Contacts of the helix formed by residues 2025 - 2044 (chain F) in PDB entry 6X34
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 PRO2025 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1973F ASN* 5.7 5.8 - - + -
2023F PRO 4.9 0.7 - - - +
2024F LEU* 1.3 109.7 - - + +
2026F ASP* 1.3 60.1 + - - +
2027F GLU* 3.0 17.1 + - + +
2028F ILE* 3.4 19.6 + - + -
2029F ARG* 4.0 2.5 + - - +
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Residues in contact with ASP2026 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013F PHE* 5.4 7.9 - - + -
2024F LEU 3.5 3.5 + - - -
2025F PRO* 1.3 70.9 - - - +
2027F GLU* 1.3 61.8 + - - +
2028F ILE 3.3 0.4 - - - -
2029F ARG* 3.4 11.3 + - + +
2030F GLN* 3.1 36.6 + - + +
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Residues in contact with GLU2027 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025F PRO* 3.0 8.9 + - + +
2026F ASP* 1.3 79.3 - - - +
2028F ILE* 1.3 66.4 + - + +
2030F GLN* 3.6 17.8 + - - +
2031F ASP* 4.2 3.5 + - - +
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Residues in contact with ILE2028 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966F TYR* 3.6 28.1 - - + +
1969F LYS* 4.8 14.4 - - + +
1970F LEU* 3.9 13.9 - - + -
1973F ASN* 3.9 28.0 - - + -
2024F LEU* 3.9 21.3 - - + -
2025F PRO* 3.4 13.1 + - + +
2026F ASP 3.3 0.2 - - - -
2027F GLU* 1.3 78.6 - - + +
2029F ARG* 1.3 63.4 + - - +
2030F GLN 3.3 0.9 + - - -
2031F ASP* 3.4 16.1 + - + +
2032F LEU 3.5 6.8 + - - -
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Residues in contact with ARG2029 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966F TYR* 4.3 6.7 + - - +
2013F PHE* 3.6 42.0 - - + -
2024F LEU* 4.8 5.7 - - + +
2025F PRO 4.0 3.0 + - - +
2026F ASP* 3.4 14.1 + - - +
2027F GLU 3.3 0.6 - - - -
2028F ILE* 1.3 75.6 - - - +
2030F GLN* 1.3 60.5 + - - +
2032F LEU* 3.2 10.9 + - + +
2033F LEU* 2.9 32.8 + - - +
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Residues in contact with GLN2030 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013F PHE* 5.1 4.7 - - - -
2026F ASP* 3.1 27.5 + - + +
2027F GLU* 3.7 11.4 - - - +
2028F ILE 3.2 1.0 - - - -
2029F ARG* 1.3 78.0 - - - +
2031F ASP* 1.3 57.2 + - - +
2033F LEU* 3.2 30.3 - - - +
2034F GLU* 2.9 30.1 + - - +
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Residues in contact with ASP2031 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962F PHE* 4.3 7.6 - - + -
1966F TYR* 5.8 2.9 - - + -
2027F GLU 4.2 3.0 + - - +
2028F ILE* 3.4 11.7 + - + +
2029F ARG 3.3 0.2 - - - -
2030F GLN* 1.3 79.0 - - - +
2032F LEU* 1.3 56.8 + - - +
2034F GLU* 3.7 6.1 - - - +
2035F PHE* 2.9 31.5 + - - +
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Residues in contact with LEU2032 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962F PHE* 3.9 28.0 - - + -
1966F TYR* 3.3 46.1 - - + +
2011F LEU 4.9 7.6 - - - +
2013F PHE* 4.8 16.4 - - + -
2028F ILE 3.5 3.0 + - - -
2029F ARG* 3.2 12.1 + - + +
2030F GLN 3.2 0.4 - - - -
2031F ASP* 1.3 78.9 - - - +
2033F LEU* 1.3 59.4 + - - +
2035F PHE* 3.4 1.9 + - - +
2036F HIS* 2.9 29.3 + - + +
3649F PHE* 4.6 10.1 - - + -
3653F TYR* 4.7 13.0 - - + -
3657F TRP* 4.4 21.8 - - + +
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Residues in contact with LEU2033 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013F PHE* 4.2 24.9 - - + -
2029F ARG 2.9 20.2 + - - +
2030F GLN* 3.2 44.6 - - - +
2032F LEU* 1.3 77.4 - - - +
2034F GLU* 1.3 63.5 + - + +
2036F HIS* 3.5 10.0 + - - +
2037F GLN* 2.9 30.8 + - + +
3657F TRP* 5.8 7.6 - - + -
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Residues in contact with GLU2034 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2030F GLN 2.9 19.4 + - - +
2031F ASP* 3.7 7.9 - - - +
2032F LEU 3.3 0.2 - - - -
2033F LEU* 1.3 83.3 - - + +
2035F PHE* 1.3 57.7 + - - +
2037F GLN* 3.3 6.1 + - - +
2038F ASP* 2.9 28.3 + - - +
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Residues in contact with PHE2035 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1746F THR* 6.1 0.9 - - - -
1747F LEU* 4.6 21.8 - - + -
