Contacts of the strand formed by residues 2024 - 2037 (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 GLY2024 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2020B LYS* 3.8 2.9 - - - +
2021B THR* 2.9 35.5 + - - +
2022B SER 3.6 1.0 - - - -
2023B TYR* 1.3 81.1 - - - +
2025B GLU* 1.3 62.7 + - - +
2053B LEU* 4.7 7.9 - - - -
2055B ASP* 4.6 0.2 - - - -
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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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2018B PRO* 4.1 24.3 - - + +
2019B PHE 3.2 15.5 - - - +
2020B LYS* 4.1 23.5 - - + +
2021B THR* 3.9 0.4 + - - -
2024B GLY* 1.3 74.5 - - - +
2026B LEU* 1.3 66.5 + - - +
2027B LYS* 3.6 13.0 - - - +
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Residues in contact with LEU2026 (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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2015B LEU* 4.1 1.3 - - + -
2018B PRO* 3.1 8.8 - - - +
2019B PHE* 2.5 50.4 + - + +
2021B THR* 4.2 16.5 - - + +
2025B GLU* 1.3 77.4 - - - +
2027B LYS* 1.3 79.9 + - - +
2028B SER 3.6 15.3 - - - +
2029B LYS* 5.4 3.4 - - + -
2030B ASP* 6.1 1.3 - - + +
2051B PHE* 4.4 20.0 - - + -
2052B PRO* 3.7 28.7 - - + -
2293B LEU* 3.7 26.0 - - + -
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Residues in contact with LYS2027 (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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2012B GLU* 4.8 6.5 + - - +
2014B PRO* 4.2 1.7 - - - +
2015B LEU* 3.2 27.7 + - - +
2018B PRO* 4.7 6.9 - - + +
2025B GLU 3.6 11.9 - - - +
2026B LEU* 1.3 103.0 - - - +
2028B SER* 1.3 77.2 + - - +
2030B ASP* 5.7 4.6 - - - +
2052B PRO* 5.0 6.0 - - - +
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Residues in contact with SER2028 (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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2012B GLU* 2.8 33.7 + - - +
2013B LEU 2.8 24.9 - - - -
2014B PRO* 4.2 2.7 - - - -
2015B LEU* 3.5 15.4 - - - +
2026B LEU* 3.5 26.9 - - - +
2027B LYS* 1.3 93.8 + - - +
2029B LYS* 1.3 58.8 + - - +
2030B ASP 3.9 2.8 + - - -
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Residues in contact with LYS2029 (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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2012B GLU* 3.4 0.7 - - - -
2013B LEU 2.9 23.2 + - - +
2015B LEU* 4.1 2.4 - - + +
2026B LEU* 5.4 2.7 - - + -
2028B SER* 1.3 75.2 - - - +
2030B ASP* 1.3 70.2 + - - +
2031B PHE* 3.1 36.1 - - + -
2047B GLU* 3.7 1.6 + - - -
2049B GLU* 3.3 43.1 + - - +
2051B PHE* 4.7 8.1 - - + -
2292B MET 3.0 18.1 + - - -
2293B LEU* 2.7 45.4 + - + +
2294B GLU* 3.7 1.4 - - - +
2295B ALA 4.9 2.2 - - - +
2324B PHE* 3.6 26.2 - - + -
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Residues in contact with ASP2030 (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* 2.7 30.6 + - - -
2011B ALA 3.3 8.0 - - - +
2012B GLU* 3.9 12.6 - - + +
2026B LEU* 6.1 1.4 - - + +
2027B LYS* 5.7 4.3 - - - +
2028B SER* 3.9 5.9 + - - +
2029B LYS* 1.3 80.2 - - - +
2031B PHE* 1.3 59.9 + - - +
2048B LEU 4.9 0.2 - - - +
2050B ALA 4.1 6.8 - - - +
2052B PRO* 5.5 19.0 - - + +
2061B LEU* 3.5 24.9 - - + +
2362B LYS* 2.9 23.5 + - - -
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Residues in contact with PHE2031 (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* 3.2 9.0 - - - -
2011B ALA* 3.1 52.0 + - + +
2013B LEU* 3.9 22.2 - - + -
2029B LYS* 3.1 45.3 - - + -
2030B ASP* 1.3 75.1 + - - +
2032B TYR* 1.3 79.4 + - - +
2033B ILE* 3.8 12.1 - - + -
