Contacts of the helix formed by residues 2056 - 2075 (chain A) in PDB entry 6AJ4
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 GLN2056 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991A GLN* 2.9 37.5 + - - +
2052A ILE* 3.3 37.3 - - + +
2053A GLY 3.4 2.8 + - - +
2054A PRO 2.9 1.6 + - - -
2055A ASP* 1.3 96.9 + - - +
2057A LYS* 1.3 59.3 + - - +
2058A GLU 3.5 1.8 - - - -
2059A TYR* 3.8 26.4 - - + -
2060A GLN 2.8 24.9 + - - -
5B LYS* 4.7 0.7 + - - -
73B PRO* 3.9 20.6 - - + +
74B GLN* 3.7 23.6 - - - +
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Residues in contact with LYS2057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052A ILE* 4.3 8.7 - - + -
2053A GLY 4.2 3.1 + - - +
2054A PRO* 3.0 25.2 + - + +
2055A ASP 3.4 1.6 - - - -
2056A GLN* 1.3 77.8 - - - +
2058A GLU* 1.3 58.9 + - - +
2060A GLN* 3.3 3.0 + - - +
2061A ARG* 2.8 51.6 + - - +
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Residues in contact with GLU2058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2055A ASP 5.0 1.0 + - - -
2056A GLN 3.5 0.2 - - - -
2057A LYS* 1.3 75.3 - - - +
2059A TYR* 1.3 67.9 + - - +
2061A ARG* 3.1 26.6 + - + +
2062A GLU* 2.9 24.2 + - + +
70B LEU* 4.1 25.7 - - + +
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Residues in contact with TYR2059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991A GLN* 3.1 41.2 + - + +
1995A GLN* 3.5 31.2 + - + +
2048A ASN* 5.0 2.9 - - - -
2055A ASP 5.2 1.3 + - - +
2056A GLN* 3.4 39.1 - - + +
2058A GLU* 1.3 79.3 - - - +
2060A GLN* 1.3 67.2 + - - +
2062A GLU* 3.2 3.7 + - + +
2063A LEU* 3.2 48.4 + - + +
5B LYS* 4.7 4.4 + - - -
56B PHE* 4.2 7.8 - - - -
70B LEU* 3.3 47.1 - - + +
71B SER* 4.1 12.5 + - - -
73B PRO* 5.7 1.1 - - + -
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Residues in contact with GLN2060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2045A LEU* 3.2 31.1 + - - +
2048A ASN* 3.2 31.4 + - - +
2049A LYS* 3.6 25.2 - - + +
2052A ILE* 3.4 18.2 - - + -
2056A GLN 2.8 19.9 + - - +
2057A LYS 3.8 3.1 - - - +
2059A TYR* 1.3 76.4 - - + +
2061A ARG* 1.3 63.1 + - - +
2063A LEU* 3.2 12.3 + - - +
2064A GLU* 2.3 62.9 + - - +
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Residues in contact with ARG2061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2049A LYS* 6.0 0.4 - - - +
2057A LYS* 2.8 43.9 + - - +
2058A GLU* 3.1 41.3 + - - +
2060A GLN* 1.3 77.0 - - - +
2062A GLU* 1.3 58.2 + - - +
2064A GLU* 3.0 15.3 + - + +
2065A ARG* 2.8 32.8 + - + +
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Residues in contact with GLU2062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058A GLU* 2.9 12.7 + - + +
2059A TYR* 3.7 8.1 - - + +
2061A ARG* 1.3 77.0 - - - +
2063A LEU* 1.3 62.2 + - + +
2064A GLU 3.0 0.2 + - - -
2065A ARG* 3.0 28.7 + - - +
2066A ASN* 2.8 60.3 + - - +
67B LEU* 3.8 31.4 - - + +
70B LEU* 3.9 20.9 - - + -
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Residues in contact with LEU2063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991A GLN* 5.2 1.6 - - + +
1994A LEU* 3.9 27.4 - - + -
1995A GLN* 3.8 33.7 - - + +
1998A VAL* 3.7 9.7 - - + +
1999A GLY* 5.2 1.3 - - - -
2045A LEU* 3.6 19.3 - - + +
2048A ASN* 4.6 8.7 - - - +
2059A TYR* 3.2 43.4 + - + +
2060A GLN* 3.2 10.7 + - - +
2062A GLU* 1.3 80.1 - - + +
2064A GLU* 1.3 55.6 + - - +
2066A ASN* 3.5 15.5 - - - +
2067A TYR* 3.1 22.0 + - - +
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Residues in contact with GLU2064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2045A LEU* 3.9 17.7 - - + -
2049A LYS* 3.0 28.2 + - - +
2060A GLN* 2.3 51.1 + - - +
2061A ARG* 3.0 12.7 + - + +
2063A LEU* 1.3 75.6 - - - +
2065A ARG* 1.3 65.9 + - - +
2066A ASN 3.0 1.6 - - - -
2067A TYR 3.3 0.7 + - - -
2068A HIS* 3.0 49.8 + - + +
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Residues in contact with ARG2065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2061A ARG* 2.8 25.4 + - + +
2062A GLU* 3.0 26.5 + - - +
2064A GLU* 1.3 72.5 - - - +
2066A ASN* 1.3 71.4 + - - +
2068A HIS* 4.3 6.0 - - - +
