Contacts of the helix formed by residues 2071 - 2085 (chain A) in PDB entry 3CMT
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 GLY2071 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069A SER 3.3 2.2 - - - -
2070A SER* 1.3 79.9 - - - +
2072A LYS* 1.3 60.0 + - - +
2074A THR* 3.8 0.6 - - - -
2075A LEU* 2.9 34.8 + - - +
2225A ILE* 3.9 7.1 - - - +
2262A ILE* 4.0 14.3 - - - +
2502A ADP 2.9 26.8 + - - -
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Residues in contact with LYS2072 (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 ILE* 4.3 13.5 - - + +
2065A TYR* 3.9 2.2 - - - -
2066A GLY 3.4 19.9 + - - +
2067A PRO 2.7 28.5 + - - -
2070A SER* 3.5 8.5 - - - +
2071A GLY* 1.3 73.8 - - - +
2073A THR* 1.3 61.2 + - - +
2075A LEU* 3.8 2.6 - - - +
2076A THR* 3.1 25.3 + - - -
2192A ILE* 3.6 26.4 - - + +
2193A ASN 3.4 25.1 - - - +
2194A GLN* 5.0 0.9 - - - +
2225A ILE* 3.6 16.8 - - + -
2501A ALF 3.2 29.7 - - - -
2502A ADP 2.6 28.3 + - - +
3217A PHE* 3.8 3.9 - - - -
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Residues in contact with THR2073 (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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2072A LYS* 1.3 72.1 - - - +
2074A THR* 1.3 68.6 + - - +
2076A THR* 3.1 4.2 + - - -
2077A LEU* 2.8 40.4 + - + +
2092A PHE* 4.1 14.4 - - + -
2099A LEU* 4.5 8.7 - - + -
2144A ASP* 2.9 19.0 + - - +
2192A ILE* 3.9 8.5 - - - +
2500A MG 2.1 33.3 - - - -
2501A ALF 3.8 0.2 - - - -
2502A ADP 2.5 15.7 + - - +
3250A LYS* 5.4 0.5 - - - -
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Residues in contact with THR2074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2071A GLY* 3.8 8.5 - - - -
2072A LYS 3.4 0.2 - - - -
2073A THR* 1.3 73.5 - - - +
2075A LEU* 1.3 63.5 + - - +
2077A LEU* 3.1 5.1 + - - +
2078A GLN* 2.9 34.5 + - + +
2103A TYR* 3.9 21.1 + - - +
2107A LEU* 3.9 21.9 - - + +
2262A ILE* 3.8 31.0 - - + -
2267A GLY* 4.7 6.3 - - - -
2268A ILE* 5.0 1.1 - - + +
2502A ADP 2.8 35.2 + - - -
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Residues in contact with LEU2075 (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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2042A THR* 4.6 5.8 - - + +
2047A LEU* 4.0 26.2 - - + -
2056A LEU* 5.7 0.9 - - + -
2064A ILE* 3.7 30.1 - - + -
2071A GLY 2.9 20.5 + - - +
2072A LYS* 3.8 3.6 - - - +
2074A THR* 1.3 73.8 - - - +
2076A THR* 1.3 64.3 + - - +
2078A GLN* 3.0 19.6 + - - +
2079A VAL* 3.1 27.4 + - + +
2223A LEU* 4.9 4.7 - - + -
2225A ILE* 4.0 14.6 - - + -
2244A VAL* 4.3 4.3 - - + -
2260A PHE* 3.9 28.5 - - + -
2262A ILE* 5.4 1.5 - - + +
2268A ILE* 4.5 12.8 - - + -
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Residues in contact with THR2076 (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 ILE* 4.1 3.5 - - - +
2072A LYS 3.1 10.0 + - - -
2073A THR 3.1 11.2 - - - +
2075A LEU* 1.3 79.5 - - - +
2077A LEU* 1.3 63.6 + - - +
2079A VAL* 3.2 13.9 + - - +
2080A ILE* 3.1 22.6 + - + +
2092A PHE* 3.5 18.8 - - + -
2142A VAL* 3.3 36.1 - - + +
2190A ILE* 4.0 14.6 - - - +
2192A ILE* 3.4 22.1 - - + +
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Residues in contact with LEU2077 (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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2073A THR* 2.8 36.6 + - + +
2074A THR* 3.6 5.8 - - - +
2076A THR* 1.3 74.9 - - + +
2078A GLN* 1.3 52.7 + - - +
2080A ILE* 3.2 9.6 + - + +
2081A ALA* 2.8 35.0 + - - +
2092A PHE* 4.0 26.2 - - + -
2099A LEU* 4.0 20.6 - - + -
2103A TYR* 4.9 6.5 - - + -
2104A ALA* 4.2 22.4 - - + +
2107A LEU* 3.8 24.0 - - + -
2109A VAL* 3.5 18.9 - - + +
2114A LEU* 5.8 3.1 - - + -
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Residues in contact with GLN2078 (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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2042A THR 3.9 11.7 - - - +
2043A GLY* 4.5 7.1 - - - +
