + +
2064B THR* 3.2 2.7 - - - +
2065B LEU* 1.3 75.2 - - - +
2067B GLU* 1.3 64.1 + - + +
2069B SER* 3.1 24.1 + - - +
2070B PHE* 3.2 12.8 + - - +
2118B LEU* 3.8 22.0 - - - +
2121B LEU* 4.5 4.2 - - - +
2125B TYR* 2.9 29.7 + - + +
2126B VAL* 4.1 18.4 - - + -
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Residues in contact with GLU2067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2018B ARG* 2.9 40.3 + - - +
2022B LEU* 6.3 3.1 - - + -
2023B TRP* 3.2 65.1 + - + +
2062B PRO* 3.8 6.1 - - + -
2063B GLN* 3.1 27.3 + - - -
2064B THR* 3.2 18.1 + - - +
2066B LYS* 1.3 78.3 - - + +
2068B THR* 1.3 56.6 + - - +
2070B PHE* 3.6 2.1 - - - +
2071B ASN* 3.1 28.2 + - - +
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Residues in contact with THR2068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2062B PRO* 3.8 21.5 - - + +
2064B THR 2.8 18.6 + - - -
2065B LEU* 3.5 14.0 - - + +
2066B LYS 3.2 0.2 - - - -
2067B GLU* 1.3 74.3 - - - +
2069B SER* 1.3 55.2 + - - +
2071B ASN* 3.0 5.6 + - + +
2072B GLN* 2.7 47.0 + - - +
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Residues in contact with SER2069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2065B LEU 3.0 13.2 + - - -
2066B LYS* 3.1 24.1 + - - +
2068B THR* 1.3 75.7 - - - +
2070B PHE* 1.3 60.7 + - - +
2072B GLN* 3.7 9.3 - - - +
2073B ALA* 3.6 18.7 + - - +
2074B TYR* 4.9 1.0 - - - -
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Residues in contact with PHE2070 (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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2023B TRP* 3.8 15.7 - + + -
2024B HIS* 3.4 40.8 - + + +
2027B TRP* 3.3 26.2 - + + -
2058B MET* 3.6 35.4 - - + -
2066B LYS 3.2 13.2 + - - +
2067B GLU* 3.6 9.4 - - - +
2068B THR 3.2 0.4 - - - -
2069B SER* 1.3 75.0 + - - +
2071B ASN* 1.3 60.5 + - - +
2073B ALA 3.2 2.1 + - - -
2074B TYR* 2.8 78.7 + + + -
2075B GLY 3.4 2.1 + - - -
2078B LEU* 4.8 6.5 - - + -
2111B ILE* 4.4 7.2 - - + -
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Residues in contact with ASN2071 (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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2023B TRP* 4.3 2.9 - - + -
2058B MET* 3.1 25.7 - - + +
2062B PRO* 3.9 25.2 - - + +
2067B GLU 3.1 15.7 + - - +
2068B THR* 3.0 9.0 + - + +
2070B PHE* 1.3 81.0 - - - +
2072B GLN* 1.3 62.7 + - - +
2075B GLY* 3.2 29.5 + - - +
2076B ARG* 3.8 3.6 + - - +
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Residues in contact with GLN2072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2068B THR* 2.7 29.5 + - - +
2069B SER* 3.7 12.8 - - - +
2071B ASN* 1.3 76.0 - - - +
2073B ALA* 1.3 62.9 + - - +
2075B GLY 4.7 0.3 + - - -
2076B ARG* 4.8 8.1 + - - +
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Residues in contact with ALA2073 (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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2069B SER 3.6 11.4 + - - +
2070B PHE 3.2 2.0 + - - -
2072B GLN* 1.3 82.5 - - + +
2074B TYR* 1.3 77.8 + - + +
2076B ARG* 4.6 3.3 + - - +
2077B ASP* 4.2 8.3 - - - +
2110B ARG* 3.7 30.3 + - - +
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Residues in contact with TYR2074 (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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2024B HIS* 5.4 1.6 - - + -
2069B SER 5.1 0.9 - - - -
2070B PHE* 2.8 62.3 + + + +
2073B ALA* 1.3 83.2 - - + +
2075B GLY* 1.3 57.5 + - - +
2076B ARG 3.2 3.1 - - - -
2077B ASP* 2.9 25.2 + - - +
2078B LEU* 3.2 19.1 + - + +
2107B VAL* 3.8 25.1 - - + -
2110B ARG* 3.6 43.6 + - + +
2111B ILE* 3.7 24.6 + - + -
2114B GLN* 2.9 31.8 + - - -
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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
------------------------------------------------------------
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