Contacts of the helix formed by residues 2052 - 2068 (chain A) in PDB entry 5G1N
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 HIS2052 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1976A THR* 3.8 14.8 + - + -
2024A ARG* 3.0 21.3 + - - -
2044A ASN 4.7 0.2 - - - -
2045A ALA* 3.2 28.2 + - - -
2046A GLY* 4.6 0.9 - - - -
2051A GLU* 1.3 75.4 - - - +
2053A PRO* 1.3 67.4 - - - +
2054A THR* 4.2 8.6 + - - -
2055A GLN* 3.2 34.2 + - + +
2056A ALA 3.3 4.9 + - - -
2085A ARG* 3.6 30.5 + - + +
2086A THR* 3.6 26.0 - - + -
2089A SER* 2.7 13.3 + - - -
2214A ARG* 4.7 0.2 - - - -
3226A PAL 3.1 14.0 + - - -
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Residues in contact with PRO2053 (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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1926A ILE* 4.1 9.4 - - + +
1927A LEU 3.4 28.3 - - - +
1928A SER* 3.8 2.2 - - - +
1929A VAL* 3.9 20.6 - - + +
1932A PHE* 3.9 26.3 - - + -
2044A ASN* 3.8 22.7 - - + +
2051A GLU* 3.5 9.9 - - + -
2052A HIS* 1.3 89.9 - - - +
2054A THR* 1.3 58.0 + - - +
2056A ALA* 3.2 4.7 + - - +
2057A LEU* 2.9 30.0 + - - +
2089A SER* 4.0 0.2 - - - +
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Residues in contact with THR2054 (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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1926A ILE* 4.3 10.5 - - + -
1976A THR* 4.8 0.2 - - - +
1980A PHE* 4.2 7.8 - - + -
2043A ILE* 3.9 24.9 - - + -
2044A ASN 4.3 7.1 + - - +
2045A ALA* 5.2 0.2 - - - -
2052A HIS* 3.4 9.0 + - - -
2053A PRO* 1.3 72.9 - - - +
2055A GLN* 1.3 68.3 + - - +
2057A LEU* 3.6 10.7 - - - +
2058A LEU* 3.2 22.3 + - - +
2213A ILE* 4.4 3.2 - - - +
2214A ARG* 2.8 29.7 + - - -
2217A LEU* 3.5 29.6 - - + -
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Residues in contact with GLN2055 (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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1975A ARG* 6.0 1.0 - - - +
1976A THR* 4.4 3.0 + - - -
2052A HIS* 3.2 34.8 + - + +
2053A PRO 3.1 0.4 - - - -
2054A THR* 1.3 79.5 + - - +
2056A ALA* 1.3 51.9 + - - +
2058A LEU* 2.8 33.6 + - - +
2059A ASP* 2.7 55.1 + - - +
2086A THR* 3.8 17.8 - - + +
2143A TYR* 4.4 1.1 - - - +
2184A PRO* 4.0 20.5 + - - +
2206A GLN* 4.4 1.2 + - - -
2214A ARG* 4.6 5.3 + - - +
3226A PAL 3.3 29.9 + - - +
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Residues in contact with ALA2056 (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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1929A VAL* 3.9 7.4 - - + -
2052A HIS 3.3 2.2 + - - -
2053A PRO 3.2 6.1 + - - +
2055A GLN* 1.3 77.6 - - - +
2057A LEU* 1.3 56.9 + - - +
2059A ASP* 4.0 11.6 + - - -
2060A ILE* 2.9 35.5 + - - +
2086A THR 4.7 0.8 + - - +
2089A SER* 3.5 33.8 - - - +
2090A LEU* 3.6 20.0 - - + +
2093A LEU* 4.1 7.2 - - + -
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Residues in contact with LEU2057 (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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1932A PHE* 3.4 47.1 - - + -
1937A MET* 3.7 36.1 - - + -
1940A LEU* 4.6 21.8 - - + -
1941A PHE* 3.3 19.1 - - + -
2053A PRO 2.9 9.9 + - - +
2054A THR* 3.6 10.8 - - - +
2056A ALA* 1.3 75.2 - - - +
2058A LEU* 1.3 58.2 + - - +
2060A ILE* 3.6 1.2 + - - +
2061A PHE 2.9 20.3 + - - -
2093A LEU* 4.1 2.9 - - + +
2213A ILE* 4.4 8.7 - - + -
2217A LEU* 4.2 25.6 - - + -
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Residues in contact with LEU2058 (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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2054A THR 3.2 14.5 + - - +
2055A GLN* 2.8 33.3 + - - +
2057A LEU* 1.3 73.1 - - - +
2059A ASP* 1.3 65.3 + - - +
2060A ILE 3.2 0.4 - - - -
2061A PHE* 3.4 8.4 - - - +
2062A THR* 2.9 36.5 + - - +
2206A GLN* 3.3 42.8 - - + +
2207A ALA* 5.3 1.3 - - - -
2209A ASN* 5.1 0.9 - - + -
2210A GLY* 3.7 20.6 - - - +
2213A ILE* 3.9 21.3 - - + -
2214A ARG* 3.9 20.9 - - - +
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Residues in contact with ASP2059 (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 GLN* 2.7 39.2 + - - +
2056A ALA* 3.7 7.5 - - - +
2058A LEU* 1.3 73.4 - - - +
2060A ILE* 1.3 61.4 + - - +
2062A THR 3.2 1.2 + - - -
2063A ILE* 3.1 29.7 + - + +
2086A THR* 4.6 1.2 - - - +
2090A LEU* 3.6 23.9 - - + +
2143A TYR* 2.7 37.4 + - - -
2182A MET* 3.5 12.7 - - + +
2206A GLN* 2.7 23.4 + - - -
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Residues in contact with ILE2060 (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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1937A MET* 3.6 21.8 - - + -
