Contacts of the helix formed by residues 2043 - 2060 (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 ASN2043 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037B LEU* 2.7 52.9 + - + +
2038B TYR* 3.8 3.0 + - - +
2041B GLU* 4.7 6.4 + - + +
2042B ARG* 1.3 74.3 - - - +
2044B VAL* 1.3 62.2 + - - +
2045B LYS* 3.9 5.0 + - - +
2046B GLY* 3.0 26.5 + - - -
2047B MET* 3.3 18.0 + - - +
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Residues in contact with VAL2044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2038B TYR* 3.9 24.0 - - + -
2042B ARG* 5.5 1.8 - - - +
2043B ASN* 1.3 73.2 + - - +
2045B LYS* 1.3 62.8 + - + +
2046B GLY 3.2 1.3 - - - -
2047B MET* 3.2 14.8 + - + +
2048B PHE* 3.0 56.8 + - + -
2088B TYR* 3.7 30.3 - - + +
2097B LEU* 3.9 12.3 - - + -
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Residues in contact with LYS2045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2043B ASN* 3.9 4.0 + - - +
2044B VAL* 1.3 77.0 - - + +
2046B GLY* 1.3 60.4 + - - +
2048B PHE* 4.3 10.3 - - + +
2049B GLU* 3.0 32.4 + - - +
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Residues in contact with GLY2046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2037B LEU* 3.7 10.3 - - - +
2043B ASN* 3.0 31.3 + - - -
2045B LYS* 1.3 75.4 - - - +
2047B MET* 1.3 62.7 + - - +
2049B GLU* 3.4 19.1 + - - +
2050B VAL* 3.6 16.3 + - - +
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Residues in contact with MET2047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034B ALA* 3.7 29.6 - - + +
2037B LEU* 4.0 10.2 - - + +
2038B TYR* 4.0 13.0 - - + -
2043B ASN 3.3 17.5 + - - +
2044B VAL* 3.2 19.6 + - + +
2046B GLY* 1.3 76.0 - - - +
2048B PHE* 1.3 92.0 - - + +
2050B VAL* 3.2 13.8 + - - +
2051B LEU* 3.3 30.6 + - + +
2085B CYS* 4.3 10.3 - - - -
2097B LEU* 4.6 5.4 - - + -
2101B TRP* 3.5 33.7 - - - +
2104B TYR* 5.7 0.2 - - + -
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Residues in contact with PHE2048 (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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2044B VAL* 3.0 41.0 + - + +
2045B LYS* 4.3 11.9 - - + +
2046B GLY 3.4 0.4 - - - -
2047B MET* 1.3 92.9 - - + +
2049B GLU* 1.3 57.4 + - + +
2051B LEU* 4.6 5.4 - - + +
2052B GLU* 3.0 41.9 + - + +
2085B CYS* 3.7 40.8 - - + -
2088B TYR* 4.0 18.8 - + - -
2089B MET* 3.7 35.2 - - + -
2097B LEU* 4.6 0.9 - - + -
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Residues in contact with GLU2049 (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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2045B LYS* 3.0 23.3 - - - +
2046B GLY* 3.4 12.3 + - - +
2047B MET 3.3 0.6 - - - -
2048B PHE* 1.3 78.0 - - + +
2050B VAL* 1.3 58.3 + - + +
2052B GLU* 4.4 14.3 - - - +
2053B PRO* 3.2 23.4 - - - +
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Residues in contact with VAL2050 (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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2030B GLY* 3.3 35.9 - - - +
2033B GLU* 3.8 19.7 - - + -
2034B ALA* 4.3 4.7 - - + +
2037B LEU* 3.5 31.4 - - + -
2046B GLY 3.6 6.1 - - - +
2047B MET 3.2 7.3 + - - +
2049B GLU* 1.3 78.4 - - + +
2051B LEU* 1.3 62.0 + - - +
2052B GLU 3.6 0.2 - - - -
2053B PRO* 3.5 9.0 - - - +
2054B LEU* 3.6 14.3 - - + +
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Residues in contact with LEU2051 (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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2027B TRP* 4.1 20.6 - - + -
2030B GLY 4.1 11.2 - - - +
2031B LEU* 4.2 11.9 - - + -
2034B ALA* 3.9 20.2 - - + -
2047B MET* 3.3 44.6 + - + +
2048B PHE* 4.3 6.5 - - + +
2050B VAL* 1.3 77.5 - - - +
2052B GLU* 1.3 59.0 + - - +
2053B PRO* 3.3 0.9 - - - -
2054B LEU* 3.0 22.7 + - + +
2055B HIS* 3.0 26.9 + - + -
2085B CYS* 5.0 2.0 - - - -
2101B TRP* 5.3 0.9 - - + -
2104B TYR* 3.7 27.8 - - + +
