Contacts of the helix formed by residues 182 - 199 (chain 3) in PDB entry 2WSF
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 LYS 182 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523 LYS* 4.9 3.6 - - - +
563 TYR* 3.9 28.6 + - + -
1803 LYS 1.9 17.7 + - - +
1813 LEU* 1.3 69.8 - - - +
1833 GLU* 1.3 53.4 + - - +
1853 LYS* 2.8 28.2 + - + +
1863 ASN* 2.3 67.3 + - - +
3023 CLA 5.7 9.7 + - - +
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Residues in contact with GLU 183 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1803 LYS 4.1 1.3 - - - -
1813 LEU 3.5 8.2 - - - +
1823 LYS* 1.3 75.5 - - - +
1843 VAL* 1.3 57.4 + - + +
1853 LYS 2.9 7.5 + - - -
1863 ASN* 3.4 26.5 + - - +
1873 GLY* 3.6 20.8 + - - -
1883 ARG* 4.4 4.2 + - - -
3073 CLA 2.8 73.7 + - + +
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Residues in contact with VAL 184 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603 ILE* 5.3 3.2 - - - +
633 ARG* 4.8 1.9 - - - -
643 TYR* 5.8 0.3 - - - -
1813 LEU* 3.4 50.5 - - + +
1823 LYS 3.2 0.4 - - - +
1833 GLU* 1.3 76.5 - - + +
1853 LYS* 1.3 57.2 + - - +
1883 ARG* 3.4 49.8 + - - +
3043 CLA 5.3 13.2 - - + -
3163 CLA 4.7 16.8 - - + -
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Residues in contact with LYS 185 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523 LYS* 3.5 11.3 - - - +
563 TYR* 2.8 56.6 - - - +
593 ILE* 5.1 4.9 - - - +
603 ILE* 3.6 20.2 - - + -
633 ARG* 2.3 63.2 + - - +
1813 LEU 4.7 2.2 - - - +
1823 LYS* 2.8 29.1 + - + +
1843 VAL* 1.3 78.2 - - - +
1863 ASN* 1.3 69.8 + - - +
1873 GLY 2.8 12.9 + - - -
1883 ARG* 2.8 8.3 + - - +
1893 LEU* 5.1 2.7 - - + +
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Residues in contact with ASN 186 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633 ARG* 3.8 3.8 - - - +
1823 LYS* 2.3 60.7 + - - +
1833 GLU* 3.4 24.9 + - - +
1853 LYS* 1.3 76.2 + - - +
1873 GLY* 1.3 59.5 + - - +
1893 LEU* 3.4 26.4 - - - +
1903 ALA* 3.6 6.1 + - - +
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Residues in contact with GLY 187 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1833 GLU* 3.6 15.6 + - - -
1853 LYS 2.8 4.4 + - - -
1863 ASN* 1.3 75.5 - - - +
1883 ARG* 1.3 63.7 + - - +
1893 LEU 3.6 0.4 - - - -
1903 ALA* 3.1 30.5 - - - +
1913 MET* 3.3 7.6 + - - +
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Residues in contact with ARG 188 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633 ARG* 3.5 37.8 - - + +
643 TYR* 3.4 39.8 + - - -
663 MET* 4.7 0.5 - - - +
1833 GLU 4.4 4.2 + - - -
1843 VAL* 3.4 56.4 + - - +
1853 LYS 2.8 3.2 + - - -
1873 GLY* 1.3 80.5 - - - +
1893 LEU* 1.3 56.1 + - - +
1913 MET* 3.2 32.5 + - + +
1923 LEU* 2.7 27.2 + - - +
3043 CLA 6.0 0.8 - - - -
3163 CLA 4.2 23.0 - - - +
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Residues in contact with LEU 189 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593 ILE* 4.1 16.6 - - + -
633 ARG* 2.7 41.4 - - - +
1853 LYS* 5.1 3.4 - - + +
1863 ASN* 3.4 17.5 - - - +
1883 ARG* 1.3 69.1 - - - +
1903 ALA* 1.3 62.8 + - + +
1913 MET 2.7 5.1 + - - -
1923 LEU* 2.9 24.6 + - + +
1933 ALA* 2.9 25.7 + - + +
1943 ILE* 4.0 2.3 - - - +
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Residues in contact with ALA 190 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1863 ASN 3.6 6.9 + - - +
1873 GLY* 3.1 24.6 - - - +
1893 LEU* 1.3 84.5 - - + +
1913 MET* 1.3 54.5 - - - +
1943 ILE* 3.5 2.9 - - - +
3033 CLA 2.9 52.3 - - + +
