Contacts of the helix formed by residues 2025 - 2044 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1973B ASN* 5.7 5.8 - - + -
2023B PRO 4.9 0.7 - - - +
2024B LEU* 1.3 110.8 - - + +
2026B ASP* 1.3 58.4 + - - +
2027B GLU* 3.0 16.7 + - + +
2028B ILE* 3.4 20.7 + - + -
2029B ARG* 4.0 1.7 + - - +
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Residues in contact with ASP2026 (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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2013B PHE* 5.4 7.6 - - + -
2024B LEU 3.5 3.3 + - - -
2025B PRO* 1.3 70.9 - - - +
2027B GLU* 1.3 61.7 + - - +
2028B ILE 3.3 0.7 - - - -
2029B ARG* 3.4 10.9 + - + +
2030B GLN* 3.1 36.4 + - + +
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Residues in contact with GLU2027 (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 PRO* 3.0 8.7 + - + +
2026B ASP* 1.3 80.3 - - - +
2028B ILE* 1.3 65.7 + - + +
2030B GLN* 3.6 17.6 + - - +
2031B ASP* 4.2 4.0 + - - +
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Residues in contact with ILE2028 (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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1966B TYR* 3.6 28.3 - - + +
1969B LYS* 4.8 13.5 - - + +
1970B LEU* 3.9 14.4 - - + -
1973B ASN* 3.9 28.3 - - + -
2024B LEU* 3.9 20.4 - - + -
2025B PRO* 3.4 13.3 + - + +
2026B ASP 3.3 0.4 - - - -
2027B GLU* 1.3 79.3 - - + +
2029B ARG* 1.3 64.2 + - - +
2030B GLN 3.3 0.9 + - - -
2031B ASP* 3.4 15.5 + - + +
2032B LEU 3.5 7.1 + - - -
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Residues in contact with ARG2029 (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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1966B TYR* 4.3 6.5 + - - +
2013B PHE* 3.6 43.3 - - + -
2024B LEU* 4.8 5.8 - - + +
2025B PRO 4.0 3.4 + - - +
2026B ASP* 3.4 14.8 + - - +
2027B GLU 3.3 0.8 - - - -
2028B ILE* 1.3 74.9 - - - +
2030B GLN* 1.3 59.8 + - - +
2031B ASP 3.3 0.2 - - - -
2032B LEU* 3.2 11.0 + - + +
2033B LEU* 2.9 32.6 + - - +
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Residues in contact with GLN2030 (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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2013B PHE* 5.1 4.9 - - - -
2026B ASP* 3.1 27.9 + - + +
2027B GLU* 3.7 11.2 - - - +
2028B ILE 3.2 0.8 - - - -
2029B ARG* 1.3 76.8 - - - +
2031B ASP* 1.3 56.9 + - - +
2033B LEU* 3.2 30.0 - - - +
2034B GLU* 2.9 30.5 + - - +
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Residues in contact with ASP2031 (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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1962B PHE* 4.3 8.8 - - + -
1966B TYR* 5.8 3.1 - - + -
2027B GLU 4.2 3.9 + - - +
2028B ILE* 3.4 11.6 + - + +
2029B ARG 3.3 0.2 - - - -
2030B GLN* 1.3 78.2 - - - +
2032B LEU* 1.3 57.0 + - - +
2034B GLU* 3.7 6.0 - - - +
2035B PHE* 2.9 31.5 + - - +
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Residues in contact with LEU2032 (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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1962B PHE* 3.9 28.5 - - + -
1966B TYR* 3.3 46.8 - - + +
2011B LEU 4.9 7.6 - - - +
2013B PHE* 4.8 16.4 - - + -
2028B ILE 3.5 3.2 + - - -
2029B ARG* 3.2 12.9 + - + +
2030B GLN 3.2 0.4 - - - -
2031B ASP* 1.3 80.0 - - - +
2033B LEU* 1.3 59.4 + - - +
2035B PHE* 3.4 1.9 + - - +
2036B HIS* 2.9 28.3 + - + +
3649B PHE* 4.6 10.8 - - + -
3653B TYR* 4.7 13.5 - - + -
3657B TRP* 4.4 22.2 - - + +
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Residues in contact with LEU2033 (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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2013B PHE* 4.2 24.7 - - + -
2029B ARG 2.9 19.0 + - - +
2030B GLN* 3.2 43.1 - - - +
2032B LEU* 1.3 77.8 - - - +
2034B GLU* 1.3 64.4 + - + +
2036B HIS* 3.5 9.2 + - - +
2037B GLN* 2.9 31.2 + - + +
3657B TRP* 5.8 7.6 - - + -
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Residues in contact with GLU2034 (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 GLN 2.9 17.7 + - - +
2031B ASP* 3.7 8.5 - - - +
2033B LEU* 1.3 83.6 - - + +
2035B PHE* 1.3 56.7 + - - +
2037B GLN* 3.3 5.7 + - - +
2038B ASP* 2.9 29.2 + - - +
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Residues in contact with PHE2035 (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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1746B THR* 6.1 1.1 - - - -
1747B LEU* 4.6 21.1 - - + -
1958B SER* 4.4 15.7 - - - -
1959B LEU* 4.6 11.0 - - + -
1962B PHE* 3.4 65.3 - + + -