2047B GLU* 4.0 16.2 - - + +
2048B LEU 3.4 13.7 - - - +
2061B LEU* 3.7 8.3 - - - -
2295B ALA* 3.7 21.8 - - + -
2328B ILE* 3.7 24.7 - - + -
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Residues in contact with TYR2032 (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 13.9 - - + -
2009B ILE 3.2 16.4 - - - -
2010B HIS* 3.2 45.6 + + + -
2031B PHE* 1.3 81.5 - - - +
2033B ILE* 1.3 63.1 + - - +
2034B ILE* 4.0 4.3 - - + -
2047B GLU* 3.4 10.9 - - - +
2048B LEU* 3.0 44.2 + - + -
2061B LEU* 3.7 28.5 - - + -
2062B SER* 5.7 0.8 - - - -
2065B ILE* 3.5 49.6 - - + +
2363B SER* 5.1 3.0 + - - -
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Residues in contact with ILE2033 (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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2007B ARG 3.3 6.2 - - - +
2008B LEU* 3.6 2.4 - - - -
2009B ILE* 2.7 60.0 + - + +
2011B ALA* 5.8 0.2 - - + -
2031B PHE* 3.8 18.2 - - + -
2032B TYR* 1.3 78.9 - - - +
2034B ILE* 1.3 70.1 + - - +
2035B GLU* 4.4 0.4 - - + +
2045B TYR* 4.4 17.7 - - + -
2046B GLY 3.5 10.1 - - - +
2047B GLU* 4.1 4.7 - - + -
2297B VAL* 3.6 32.3 - - + -
2328B ILE* 4.0 15.5 - - + -
2352B LEU* 4.8 7.6 - - + -
2357B LEU* 5.3 6.7 - - + -
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Residues in contact with ILE2034 (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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2007B ARG 4.0 2.0 - - - -
2008B LEU* 3.6 22.4 - - + -
2032B TYR* 4.0 21.5 - - + +
2033B ILE* 1.3 78.3 - - - +
2035B GLU* 1.3 59.7 + - - +
2036B LEU* 3.8 24.9 - - + -
2044B GLY 3.4 1.4 - - - +
2045B TYR* 3.4 5.2 - - - +
2046B GLY 2.9 33.8 + - - +
2048B LEU* 4.4 2.0 - - + +
2065B ILE* 4.3 0.2 - - + -
2068B ILE* 3.9 29.6 - - + -
2073B LEU* 5.4 1.1 - - + -
2103B ALA* 3.9 26.7 - - + +
2104B VAL* 4.2 12.8 - - + -
2107B ALA* 3.9 12.5 - - + +
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Residues in contact with GLU2035 (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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2006B ALA* 3.3 4.7 - - - -
2007B ARG* 2.8 83.3 + - + +
2009B ILE* 3.7 16.4 - - + +
2033B ILE* 3.6 0.6 + - + -
2034B ILE* 1.3 71.4 - - - +
2036B LEU* 1.3 62.1 + - - +
2037B ILE* 3.8 5.6 + - + +
2043B HIS* 2.7 37.7 - - + -
2044B GLY 3.3 4.7 - - - +
2045B TYR* 3.4 32.6 + - + -
2352B LEU* 5.2 1.7 - - - +
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Residues in contact with LEU2036 (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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2003B PHE* 3.6 27.9 - - + -
2005B LYS 3.9 0.4 - - - -
2006B ALA* 3.7 26.2 - - + -
2034B ILE* 3.8 15.2 + - + -
2035B GLU* 1.3 72.9 - - - +
2037B ILE* 1.3 60.3 + - - +
2038B ASN 3.9 0.6 + - - -
2042B ILE 3.6 1.4 - - - +
2043B HIS* 3.5 1.4 - - - -
2044B GLY* 2.7 44.5 + - - +
2073B LEU* 4.4 11.0 - - + -
2076B LEU* 4.2 5.2 - - + -
2104B VAL* 3.6 22.2 - - + +
2107B ALA* 3.4 25.4 - - + -
2108B VAL* 3.7 17.7 - - + +
2369B LEU* 4.5 5.4 - - + -
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Residues in contact with ILE2037 (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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2003B PHE* 3.7 5.8 - - - -
2004B GLN* 2.9 31.6 + - - +
2005B LYS* 2.9 49.6 + - + +
2007B ARG* 4.0 21.8 - - + +
2035B GLU* 4.2 9.9 - - + +
2036B LEU* 1.3 73.9 - - - +
2038B ASN* 1.3 75.3 + - - +
2041B GLY* 4.7 5.4 - - - -
2042B ILE 3.4 7.9 - - - +
2043B HIS* 3.4 44.6 - - + +
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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