2069A ARG* 3.2 54.5 + - - +
67B LEU* 6.0 2.4 - - - +
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Residues in contact with ASN2066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998A VAL 3.5 20.0 - - - +
1999A GLY* 3.5 23.0 - - - -
2062A GLU* 2.8 52.6 + - - +
2063A LEU* 3.5 12.0 - - - +
2065A ARG* 1.3 81.3 + - - +
2067A TYR* 1.3 68.3 + - - +
2069A ARG* 2.9 32.8 + - - +
2070A LEU* 2.9 14.3 + - - +
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Residues in contact with TYR2067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998A VAL* 3.8 18.3 - - + +
2038A THR* 3.5 41.2 + - - -
2041A CYS* 3.8 19.5 - - + -
2042A GLU* 3.5 29.9 + - + -
2045A LEU* 3.5 28.9 - - + -
2063A LEU 3.1 7.9 + - - +
2064A GLU 3.3 1.1 + - - +
2066A ASN* 1.3 79.3 - - - +
2068A HIS* 1.3 80.5 + + - +
2070A LEU* 3.7 10.2 - - + +
2071A LYS* 2.9 54.2 + - + +
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Residues in contact with HIS2068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2045A LEU* 5.0 2.6 - - - +
2064A GLU* 3.0 39.3 + - + +
2065A ARG* 4.3 4.8 + - - +
2067A TYR* 1.3 102.0 - + - +
2069A ARG* 1.3 69.5 + - - +
2071A LYS* 4.4 3.1 - - + +
2072A GLU* 3.1 36.0 + - + +
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Residues in contact with ARG2069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998A VAL 5.7 2.0 + - - -
2007A LEU* 5.9 2.2 - - - +
2065A ARG* 3.2 43.1 + - - +
2066A ASN* 2.9 24.0 + - - +
2068A HIS* 1.3 79.7 - - - +
2070A LEU* 1.3 62.1 + - - +
2072A GLU* 3.6 7.0 - - - +
2073A ALA* 3.2 19.6 + - - +
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Residues in contact with LEU2070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1997A SER 4.6 2.7 - - - +
1998A VAL* 4.4 28.7 - - + +
2006A PRO* 4.2 19.5 - - + -
2007A LEU* 3.7 35.4 - - + +
2037A PHE* 4.9 7.2 - - + -
2066A ASN 2.9 14.8 + - - +
2067A TYR* 3.7 8.5 - - + +
2069A ARG* 1.3 78.4 - - - +
2071A LYS* 1.3 55.8 + - - +
2073A ALA* 3.0 5.2 + - - -
2074A LEU* 2.7 59.2 + - + +
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Residues in contact with LYS2071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2038A THR* 3.2 42.6 + - - +
2039A LYS* 5.8 0.4 - - - +
2042A GLU* 5.4 3.7 + - - -
2067A TYR* 2.9 44.6 + - + +
2068A HIS* 3.4 3.8 + - + +
2070A LEU* 1.3 76.2 - - - +
2072A GLU* 1.3 67.2 + - - +
2074A LEU* 3.8 9.1 - - + +
2075A GLN* 3.0 39.8 + - + +
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Residues in contact with GLU2072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2068A HIS* 3.1 27.2 + - + +
2069A ARG* 3.6 6.1 - - - +
2071A LYS* 1.3 82.5 - - - +
2073A ALA* 1.3 62.3 + - - +
2075A GLN* 3.3 9.7 + - - +
2076A PRO* 3.1 19.6 - - - +
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Residues in contact with ALA2073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007A LEU* 3.4 35.0 - - + +
2069A ARG 3.2 9.2 + - - +
2070A LEU 3.0 4.7 + - - +
2072A GLU* 1.3 79.4 - - - +
2074A LEU* 1.3 64.7 + - - +
2076A PRO* 3.4 12.6 - - - +
2077A LEU* 4.2 10.4 - - - +
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Residues in contact with LEU2074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006A PRO* 5.9 0.4 - - + -
2007A LEU* 4.2 17.5 - - + -
2010A ALA* 4.0 27.4 - - + -
2034A PHE* 3.8 27.4 - - + +
2037A PHE* 5.5 4.0 - - + -
2038A THR* 5.0 13.7 - - - +
2070A LEU* 2.7 46.2 + - + +
2071A LYS* 3.8 10.5 - - + +
2072A GLU 3.2 0.2 - - - -
2073A ALA* 1.3 74.5 - - - +
2075A GLN* 1.3 53.7 + - - +
2077A LEU* 2.7 34.9 + - + +
2078A ILE* 3.1 24.6 - - + +
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Residues in contact with GLN2075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2071A LYS* 3.0 33.3 + - + +
2072A GLU* 3.9 10.2 - - - +
2074A LEU* 1.3 75.3 - - - +
2076A PRO* 1.3 68.9 - - + +
2078A ILE* 3.7 8.5 + - + -
2079A ASN* 3.2 45.8 + - - +
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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
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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