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Residues in contact with GLU2052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2048B PHE* 3.0 25.8 + - + +
2049B GLU* 4.4 14.3 - - - +
2051B LEU* 1.3 77.0 - - - +
2053B PRO* 1.4 68.0 - - + +
2055B HIS* 4.0 9.6 - - - +
2056B ALA* 3.1 28.6 + - - +
2082B GLN* 5.5 2.2 - - - +
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Residues in contact with PRO2053 (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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2049B GLU 3.2 26.0 - - - +
2050B VAL 3.5 7.2 - - - +
2051B LEU 3.4 4.5 - - - -
2052B GLU* 1.4 97.4 - - + +
2054B LEU* 1.3 54.9 + - + +
2056B ALA* 3.7 4.9 - - + +
2057B MET* 2.8 34.7 + - - +
2060B ARG* 5.4 1.0 + - - -
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Residues in contact with LEU2054 (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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2026B MET* 3.7 47.8 - - + +
2027B TRP* 3.2 43.4 - - + +
2029B GLU* 6.0 0.4 - - - +
2030B GLY* 3.8 28.3 - - - -
2050B VAL* 3.6 20.4 - - + +
2051B LEU* 3.0 11.0 + - + +
2053B PRO* 1.3 76.1 - - + +
2055B HIS* 1.3 63.7 + - - +
2057B MET* 3.6 26.5 - - + +
2058B MET* 3.8 4.0 + - - +
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Residues in contact with HIS2055 (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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2027B TRP* 3.5 25.0 - + - -
2051B LEU* 3.0 35.8 + - + +
2052B GLU* 4.1 6.7 - - - +
2054B LEU* 1.3 74.4 - - - +
2056B ALA* 1.3 58.6 + - - +
2057B MET 3.2 0.2 - - - -
2058B MET* 3.3 6.7 + - - +
2059B GLU* 3.0 27.1 + - - +
2078B LEU* 3.4 28.9 + - + +
2079B MET* 5.5 0.4 - - - -
2082B GLN* 3.2 46.2 + - + +
2104B TYR* 2.9 31.5 + + - -
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Residues in contact with ALA2056 (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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2052B GLU 3.1 20.6 + - - +
2053B PRO* 3.9 6.1 - - + +
2055B HIS* 1.3 73.3 - - - +
2057B MET* 1.3 64.5 + - - +
2059B GLU* 3.4 30.7 + - + +
2060B ARG* 3.5 22.1 + - - +
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Residues in contact with MET2057 (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 41.9 - - + +
2026B MET* 3.5 36.8 - - + +
2027B TRP* 3.9 16.4 - - + +
2053B PRO 2.8 18.8 + - - +
2054B LEU* 3.6 17.5 - - + +
2056B ALA* 1.3 79.1 - - - +
2058B MET* 1.3 83.0 + - + +
2060B ARG* 3.5 39.9 + - - +
2063B GLN* 5.6 0.7 + - - -
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Residues in contact with MET2058 (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* 3.7 28.5 - - + -
2027B TRP* 3.3 33.2 - - - -
2054B LEU 3.9 2.0 - - - +
2055B HIS* 3.3 8.7 + - - +
2057B MET* 1.3 89.4 - - + +
2059B GLU* 1.3 57.1 + - - +
2060B ARG 3.1 3.1 - - - -
2061B GLY* 2.8 26.8 + - - -
2062B PRO* 5.0 0.5 - - - +
2070B PHE* 3.6 26.2 - - + -
2071B ASN* 3.1 28.8 - - - +
2075B GLY* 4.0 11.2 - - - +
2078B LEU* 5.3 5.2 - - + -
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Residues in contact with GLU2059 (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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2055B HIS 3.0 12.9 + - - +
2056B ALA* 3.4 26.8 + - - +
2057B MET 3.4 0.2 - - - -
2058B MET* 1.3 76.2 - - - +
2060B ARG* 1.3 60.1 + - - +
2061B GLY* 3.3 0.7 + - - -
2082B GLN* 5.5 3.6 + - - +
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Residues in contact with ARG2060 (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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2053B PRO 5.4 1.0 + - - -
2056B ALA* 3.5 23.4 + - - +
2057B MET* 3.5 31.3 + - - +
2058B MET 3.1 0.4 - - - -
2059B GLU* 1.3 77.5 - - + +
2061B GLY* 1.3 63.5 + - - +
2063B GLN* 5.1 10.8 - - - +
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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