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Residues in contact with MET 191 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633 ARG 5.3 1.8 - - - +
663 MET* 3.3 28.9 - - + +
693 ALA* 4.9 9.0 - - - +
703 VAL* 4.7 23.3 - - + -
1873 GLY 3.6 9.6 - - - +
1883 ARG* 3.2 33.4 - - + +
1893 LEU 2.7 0.6 - - - -
1903 ALA* 1.3 82.7 - - - +
1923 LEU* 1.3 60.6 - - - +
1943 ILE* 3.8 10.9 - - - +
1953 LEU* 3.2 22.9 - - - +
3033 CLA 4.9 7.0 - - + -
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Residues in contact with LEU 192 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593 ILE* 3.7 27.1 - - + -
623 GLY* 3.6 27.1 - - - +
653 ALA 5.9 0.4 - - - +
663 MET* 4.2 6.5 - - - -
1883 ARG 2.7 17.5 + - - +
1893 LEU* 2.9 10.1 + - + -
1913 MET* 1.3 71.3 - - - +
1933 ALA* 1.3 58.3 + - + +
1943 ILE 2.7 15.6 + - - -
1953 LEU* 3.2 27.5 + - + +
1963 GLY* 3.6 5.2 + - - -
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Residues in contact with ALA 193 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1893 LEU* 2.9 18.0 + - + +
1923 LEU* 1.3 79.8 - - + +
1943 ILE* 1.3 63.4 + - + +
1953 LEU 3.7 0.2 - - - -
1963 GLY* 3.6 12.7 + - - +
1973 TYR* 3.1 22.7 + - - -
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Residues in contact with ILE 194 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1893 LEU 4.0 6.1 - - - +
1903 ALA* 3.5 17.5 - - - +
1913 MET* 3.8 9.2 - - - +
1923 LEU 2.7 6.9 + - - -
1933 ALA* 1.3 80.5 - - + +
1953 LEU* 1.3 63.7 + - + +
1963 GLY 3.1 0.9 - - - -
1973 TYR* 3.0 58.4 - - + +
1983 PHE* 3.4 13.7 + - + -
3033 CLA 3.2 63.5 - - + +
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Residues in contact with LEU 195 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663 MET* 3.6 46.0 - - + +
683 GLY* 4.5 12.6 - - - -
693 ALA* 4.6 3.4 - - + +
1913 MET 3.2 25.4 - - - +
1923 LEU* 3.2 16.1 + - + +
1943 ILE* 1.3 75.7 - - + +
1963 GLY* 1.3 56.8 + - - +
1983 PHE* 2.8 27.6 + - + -
1993 VAL* 2.9 19.5 + - - +
3053 CLA 4.2 17.4 - - + -
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Residues in contact with GLY 196 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1923 LEU* 3.6 8.3 + - - -
1933 ALA* 3.7 11.2 - - - -
1943 ILE 3.1 1.6 - - - -
1953 LEU* 1.3 79.7 - - - +
1973 TYR* 1.3 50.3 + - - +
1993 VAL* 3.3 15.2 - - - +
2003 GLN* 2.7 26.4 + - - -
3053 CLA 5.3 3.5 - - - -
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Residues in contact with TYR 197 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1933 ALA 3.1 29.1 + - - -
1943 ILE* 3.0 40.1 - - + +
1963 GLY* 1.3 70.4 - - - +
1983 PHE* 1.3 71.6 + + - +
1993 VAL 3.2 5.2 - - - -
2003 GLN* 3.1 19.7 + - - +
2013 ALA* 2.7 34.7 + - + +
3033 CLA 3.0 57.0 + + + +
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Residues in contact with PHE 198 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1943 ILE* 3.4 24.9 - - + +
1953 LEU* 2.8 17.0 + - + +
1973 TYR* 1.3 98.7 - + - +
1993 VAL* 1.3 62.1 + - - +
2013 ALA* 3.1 28.3 + - + +
2023 LEU* 5.3 0.9 - - - +
3033 CLA 5.0 34.5 - + + -
3053 CLA 5.5 2.2 - - - +
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Residues in contact with VAL 199 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1953 LEU 2.9 15.7 + - - +
1963 GLY* 3.3 13.7 - - - +
1983 PHE* 1.3 78.1 - - - +
2003 GLN* 1.3 65.5 + - + +
2013 ALA 3.3 0.4 + - - -
2023 LEU* 4.0 9.0 - - - +
3053 CLA 3.1 87.6 - - + +
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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
------------------------------------------------------------
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