1958F SER* 4.4 16.2 - - - -
1959F LEU* 4.6 9.6 - - + -
1962F PHE* 3.4 66.9 - + + -
1965F ARG* 5.4 2.2 - - - -
2031F ASP 2.9 18.0 + - - +
2032F LEU 3.8 0.7 - - - +
2034F GLU* 1.3 75.9 - - - +
2036F HIS* 1.3 61.5 + - - +
2038F ASP* 3.3 9.5 + - + +
2039F LEU* 2.9 48.1 + - + +
3653F TYR* 5.5 5.2 - + - -
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Residues in contact with HIS2036 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2032F LEU* 2.9 19.8 + - + +
2033F LEU* 3.5 10.5 + - - +
2034F GLU 3.2 0.4 - - - -
2035F PHE* 1.3 77.9 - - - +
2037F GLN* 1.3 57.6 + - - +
2039F LEU* 3.2 5.3 + - + +
2040F LEU* 2.9 74.3 + - + +
3653F TYR* 3.1 31.2 - + + +
3657F TRP* 3.3 56.6 + + + +
3658F ILE* 5.0 3.2 - - + +
3661F GLU* 4.8 5.8 - - + -
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Residues in contact with GLN2037 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2033F LEU* 2.9 17.0 + - + +
2034F GLU* 3.7 6.5 - - - +
2036F HIS* 1.3 79.1 + - - +
2038F ASP* 1.3 57.5 + - - +
2040F LEU* 3.3 9.2 + - - +
2041F THR* 2.8 35.9 + - + +
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Residues in contact with ASP2038 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747F LEU* 5.7 6.1 - - + -
1748F PHE* 3.5 24.1 - - + -
2034F GLU 2.9 17.4 + - - +
2035F PHE* 3.6 13.5 - - + +
2037F GLN* 1.3 77.4 - - - +
2039F LEU* 1.3 56.4 + - - +
2041F THR* 2.7 20.0 + - - -
2042F HIS* 2.9 19.7 + - - +
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Residues in contact with LEU2039 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747F LEU* 6.0 5.1 - - + +
1955F ARG* 4.8 19.7 - - + +
1959F LEU* 3.7 33.0 - - + -
2035F PHE* 2.9 38.2 + - + +
2036F HIS* 3.2 6.3 + - + +
2038F ASP* 1.3 76.5 - - - +
2040F LEU* 1.3 70.7 + - + +
2042F HIS* 3.8 7.0 + - + +
2043F CYS* 2.9 33.2 + - + +
2132F LEU* 5.6 1.8 - - + -
2135F LEU* 4.4 25.6 - - + -
3653F TYR* 5.1 9.6 - - + +
3658F ILE* 5.5 5.4 - - + -
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Residues in contact with LEU2040 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036F HIS* 2.9 63.3 + - + +
2037F GLN* 3.7 9.2 - - - +
2039F LEU* 1.3 87.8 - - + +
2041F THR* 1.3 61.1 + - + +
2043F CYS* 3.4 5.1 + - - -
2044F GLY 3.3 4.3 + - - -
2045F ILE* 2.8 47.8 + - + +
2132F LEU* 5.3 10.5 - - + -
3658F ILE* 5.9 3.1 - - + -
3661F GLU* 4.1 23.1 - - + +
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Residues in contact with THR2041 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1748F PHE* 3.8 11.1 - - - -
1761F HIS* 4.2 8.7 + - - -
2037F GLN* 2.8 18.9 + - + +
2038F ASP* 2.7 22.3 + - - -
2040F LEU* 1.3 75.2 - - + +
2042F HIS* 1.3 59.9 + - - +
2044F GLY* 3.5 10.4 + - - -
2045F ILE 3.5 14.5 - - - +
2046F GLN* 5.6 4.3 - - - +
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Residues in contact with HIS2042 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747F LEU* 4.5 16.4 + - + +
1748F PHE* 3.6 24.2 - + + -
1761F HIS* 3.4 48.0 + + + +
1762F GLY 5.9 0.6 + - - -
1951F GLU* 3.9 14.4 + - + +
1954F HIS* 5.9 6.5 - + - -
1955F ARG* 3.2 47.4 + - + +
2038F ASP 2.9 17.6 + - - +
2039F LEU* 3.8 8.3 + - - +
2041F THR* 1.3 77.0 + - - +
2043F CYS* 1.3 60.1 + - - +
2044F GLY* 3.1 2.8 + - - -
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Residues in contact with CYS2043 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1955F ARG* 4.6 19.1 - - - +
2039F LEU* 2.9 18.1 + - + +
2040F LEU* 3.4 6.2 + - - +
2042F HIS* 1.3 78.7 + - - +
2044F GLY* 1.3 57.2 + - - +
2045F ILE 3.6 1.6 - - - +
2128F GLN 5.6 1.2 - - - +
2131F GLY* 3.6 41.3 + - - -
2132F LEU* 3.8 16.2 - - + -
2135F LEU* 3.7 18.2 - - + -
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Residues in contact with GLY2044 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040F LEU 3.3 1.2 + - - -
2041F THR 3.5 7.1 + - - -
2042F HIS 3.1 5.8 + - - -
2043F CYS* 1.3 78.9 - - - +
2045F ILE* 1.3 64.3 + - - +
2046F GLN* 3.6 3.6 + - - +
3663F HIS* 4.8 2.8 + - - -
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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