1941A PHE* 3.7 9.9 - - + -
2056A ALA 2.9 14.8 + - - +
2057A LEU 3.9 2.2 - - - +
2059A ASP* 1.3 73.6 - - - +
2061A PHE* 1.3 65.0 + - - +
2062A THR 3.3 0.5 + - - -
2063A ILE* 3.5 7.9 + - + +
2064A ARG* 3.3 21.5 + - + +
2070A VAL* 4.2 8.9 - - + +
2090A LEU* 3.6 17.7 - - + -
2093A LEU* 3.4 53.4 - - + +
2094A LEU* 4.0 17.3 - - + +
2097A TYR* 3.8 17.7 - - + +
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Residues in contact with PHE2061 (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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1941A PHE* 3.3 46.9 - + + -
1944A ALA* 4.4 11.7 - - + -
1945A HIS* 3.6 26.2 - + - -
1948A ARG* 5.1 4.0 - - - -
2057A LEU 2.9 19.0 + - - +
2058A LEU* 3.3 6.5 + - - +
2060A ILE* 1.3 76.9 - - - +
2062A THR* 1.3 59.0 + - - +
2064A ARG* 3.3 10.1 - - - +
2065A GLU* 3.2 51.4 + - + +
2209A ASN* 3.9 39.3 - - + -
2212A TYR* 6.0 2.7 - - + -
2213A ILE* 3.6 17.7 - - + -
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Residues in contact with THR2062 (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 LEU 2.9 18.2 + - - -
2059A ASP 3.8 4.0 - - - -
2060A ILE 3.2 0.4 - - - -
2061A PHE* 1.3 74.7 - - - +
2063A ILE* 1.3 67.7 + - - +
2064A ARG 3.1 1.3 - - - -
2065A GLU* 3.0 4.5 + - - +
2066A GLU* 2.9 41.1 + - + +
2182A MET* 4.0 23.3 - - + -
2202A ALA* 4.7 3.1 - - + -
2206A GLN* 3.9 20.1 + - + +
2209A ASN* 3.1 33.9 + - - +
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Residues in contact with ILE2063 (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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2059A ASP* 3.1 28.1 + - + +
2060A ILE* 3.8 10.5 - - + +
2062A THR* 1.3 74.9 - - - +
2064A ARG* 1.3 63.9 + - - +
2066A GLU* 4.9 2.5 - - - -
2067A LEU* 3.0 33.5 + - + +
2069A THR 3.9 13.9 - - - +
2070A VAL* 3.9 17.5 - - + -
2073A MET* 5.0 2.5 - - + -
2075A ILE* 4.0 23.8 - - + -
2090A LEU* 4.7 13.5 - - + -
2094A LEU* 4.7 3.8 - - + -
2141A VAL* 3.8 29.6 - - + -
2143A TYR* 6.2 0.4 - - + -
2180A VAL* 5.2 1.3 - - - -
2182A MET* 3.6 20.2 - - + -
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Residues in contact with ARG2064 (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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1938A SER* 4.8 12.5 + - - +
1941A PHE* 3.4 50.2 - - - +
1942A ASN* 5.1 9.1 + - - +
1945A HIS* 4.7 14.7 + - - -
2060A ILE* 3.3 9.0 + - + +
2061A PHE* 3.3 13.6 - - - +
2063A ILE* 1.3 79.8 - - - +
2065A GLU* 1.3 59.9 + - - +
2068A GLY* 2.7 36.3 + - - +
2069A THR* 3.5 24.6 + - - +
2070A VAL* 4.5 7.2 - - + +
2097A TYR* 5.5 4.0 + - + -
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Residues in contact with GLU2065 (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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1945A HIS* 2.8 39.4 + - - -
1948A ARG* 4.5 9.4 + - - -
2061A PHE* 3.2 32.8 + - + +
2062A THR* 3.0 9.0 + - - +
2064A ARG* 1.3 81.8 - - - +
2066A GLU* 1.3 66.2 + - + +
2068A GLY 4.8 0.7 + - - -
2209A ASN* 4.4 13.0 - - - +
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Residues in contact with GLU2066 (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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2062A THR* 2.9 32.9 + - + +
2063A ILE 4.0 2.2 - - - +
2065A GLU* 1.3 84.6 - - + +
2067A LEU* 1.3 63.3 + - + +
2068A GLY 3.8 0.2 - - - -
2180A VAL* 3.4 33.0 - - + +
2199A PRO 4.8 0.2 - - - +
2202A ALA* 4.1 4.3 - - + -
2205A ARG* 2.8 53.6 + - - +
2209A ASN* 5.1 2.8 + - - -
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Residues in contact with LEU2067 (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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2063A ILE* 3.0 19.8 + - + +
2066A GLU* 1.3 88.7 - - + +
2068A GLY* 1.3 56.7 + - - +
2069A THR* 3.4 5.7 + - - +
2073A MET* 3.6 38.5 - - + +
2140A ASP* 3.6 20.2 - - + +
2141A VAL* 3.8 19.5 - - + -
2178A LYS* 4.2 22.2 - - + +
2179A MET* 4.3 7.9 - - - +
2180A VAL* 4.2 20.2 - - + -
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Residues in contact with GLY2068 (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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2064A ARG* 2.7 21.5 + - - +
2065A GLU 4.7 1.0 + - - -
2066A GLU 3.8 0.8 - - - -
2067A LEU* 1.3 73.6 - - - +
2069A THR* 1.3 62.6 + - - +
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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
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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