Contacts of the helix formed by residues 1972 - 1981 (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 LEU1972 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1939B ILE* 4.2 9.6 - - + -
1943B ILE* 3.8 20.2 - - + -
1961B LEU* 3.1 51.4 - - + +
1964B ILE* 3.6 22.4 - - + -
1965B GLY* 3.5 17.3 - - - +
1968B HIS 4.6 1.6 - - - +
1969B PRO 3.0 8.2 + - - +
1971B ALA* 1.3 80.4 - - - +
1973B ILE* 1.3 64.6 + - - +
1974B TYR 3.5 1.3 - - - -
1975B PRO* 3.4 5.8 - - - +
1976B LEU* 3.1 46.0 + - + +
1998B MET* 4.5 6.3 - - + -
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Residues in contact with ILE1973 (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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1969B PRO 3.1 19.3 + - - +
1970B GLN* 3.5 19.7 + - - +
1971B ALA 3.8 0.6 - - - -
1972B LEU* 1.3 77.3 - - - +
1974B TYR* 1.3 61.9 + - + +
1976B LEU* 3.9 3.9 - - - +
1977B THR* 2.5 35.7 + - - +
1995B LEU* 4.6 6.2 - - + +
1998B MET* 4.6 8.5 - - + -
2005B LEU* 3.4 22.9 - - + +
2006B VAL* 4.0 28.3 - - + +
2009B ALA* 3.4 23.6 - - + -
2138B LEU* 3.3 33.4 - - + -
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Residues in contact with TYR1974 (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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1970B GLN 4.8 11.2 + - - -
1973B ILE* 1.3 79.3 - - + +
1975B PRO* 1.4 70.8 - - + +
1977B THR* 3.1 16.6 + - - -
1978B VAL* 3.2 16.9 + - - +
2009B ALA* 5.3 7.6 - - + -
2012B VAL* 5.0 9.0 - - + +
2013B SER* 5.1 7.0 - - - -
2016B LEU* 5.9 1.1 - - + -
2138B LEU* 3.3 40.9 - - + +
2139B ALA* 2.8 27.3 + - + -
2140B VAL 4.8 0.9 - - - -
2141B PRO* 3.5 36.9 - - + +
2142B GLY 4.9 2.7 - - - -
2153B ILE* 3.7 2.6 - - - +
2228B ILE* 4.3 25.8 - - + -
2229B PRO 4.8 2.4 - - - +
2230B LEU* 4.9 16.4 - - + +
2236B LEU* 6.0 0.4 - - + -
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Residues in contact with PRO1975 (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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1939B ILE* 4.4 7.6 - - + -
1940B PRO* 6.1 2.5 - - + -
1943B ILE* 3.7 30.7 - - + +
1971B ALA 3.8 17.3 - - - +
1972B LEU* 3.4 16.2 - - - +
1974B TYR* 1.4 96.1 - - + +
1976B LEU* 1.3 58.0 + - - +
1978B VAL* 3.5 13.0 - - + +
1979B ALA* 3.4 18.5 + - - +
2196B GLU* 5.7 4.9 - - - +
2229B PRO 5.5 0.4 - - - +
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Residues in contact with LEU1976 (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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1943B ILE* 4.5 5.6 - - + -
1946B ILE* 3.6 30.7 - - + -
1961B LEU* 5.2 0.4 - - + -
1972B LEU* 3.1 42.0 + - + +
1975B PRO* 1.3 73.7 - - - +
1977B THR* 1.3 59.6 + - - +
1979B ALA* 3.1 5.4 + - + +
1980B SER* 2.9 28.6 + - - -
1991B ALA* 3.9 17.1 - - + +
1994B ILE* 3.6 37.5 - - + -
1995B LEU* 3.9 21.0 - - + +
1998B MET* 4.0 18.6 - - - -
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Residues in contact with THR1977 (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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1973B ILE* 2.5 26.5 + - - +
1974B TYR* 3.1 7.7 + - - -
1976B LEU* 1.3 72.5 - - - +
1978B VAL* 1.3 66.3 + - - +
1980B SER* 2.7 22.8 + - - +
1981B LYS* 3.4 22.4 - - + +
1995B LEU* 4.5 6.2 - - - +
2009B ALA* 4.0 15.7 + - - +
2010B MET* 3.9 26.4 - - + -
2013B SER* 3.1 29.2 - - - +
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Residues in contact with VAL1978 (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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1974B TYR 3.2 13.6 + - - +
1975B PRO* 3.5 13.0 - - + +
1976B LEU 3.3 0.2 - - - -
1977B THR* 1.3 75.6 - - - +
1979B ALA* 1.3 63.6 + - - +
1981B LYS* 3.1 25.7 + - - +
1982B SER* 4.6 1.2 - - - -
2193B ARG* 5.8 5.4 - - - -
2229B PRO* 3.1 37.0 - - + +
2230B LEU* 3.6 25.8 - - + +
2231B SER* 4.0 17.5 - - - +
2232B THR* 5.1 0.7 - - + +
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Residues in contact with ALA1979 (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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1943B ILE* 4.5 7.0 - - + -
1946B ILE* 4.9 4.7 - - + -
1975B PRO 3.4 9.1 + - - +
1976B LEU* 3.1 8.3 + - - +
1978B VAL* 1.3 80.3 - - - +
1980B SER* 1.3 62.1 + - - +
1981B LYS 3.3 0.5 + - - -
1982B SER* 3.4 15.9 - - - -
1987B ARG* 4.0 26.3 - - + +
1988B HIS* 3.3 19.6 + - - +
1991B ALA* 3.5 19.5 - - + -
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Residues in contact with SER1980 (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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1976B LEU 2.9 12.3 + - - -
1977B THR* 2.7 30.3 + - - +
1979B ALA* 1.3 73.9 - - - +
1981B LYS* 1.3 59.1 + - - +
1988B HIS* 3.3 23.9 - - - +
1991B ALA* 3.6 5.6 - - - +
1992B ASN* 3.3 31.5 + - - -
1995B LEU* 3.8 10.8 - - - +
2010B MET* 4.4 6.5 - - - -
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Residues in contact with LYS1981 (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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1977B THR* 3.4 28.6 - - + +
1978B VAL* 3.1 12.8 + - - +
1980B SER* 1.3 78.9 + - - +
1982B SER* 1.3 57.1 + - - +
1988B HIS* 5.5 0.2 - - - -
2010B MET* 6.1 0.2 - - - +
2013B SER* 3.3 29.2 + - - -
2014B GLU* 3.4 29.7 - - + +
2017B ILE* 3.6 23.6 - - + +
2230B LEU 3.8 11.4 - - - +
2231B SER* 5.5 8.0 - - - -
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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