Contacts of the helix formed by residues 2069 - 2083 (chain C) in PDB entry 1G24
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 SER2069 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2067C GLY 3.7 1.2 + - - -
2068C LEU* 1.3 74.8 - - - +
2070C LYS* 1.3 64.8 + - - +
2071C SER* 3.6 7.6 + - - -
2072C GLU* 2.9 45.3 + - - +
2073C LYS* 3.0 24.1 + - - +
2110C LEU* 5.1 0.5 - - - +
2117C LYS* 4.4 5.4 - - - +
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Residues in contact with LYS2070 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069C SER* 1.3 74.0 - - - +
2071C SER* 1.3 59.3 + - - +
2073C LYS* 3.3 9.8 + - - +
2074C GLU* 3.0 54.7 + - + +
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Residues in contact with SER2071 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069C SER* 3.2 7.1 + - - -
2070C LYS* 1.3 79.9 - - - +
2072C GLU* 1.3 59.2 + - - +
2074C GLU* 3.4 11.1 + - - +
2075C ALA* 3.0 28.2 + - - +
2106C LYS* 6.2 0.2 - - - -
2110C LEU* 3.8 28.2 - - - +
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Residues in contact with GLU2072 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2068C LEU* 3.4 13.1 - - + +
2069C SER* 2.9 35.2 + - - +
2071C SER* 1.3 74.2 - - - +
2073C LYS* 1.3 66.6 + - - +
2075C ALA* 3.3 7.2 + - - +
2076C ILE* 3.1 28.4 + - - +
2110C LEU* 4.2 21.0 - - + +
2111C LEU* 5.9 0.2 - - - -
2113C LYS* 4.3 10.9 + - - +
2114C SER* 3.6 37.5 + - - -
2117C LYS* 2.8 37.4 + - - -
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Residues in contact with LYS2073 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063C TYR* 3.5 25.5 + - - +
2068C LEU* 3.7 42.0 + - + +
2069C SER 3.0 15.8 + - - +
2070C LYS* 3.7 9.8 - - - +
2072C GLU* 1.3 76.0 - - - +
2074C GLU* 1.3 59.0 + - + +
2076C ILE* 3.1 6.3 + - - +
2077C VAL* 2.9 34.8 + - + +
2206C ILE* 3.9 19.1 - - + +
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Residues in contact with GLU2074 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2070C LYS* 3.0 53.1 + - + +
2071C SER* 3.6 10.3 + - - +
2073C LYS* 1.3 76.6 - - + +
2075C ALA* 1.3 56.6 + - - +
2077C VAL* 3.2 9.3 + - + +
2078C SER* 2.9 33.2 + - - +
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Residues in contact with ALA2075 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2071C SER 3.0 16.5 + - - +
2072C GLU* 3.6 5.6 - - - +
2073C LYS 3.3 0.2 - - - -
2074C GLU* 1.3 75.5 - - - +
2076C ILE* 1.3 57.0 + - - +
2078C SER* 3.3 8.1 + - - -
2079C TYR* 2.9 23.4 + - - +
2107C GLN* 3.8 35.1 - - + +
2110C LEU* 3.9 15.7 - - + -
2111C LEU* 3.5 18.6 - - + +
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Residues in contact with ILE2076 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2068C LEU* 3.9 15.5 - - + -
2072C GLU 3.1 16.5 + - - +
2073C LYS* 3.1 7.2 + - - +
2075C ALA* 1.3 75.4 - - - +
2077C VAL* 1.3 66.2 + - - +
2079C TYR* 3.2 4.7 + - + +
2080C THR* 3.0 24.9 + - + +
2111C LEU* 3.6 18.4 - - + -
2114C SER* 4.5 7.9 - - - +
2118C MET* 4.3 15.0 - - + -
2203C ILE* 3.7 40.6 - - + -
2206C ILE* 3.8 33.4 - - + -
2207C SER* 5.2 0.7 - - - -
2216C LEU* 5.4 4.5 - - + -
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Residues in contact with VAL2077 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2073C LYS* 2.9 20.9 + - + +
2074C GLU* 3.6 9.9 - - - +
2076C ILE* 1.3 75.2 - - - +
2078C SER* 1.3 63.1 + - - +
2080C THR* 2.6 24.1 + - - -
2081C LYS* 3.1 33.9 + - + +
2206C ILE* 3.6 26.2 - - + +
2207C SER* 4.0 14.4 - - - +
2208C ALA 5.9 0.2 - - - +
2209C PHE* 5.6 0.2 - - + -
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Residues in contact with SER2078 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2074C GLU* 2.9 19.4 + - - +
2075C ALA 3.6 5.8 - - - -
2077C VAL* 1.3 78.1 - - - +
2079C TYR* 1.3 62.1 + - - +
2081C LYS* 3.2 10.8 + - - +
2082C SER* 3.1 25.8 + - - -
2086C ILE* 4.4 2.8 - - - +
2107C GLN* 3.1 35.5 + - - -
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Residues in contact with TYR2079 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2075C ALA 2.9 14.4 + - - +
2076C ILE* 3.2 9.2 + - - +
2078C SER* 1.3 76.8 - - - +
2080C THR* 1.3 69.5 + - + +
2082C SER 3.1 0.2 + - - -
2083C ALA* 2.7 57.9 + - + +
2086C ILE* 3.9 23.0 - - + +
2087C ASN* 3.1 25.4 + - - -
2111C LEU* 4.1 16.8 - - + -
2172C TYR* 3.8 37.5 + + + +
2174C SER* 3.0 28.5 + - - -
2203C ILE* 4.8 1.8 - - + -
2214C GLU* 4.1 5.2 - - - -
2216C LEU* 3.6 26.0 - - + -
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Residues in contact with THR2080 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2076C ILE* 3.0 13.6 + - + +
2077C VAL 2.6 18.2 + - - -
2079C TYR* 1.3 83.2 - - + +
2081C LYS* 1.3 60.4 + - - +
2083C ALA* 4.4 6.4 + - - +
2203C ILE* 4.0 21.1 - - + -
2207C SER* 2.7 33.9 + - - -
2209C PHE* 3.8 25.5 - - - +
2210C ALA* 3.9 14.4 - - - -
2214C GLU* 4.8 1.8 - - - +
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Residues in contact with LYS2081 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2077C VAL* 3.1 35.7 + - + +
2078C SER* 3.7 10.1 - - - +
2079C TYR 3.1 0.8 - - - -
2080C THR* 1.3 78.1 - - - +
2082C SER* 1.3 64.4 + - - +
2083C ALA 3.8 0.7 - - - -
2209C PHE* 3.0 44.3 - - + -
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Residues in contact with SER2082 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2078C SER 3.1 12.7 + - - -
2079C TYR 3.4 2.0 - - - -
2081C LYS* 1.3 82.5 + - - +
2083C ALA* 1.3 66.2 + - - +
2084C SER* 3.3 3.6 - - - -
2085C GLU* 3.2 23.5 + - - +
2086C ILE* 2.9 33.6 + - - +
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Residues in contact with ALA2083 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2079C TYR* 2.7 52.6 + - + +
2080C THR* 4.4 6.2 + - - +
2081C LYS 3.8 0.8 - - - -
2082C SER* 1.3 73.2 - - - +
2084C SER* 1.3 64.0 + - - +
2086C ILE* 4.5 0.4 - - - -
2087C ASN* 2.9 33.8 + - - +
2174C SER* 5.3 1.1 - - - +
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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