2074A THR* 2.9 23.7 + - + +
2075A LEU 3.0 7.8 + - - +
2077A LEU* 1.3 76.4 - - - +
2079A VAL* 1.3 56.9 + - - +
2081A ALA* 3.4 5.5 + - - +
2082A ALA* 3.0 28.8 + - - +
2085A ARG* 4.5 2.2 + - - +
2107A LEU* 2.9 42.2 + - + +
2266A GLU 4.5 1.1 + - - +
2267A GLY* 3.4 8.1 - - - -
2268A ILE* 2.7 55.3 + - + +
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Residues in contact with VAL2079 (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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2040A ILE* 4.4 9.0 - - + +
2041A SER 3.7 19.6 - - - +
2042A THR* 3.6 19.7 + - - +
2056A LEU* 4.5 13.0 - - + -
2075A LEU* 3.1 28.5 + - + +
2076A THR* 3.2 10.3 + - - +
2078A GLN* 1.3 70.7 - - - +
2080A ILE* 1.3 64.9 + - + +
2082A ALA* 3.3 3.4 + - - +
2083A ALA* 2.9 28.6 + - - +
2140A VAL* 4.5 12.8 - - + -
2188A LEU* 4.9 2.2 - - + -
2190A ILE* 3.9 23.3 - - + -
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Residues in contact with ILE2080 (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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2076A THR* 3.1 17.4 + - + +
2077A LEU* 3.4 13.9 - - + +
2079A VAL* 1.3 77.6 - - + +
2081A ALA* 1.3 53.3 + - - +
2083A ALA* 3.0 3.2 + - - +
2084A GLN* 2.8 49.8 + - - +
2090A CYS* 3.8 31.6 - - + -
2091A ALA 4.7 1.3 - - - +
2092A PHE* 3.9 18.8 - - + -
2109A VAL* 4.0 9.4 - - + -
2114A LEU* 3.9 18.4 - - + -
2140A VAL* 4.3 7.2 - - + -
2142A VAL* 3.4 32.1 - - + -
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Residues in contact with ALA2081 (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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2077A LEU 2.8 20.3 + - - +
2078A GLN* 3.5 8.7 - - - +
2079A VAL 3.3 0.2 - - - -
2080A ILE* 1.3 73.2 - - - +
2082A ALA* 1.3 57.7 + - - +
2084A GLN* 3.3 9.2 + - - +
2085A ARG* 2.9 43.5 + - - +
2107A LEU 3.9 10.8 - - - +
2108A GLY 3.4 32.9 - - - +
2109A VAL* 4.1 2.9 - - - +
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Residues in contact with ALA2082 (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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2040A ILE* 5.4 1.6 - - + -
2041A SER* 4.2 28.5 - - - +
2043A GLY* 5.0 5.8 - - - +
2078A GLN 3.0 16.4 + - - +
2079A VAL 3.6 4.3 - - - +
2081A ALA* 1.3 76.0 - - - +
2083A ALA* 1.3 60.9 + - - +
2085A ARG* 3.2 35.2 + - - +
2086A GLU* 3.5 16.5 + - - +
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Residues in contact with ALA2083 (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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2040A ILE* 4.4 13.4 - - + +
2079A VAL 2.9 17.5 + - - +
2080A ILE 3.5 4.0 - - - +
2082A ALA* 1.3 74.7 - - - +
2084A GLN* 1.3 60.1 + - - +
2086A GLU* 3.0 24.4 + - - +
2088A LYS* 3.1 31.7 + - + +
2090A CYS* 4.0 4.5 - - - -
2140A VAL* 3.8 28.0 - - + -
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Residues in contact with GLN2084 (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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2080A ILE* 2.8 29.7 + - - +
2081A ALA* 3.7 4.7 - - - +
2083A ALA* 1.3 68.2 - - - +
2085A ARG* 1.3 57.6 + - - +
2086A GLU 2.9 10.1 + - - -
2087A GLY* 2.9 14.6 + - - -
2088A LYS 3.8 18.4 + - - +
2089A THR* 6.1 0.2 - - - +
2090A CYS* 3.9 11.4 - - - +
2108A GLY 5.9 0.2 - - - +
2109A VAL* 3.4 9.4 - - - +
2110A ASP* 2.7 58.1 + - + +
2113A ASN* 3.9 8.3 + - - +
2114A LEU* 3.7 24.4 - - - +
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Residues in contact with ARG2085 (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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2078A GLN* 4.5 2.2 + - - +
2081A ALA* 2.9 24.6 + - - +
2082A ALA* 3.2 45.5 - - - +
2084A GLN* 1.3 74.4 - - - +
2086A GLU* 1.3 60.3 + - + +
2087A GLY 3.6 0.8 + - - -
2107A LEU 5.5 1.0 + - - -
2108A GLY* 4.6 7.3 + - - -
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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