Contacts of the helix formed by residues 2022 - 2039 (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 LEU2022 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2018B ARG* 3.8 13.9 - - + +
2019B VAL 4.4 2.9 - - - +
2021B ILE* 1.3 76.3 - - - +
2023B TRP* 1.3 67.9 + - - +
2024B HIS* 3.4 33.2 - - + +
2025B GLU* 3.1 11.8 + - + -
2026B MET* 3.1 23.8 + - - +
2066B LYS* 4.1 21.5 - - + -
2067B GLU* 6.3 2.9 - - + -
2118B LEU* 4.1 4.0 - - + -
2121B LEU* 3.8 27.4 - - + -
2126B VAL* 3.7 28.7 - - + +
2170B ARG* 3.6 14.4 - - - +
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Residues in contact with TRP2023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2018B ARG* 6.1 0.9 - - + -
2021B ILE 5.7 0.7 - - - -
2022B LEU* 1.3 75.1 - - - +
2024B HIS* 1.3 63.5 + - - +
2026B MET* 3.3 10.0 + - - +
2027B TRP* 3.1 28.4 + - - -
2057B MET* 3.8 39.7 - - + +
2058B MET* 3.7 41.5 - - + -
2061B GLY 4.0 6.7 - - - -
2062B PRO* 3.7 26.9 - - + -
2063B GLN* 4.7 4.4 - - - +
2067B GLU* 3.2 69.2 + - + +
2070B PHE* 3.8 27.1 - + + -
2071B ASN* 4.3 5.4 - - + -
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Residues in contact with HIS2024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2022B LEU* 3.5 32.2 - - + +
2023B TRP* 1.3 76.6 + - - +
2025B GLU* 1.3 82.5 + - + +
2027B TRP* 3.3 4.4 + - - +
2028B HIS* 2.9 28.1 + - - +
2066B LYS* 4.3 14.7 - - - +
2070B PHE* 3.4 34.5 - - + +
2074B TYR* 5.4 1.3 - - + -
2111B ILE* 3.7 19.0 - - + +
2114B GLN* 5.8 7.5 + - + -
2115B LEU* 3.7 18.3 - - + +
2118B LEU* 3.3 28.1 - - + +
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Residues in contact with GLU2025 (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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2020B ALA 4.0 0.7 - - - +
2021B ILE* 3.6 16.3 - - + +
2022B LEU* 3.1 20.7 + - + +
2024B HIS* 1.3 94.5 - - + +
2026B MET* 1.3 62.4 + - - +
2028B HIS* 3.4 8.6 + - - +
2029B GLU* 3.3 21.8 + - - +
2115B LEU* 5.0 0.4 - - - -
2118B LEU* 3.5 15.7 - - - +
2167B GLN 6.0 0.7 - - - -
2168B ARG* 2.8 37.0 + - - +
2170B ARG* 2.8 39.4 + - - -
2189B HIS* 5.0 3.4 + - - +
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Residues in contact with MET2026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2021B ILE* 3.6 27.8 - - + +
2022B LEU 3.1 18.4 + - - +
2023B TRP* 3.6 8.5 - - - +
2025B GLU* 1.3 75.0 - - - +
2027B TRP* 1.3 59.6 + - - +
2029B GLU* 3.2 18.8 - - - +
2030B GLY* 2.9 26.5 + - - -
2054B LEU* 3.7 24.5 - - + +
2057B MET* 3.5 32.1 - - + +
2189B HIS* 5.1 1.1 - - + -
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Residues in contact with TRP2027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2023B TRP 3.1 24.8 + - - -
2024B HIS 3.6 8.3 - - - +
2026B MET* 1.3 73.4 - - - +
2028B HIS* 1.3 59.8 + - - +
2030B GLY 3.9 0.4 - - - +
2031B LEU* 3.0 49.4 + - + +
2051B LEU* 4.1 20.9 - - + -
2054B LEU* 3.2 45.8 - - + -
2055B HIS* 3.5 36.6 - + - -
2057B MET* 3.9 9.8 - - + +
2058B MET* 3.3 27.8 - - - -
2070B PHE* 3.3 22.1 - + - -
2078B LEU* 4.0 26.7 - - + -
2104B TYR* 4.4 3.4 - + - -
2107B VAL* 6.6 0.2 - - + -
2111B ILE* 4.3 14.1 - - + -
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Residues in contact with HIS2028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2024B HIS 2.9 17.2 + - - +
2025B GLU* 3.5 9.6 - - - +
2026B MET 3.2 0.2 - - - -
2027B TRP* 1.3 77.5 - - - +
2029B GLU* 1.3 60.2 + - + +
2032B GLU* 3.1 51.4 + - - +
2108B PHE* 3.4 35.7 - + - -
2111B ILE* 4.1 13.1 - - + +
2112B SER* 3.3 26.4 + - - -
2115B LEU* 3.4 33.3 - - + +
2166B LYS* 4.7 8.1 + - - -
2168B ARG* 6.1 1.8 - - - -
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Residues in contact with GLU2029 (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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2025B GLU 3.3 10.6 + - - +
2026B MET* 3.2 22.4 - - - +
2028B HIS* 1.3 78.5 - - + +
2030B GLY* 1.3 59.8 + - - +
2032B GLU* 3.3 14.6 + - - +
2033B GLU* 3.0 30.3 + - - +
2054B LEU* 6.0 0.3 - - - +
2189B HIS* 3.4 38.8 + - - +
2233B ASN* 5.1 3.1 + - - -
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Residues in contact with GLY2030 (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 2.9 17.7 + - - -
2027B TRP 3.9 0.7 - - - -
2028B HIS 3.3 0.2 - - - -
2029B GLU* 1.3 78.6 - - - +
2031B LEU* 1.3 58.6 + - - +
2033B GLU* 4.8 0.2 - - - -