1965B ARG* 5.4 2.2 - - - -
2031B ASP 2.9 17.1 + - - +
2032B LEU 3.8 0.7 - - - +
2034B GLU* 1.3 77.4 - - - +
2036B HIS* 1.3 59.0 + - - +
2038B ASP* 3.6 9.5 - - + +
2039B LEU* 2.9 48.0 + - + +
3653B TYR* 5.5 5.4 - + - -
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Residues in contact with HIS2036 (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 LEU* 2.9 20.9 + - + +
2033B LEU* 3.5 9.8 + - - +
2035B PHE* 1.3 79.4 - - - +
2037B GLN* 1.3 58.8 + - - +
2039B LEU* 3.2 5.0 + - + +
2040B LEU* 2.9 74.0 + - + +
3653B TYR* 3.1 30.1 - + + +
3657B TRP* 3.3 58.0 + + + +
3658B ILE* 5.0 3.0 - - + +
3661B GLU* 4.8 5.8 - - + +
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Residues in contact with GLN2037 (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 LEU* 2.9 18.2 + - + +
2034B GLU* 3.7 5.4 - - - +
2036B HIS* 1.3 77.6 + - - +
2038B ASP* 1.3 58.1 + - - +
2040B LEU* 3.3 9.6 + - - +
2041B THR* 2.8 35.7 + - + +
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Residues in contact with ASP2038 (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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1747B LEU* 5.7 6.7 - - + -
1748B PHE* 3.5 24.7 - - + -
2034B GLU 2.9 18.4 + - - +
2035B PHE* 3.6 13.5 - - + +
2036B HIS 3.2 0.2 - - - -
2037B GLN* 1.3 77.2 - - - +
2039B LEU* 1.3 56.3 + - - +
2041B THR* 2.7 20.3 + - - -
2042B HIS* 2.9 19.6 + - - +
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Residues in contact with LEU2039 (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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1747B LEU* 6.0 5.4 - - + +
1955B ARG* 4.8 18.6 - - + -
1959B LEU* 3.7 32.1 - - + -
2035B PHE* 2.9 38.0 + - + +
2036B HIS* 3.2 6.0 + - + +
2038B ASP* 1.3 76.1 - - - +
2040B LEU* 1.3 71.4 + - + +
2042B HIS* 3.3 7.3 + - + +
2043B CYS* 2.9 33.4 + - + +
2132B LEU* 5.6 2.0 - - + -
2135B LEU* 4.4 25.8 - - + -
3653B TYR* 5.1 9.9 - - + +
3658B ILE* 5.5 5.4 - - + -
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Residues in contact with LEU2040 (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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2036B HIS* 2.9 64.9 + - + +
2037B GLN* 3.7 8.5 - - - +
2038B ASP 3.3 0.2 - - - -
2039B LEU* 1.3 87.6 - - + +
2041B THR* 1.3 60.7 + - + +
2043B CYS* 3.4 4.9 + - - +
2044B GLY 3.3 4.2 + - - -
2045B ILE* 2.8 48.1 + - + +
2132B LEU* 5.3 10.8 - - + -
3658B ILE* 5.9 2.7 - - + -
3661B GLU* 4.1 23.3 - - + +
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Residues in contact with THR2041 (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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1748B PHE* 3.8 10.5 - - - -
1761B HIS* 4.2 8.5 + - - -
2037B GLN* 2.8 19.7 + - + +
2038B ASP* 2.7 22.2 + - - -
2040B LEU* 1.3 75.4 - - + +
2042B HIS* 1.3 59.4 + - - +
2044B GLY* 3.5 9.9 + - - -
2045B ILE 3.5 13.4 - - - +
2046B GLN* 5.6 4.5 - - - +
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Residues in contact with HIS2042 (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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1747B LEU* 4.5 17.2 + - + +
1748B PHE* 3.6 25.1 - + + -
1761B HIS* 3.4 47.1 + + + +
1762B GLY 5.9 0.6 + - - -
1951B GLU* 3.9 15.1 + - + +
1954B HIS* 5.9 7.1 - + - -
1955B ARG* 3.2 49.2 + - + +
2038B ASP 2.9 17.7 + - - +
2039B LEU* 3.8 7.6 + - - +
2041B THR* 1.3 78.1 - - - +
2043B CYS* 1.3 59.8 + - - +
2044B GLY* 3.1 3.2 + - - -
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Residues in contact with CYS2043 (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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1955B ARG* 4.6 18.6 - - - +
2039B LEU* 2.9 19.5 + - + +
2040B LEU* 3.4 5.1 + - - +
2042B HIS* 1.3 79.4 + - - +
2044B GLY* 1.3 57.5 + - - +
2045B ILE* 4.8 0.9 - - + +
2128B GLN 5.6 1.0 - - - +
2131B GLY* 3.6 40.3 + - - -
2132B LEU* 3.8 16.2 - - + -
2135B LEU* 3.7 17.7 - - + -
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Residues in contact with GLY2044 (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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2040B LEU 3.3 1.2 + - - -
2041B THR 3.5 6.4 + - - -
2042B HIS 3.1 6.0 + - - -
2043B CYS* 1.3 79.2 - - - +
2045B ILE* 1.3 63.5 + - - +
2046B GLN* 3.6 4.2 + - - +
3663B HIS* 4.8 3.2 + - - -
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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
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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