Contacts of the helix formed by residues 2025 - 2044 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1973D ASN* 5.7 6.1 - - + -
2024D LEU* 1.3 110.4 - - + +
2026D ASP* 1.3 60.3 + - - +
2027D GLU* 3.0 16.5 + - + +
2028D ILE* 3.4 20.5 + - + -
2029D ARG* 4.0 1.9 + - - +
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Residues in contact with ASP2026 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013D PHE* 5.4 7.6 - - + -
2024D LEU 3.5 3.3 + - - -
2025D PRO* 1.3 71.8 - - - +
2027D GLU* 1.3 61.5 + - - +
2028D ILE 3.3 0.4 - - - -
2029D ARG* 3.4 11.1 + - + +
2030D GLN* 3.1 35.9 + - + +
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Residues in contact with GLU2027 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025D PRO* 3.0 9.0 + - + +
2026D ASP* 1.3 79.7 - - - +
2028D ILE* 1.3 66.8 + - + +
2030D GLN* 3.6 17.7 + - - +
2031D ASP* 4.2 3.3 + - - +
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Residues in contact with ILE2028 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966D TYR* 3.6 27.1 - - + +
1969D LYS* 4.8 14.6 - - + +
1970D LEU* 3.9 14.4 - - + -
1973D ASN* 3.9 27.6 - - + -
2024D LEU* 3.9 22.2 - - + -
2025D PRO* 3.4 13.6 + - + +
2026D ASP 3.3 0.4 - - - -
2027D GLU* 1.3 77.1 - - + +
2029D ARG* 1.3 64.7 + - - +
2030D GLN 3.3 0.7 + - - -
2031D ASP* 3.4 15.1 + - + +
2032D LEU 3.5 7.4 + - - -
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Residues in contact with ARG2029 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966D TYR* 4.3 6.0 + - - +
2013D PHE* 3.6 42.4 - - + -
2024D LEU* 4.8 5.1 - - + +
2025D PRO 4.0 3.6 + - - +
2026D ASP* 3.4 15.0 + - - +
2027D GLU 3.3 0.4 - - - -
2028D ILE* 1.3 77.3 - - - +
2030D GLN* 1.3 60.0 + - - +
2032D LEU* 3.2 10.3 + - + +
2033D LEU* 2.9 32.4 + - - +
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Residues in contact with GLN2030 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013D PHE* 5.1 4.2 - - - -
2026D ASP* 3.1 27.4 + - - +
2027D GLU* 3.7 11.4 - - - +
2028D ILE 3.2 0.8 - - - -
2029D ARG* 1.3 77.8 - - - +
2031D ASP* 1.3 57.8 + - - +
2033D LEU* 3.2 30.9 - - - +
2034D GLU* 2.9 30.2 + - - +
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Residues in contact with ASP2031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962D PHE* 4.3 8.1 - - + -
1966D TYR* 5.9 2.7 - - + -
2027D GLU 4.2 3.4 + - - +
2028D ILE* 3.4 11.7 + - + +
2029D ARG 3.3 0.2 - - - -
2030D GLN* 1.3 77.8 - - - +
2032D LEU* 1.3 57.8 + - - +
2034D GLU* 3.3 7.6 + - - +
2035D PHE* 2.9 30.8 + - - +
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Residues in contact with LEU2032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962D PHE* 3.9 28.5 - - + -
1966D TYR* 3.3 46.4 - - + +
2011D LEU 4.9 7.2 - - - +
2013D PHE* 4.8 17.0 - - + -
2028D ILE 3.5 2.2 + - - -
2029D ARG* 3.2 11.8 + - + +
2030D GLN 3.2 0.8 - - - -
2031D ASP* 1.3 79.4 - - - +
2033D LEU* 1.3 57.7 + - - +
2035D PHE* 3.4 1.9 + - - +
2036D HIS* 2.9 29.1 + - + +
3649D PHE* 4.6 10.3 - - + -
3653D TYR* 4.7 13.0 - - + -
3657D TRP* 4.4 21.8 - - + +
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Residues in contact with LEU2033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013D PHE* 4.2 25.5 - - + -
2029D ARG 2.9 19.4 + - - +
2030D GLN* 3.2 42.8 - - - +
2032D LEU* 1.3 78.1 - - - +
2034D GLU* 1.3 64.0 + - + +
2036D HIS* 3.3 10.3 + - - +
2037D GLN* 2.9 30.6 + - + +
3657D TRP* 5.8 7.0 - - + -
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Residues in contact with GLU2034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2030D GLN 2.9 19.1 + - - +
2031D ASP* 3.7 7.6 - - - +
2033D LEU* 1.3 82.6 - - + +
2035D PHE* 1.3 56.8 + - - +
2037D GLN* 3.3 6.4 + - - +
2038D ASP* 2.9 27.9 + - - +
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Residues in contact with PHE2035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1746D THR* 6.1 0.9 - - - -
1747D LEU* 4.6 22.7 - - + -
1958D SER* 4.4 15.9 - - - -
1959D LEU* 4.6 10.5 - - + -
1962D PHE* 3.4 65.3 - + + -