2034B ALA* 3.0 29.8 + - - +
2050B VAL* 3.3 16.2 - - - +
2051B LEU* 4.1 5.4 - - - +
2054B LEU* 3.8 17.9 - - - -
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Residues in contact with LEU2031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2027B TRP* 3.0 38.6 + - + +
2030B GLY* 1.3 73.1 - - - +
2032B GLU* 1.3 62.0 + - - +
2034B ALA* 3.9 2.7 - - - -
2035B SER* 3.0 27.7 + - - -
2051B LEU* 4.2 14.8 - - + -
2101B TRP* 4.4 12.6 - - + -
2104B TYR* 3.7 43.1 - - + +
2105B TYR* 6.0 0.7 - - - -
2107B VAL* 4.4 10.3 - - + -
2108B PHE* 3.8 46.0 - - + -
2111B ILE* 5.0 1.6 - - + -
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Residues in contact with GLU2032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2028B HIS* 3.1 42.7 + - - +
2029B GLU* 3.3 15.0 + - - +
2031B LEU* 1.3 76.6 - - - +
2033B GLU* 1.3 59.6 + - - +
2035B SER* 2.9 18.9 + - - -
2036B ARG* 3.3 18.8 + - - +
2108B PHE* 4.2 15.3 - - + -
2166B LYS* 3.5 22.9 + - - -
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Residues in contact with GLU2033 (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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2029B GLU 3.0 16.2 + - - +
2030B GLY 4.1 3.4 - - - +
2032B GLU* 1.3 77.5 - - - +
2034B ALA* 1.3 61.4 + - - +
2036B ARG* 3.4 10.7 + - - +
2037B LEU* 3.2 38.3 + - + +
2041B GLU* 5.4 1.0 - - - +
2050B VAL* 3.8 26.5 - - + -
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Residues in contact with ALA2034 (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 3.0 21.7 + - - +
2031B LEU* 4.3 2.0 - - - -
2032B GLU 3.4 0.2 - - - -
2033B GLU* 1.3 77.3 - - - +
2035B SER* 1.3 57.3 + - - +
2037B LEU* 3.9 5.3 - - - +
2038B TYR* 3.2 23.4 + - - +
2047B MET* 3.7 21.1 - - + +
2050B VAL* 4.3 5.3 - - + +
2051B LEU* 3.9 19.1 - - + -
2101B TRP* 3.5 24.3 - - + -
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Residues in contact with SER2035 (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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2031B LEU 3.0 15.1 + - - -
2032B GLU* 2.9 22.2 + - - -
2034B ALA* 1.3 75.2 - - - +
2036B ARG* 1.3 78.4 + - - +
2039B PHE* 3.0 33.6 + - - +
2040B GLY 3.3 4.5 + - - -
2101B TRP* 3.5 14.0 - - - -
2105B TYR* 3.6 26.2 - - - -
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Residues in contact with ARG2036 (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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2032B GLU* 3.3 15.0 - - - +
2033B GLU* 3.4 15.4 + - - +
2034B ALA 3.4 0.6 - - - -
2035B SER* 1.3 107.2 + - - +
2037B LEU* 1.3 56.3 + - - +
2039B PHE* 5.6 1.6 - - - +
2040B GLY* 3.2 11.5 - - - +
2041B GLU* 2.7 44.0 + - + +
2105B TYR* 5.3 1.2 + - - -
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Residues in contact with LEU2037 (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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2033B GLU* 3.2 35.5 + - - +
2034B ALA* 3.9 4.7 - - - +
2035B SER 3.4 0.2 - - - -
2036B ARG* 1.3 79.0 - - - +
2038B TYR* 1.3 51.5 + - - +
2041B GLU* 3.6 19.8 - - - +
2042B ARG 3.0 11.4 + - - -
2043B ASN* 2.7 69.6 + - - +
2046B GLY* 3.7 13.7 - - - +
2047B MET* 4.0 4.7 - - - +
2050B VAL* 3.5 27.6 - - + -
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Residues in contact with TYR2038 (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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2034B ALA 3.2 15.1 + - - +
2037B LEU* 1.3 76.1 - - - +
2039B PHE* 1.3 88.0 + + - +
2042B ARG* 2.6 51.8 + - - -
2043B ASN 3.8 5.5 + - - +
2044B VAL* 3.9 24.5 - - + -
2047B MET* 4.0 16.2 - - + -
2094B VAL* 3.8 23.0 + - - +
2097B LEU* 3.3 37.2 - - + +
2098B THR* 5.1 2.5 + - - -
2101B TRP* 3.2 34.3 - + + +
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Residues in contact with PHE2039 (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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2035B SER* 3.0 21.2 + - - +
2036B ARG* 5.6 1.8 - - - +
2038B TYR* 1.3 103.6 - + - +
2040B GLY* 1.3 63.8 + - - +
2042B ARG* 4.2 23.3 + - - +
2101B TRP* 3.6 40.4 - + + -
2105B TYR* 3.6 33.2 - + - -
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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
------------------------------------------------------------
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