1965D ARG* 5.4 3.1 - - - -
2031D ASP 2.9 18.0 + - - +
2032D LEU 3.8 0.4 - - - +
2034D GLU* 1.3 76.7 - - - +
2036D HIS* 1.3 59.8 + - - +
2038D ASP* 3.3 8.9 + - + +
2039D LEU* 2.9 48.7 + - + +
3653D TYR* 5.5 4.7 - + - -
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Residues in contact with HIS2036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2032D LEU* 2.9 19.8 + - + +
2033D LEU* 3.5 10.2 + - - +
2035D PHE* 1.3 77.6 - - - +
2037D GLN* 1.3 58.3 + - - +
2039D LEU* 3.2 5.5 + - + +
2040D LEU* 2.9 73.7 + - + +
3653D TYR* 3.1 30.3 - + + +
3657D TRP* 3.3 57.6 + + + +
3658D ILE* 5.0 3.4 - - + +
3661D GLU* 4.8 6.5 - - + +
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Residues in contact with GLN2037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2033D LEU* 2.9 17.8 + - + +
2034D GLU* 3.7 5.6 - - - +
2036D HIS* 1.3 78.1 + - - +
2038D ASP* 1.3 58.3 + - - +
2040D LEU* 3.3 9.3 + - - +
2041D THR* 2.8 36.3 + - + +
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Residues in contact with ASP2038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747D LEU* 5.7 5.8 - - + -
1748D PHE* 3.5 23.9 - - + -
2034D GLU 2.9 17.6 + - - +
2035D PHE* 3.6 13.5 - - + +
2037D GLN* 1.3 77.0 - - - +
2039D LEU* 1.3 56.8 + - - +
2041D THR* 2.7 21.0 + - - -
2042D HIS* 2.9 19.4 + - - +
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Residues in contact with LEU2039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747D LEU* 6.0 5.6 - - + +
1955D ARG* 4.8 19.5 - - + -
1959D LEU* 3.7 33.2 - - + -
2035D PHE* 2.9 37.9 + - + +
2036D HIS* 3.6 6.3 - - - +
2038D ASP* 1.3 75.9 - - - +
2040D LEU* 1.3 71.8 + - + +
2042D HIS* 3.3 6.7 + - + +
2043D CYS* 2.9 33.5 + - + +
2132D LEU* 5.6 2.0 - - + -
2135D LEU* 4.4 25.1 - - + -
3653D TYR* 5.1 10.3 - - + +
3658D ILE* 5.5 5.2 - - + -
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Residues in contact with LEU2040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036D HIS* 2.9 65.3 + - + +
2037D GLN* 3.7 9.6 - - - +
2039D LEU* 1.3 87.8 - - + +
2041D THR* 1.3 60.5 + - + +
2043D CYS* 3.4 4.5 + - - -
2044D GLY 3.3 4.3 + - - -
2045D ILE* 2.8 48.1 + - + +
2132D LEU* 5.3 10.3 - - + -
3657D TRP 5.8 0.2 - - - +
3658D ILE* 5.9 3.4 - - + -
3661D GLU* 4.1 22.4 - - + +
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Residues in contact with THR2041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1748D PHE* 3.8 10.5 - - - -
1761D HIS* 4.2 8.8 + - - -
2037D GLN* 2.8 18.3 + - + +
2038D ASP* 2.7 22.3 + - - -
2040D LEU* 1.3 76.1 - - + +
2042D HIS* 1.3 59.2 + - - +
2044D GLY* 3.5 10.0 + - - -
2045D ILE 3.5 14.4 - - - +
2046D GLN* 5.6 4.0 - - - +
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Residues in contact with HIS2042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747D LEU* 4.5 17.5 + - + +
1748D PHE* 3.6 25.1 - + + -
1761D HIS* 3.4 47.0 + + + +
1762D GLY 5.9 0.6 + - - -
1951D GLU* 3.9 16.5 + - + +
1954D HIS* 5.9 6.3 - + - -
1955D ARG* 3.2 48.2 + - + +
2038D ASP 2.9 17.7 + - - +
2039D LEU* 3.8 7.7 + - - +
2040D LEU 3.2 0.2 - - - -
2041D THR* 1.3 78.5 - - - +
2043D CYS* 1.3 60.6 + - - +
2044D GLY* 3.1 3.0 + - - -
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Residues in contact with CYS2043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1955D ARG* 4.6 18.6 - - - +
2039D LEU* 2.9 20.5 + - + +
2040D LEU 3.4 4.7 + - - +
2042D HIS* 1.3 79.4 + - - +
2044D GLY* 1.3 57.0 + - - +
2045D ILE* 3.6 1.3 - - + +
2128D GLN 5.6 1.6 - - - +
2131D GLY* 3.6 41.2 + - - -
2132D LEU* 3.8 15.5 - - + -
2135D LEU* 3.7 17.9 - - + -
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Residues in contact with GLY2044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040D LEU 3.3 1.2 + - - -
2041D THR 3.5 6.0 + - - -
2042D HIS 3.1 6.2 - - - -
2043D CYS* 1.3 77.9 - - - +
2045D ILE* 1.3 64.3 + - - +
2046D GLN* 3.6 3.5 + - - +
3663D HIS* 4.8 2.9 + - - -
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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