Contacts of the helix formed by residues 2082 - 2093 (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 SER2082 (chain C).
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Specific contacts
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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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Residues in contact with SER2084 (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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2082C SER 3.3 0.8 - - - -
2083C ALA* 1.3 78.3 - - - +
2085C GLU* 1.3 57.3 + - - +
2087C ASN* 4.2 2.0 - - - +
2088C GLY* 3.0 27.0 + - - -
2091C ARG* 5.1 1.6 + - - +
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Residues in contact with GLU2085 (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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2082C SER* 3.2 24.6 + - - +
2084C SER* 1.3 75.5 - - - +
2086C ILE* 1.3 62.3 + - + +
2088C GLY* 3.2 1.7 + - - -
2089C LYS* 2.9 65.8 + - + +
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Residues in contact with ILE2086 (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* 4.4 2.7 - - - +
2079C TYR* 3.9 32.5 - - + +
2082C SER* 2.9 29.1 + - - +
2083C ALA* 3.9 3.8 - - - +
2085C GLU* 1.3 77.8 - - + +
2087C ASN* 1.3 64.1 + - - +
2089C LYS* 3.2 8.6 + - - +
2090C LEU* 2.9 40.0 + - + +
2100C PHE* 5.2 0.8 - - + -
2104C LEU* 4.1 26.7 - - + -
2107C GLN* 4.9 7.0 - - + +
2108C VAL* 4.7 11.7 - - + -
2111C LEU* 5.2 5.2 - - + -
2172C TYR* 4.2 17.3 - - + -
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Residues in contact with ASN2087 (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* 3.1 24.9 + - - -
2083C ALA* 2.9 26.5 + - - +
2084C SER* 4.3 2.6 - - - +
2086C ILE* 1.3 72.8 - - - +
2088C GLY* 1.3 57.4 + - - +
2090C LEU* 3.3 6.2 + - - +
2091C ARG* 2.9 60.2 + - - +
2171C GLY* 3.4 3.1 - - - -
2172C TYR* 2.8 50.1 + - - -
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Residues in contact with GLY2088 (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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2084C SER 3.0 18.8 + - - -
2085C GLU* 3.6 2.0 - - - -
2086C ILE 3.1 0.4 - - - -
2087C ASN* 1.3 77.4 - - - +
2089C LYS* 1.3 56.3 + - - +
2091C ARG* 3.3 12.7 + - - +
2092C GLN* 3.0 32.4 + - - +
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Residues in contact with LYS2089 (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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2085C GLU* 2.9 48.8 + - + +
2086C ILE* 3.2 5.1 + - - +
2088C GLY* 1.3 72.9 - - - +
2090C LEU* 1.3 65.4 + - - +
2092C GLN* 3.5 2.9 + - - -
2093C ASN* 2.9 37.0 + - - +
2100C PHE* 3.7 23.0 - - + -
2101C PRO* 4.4 17.4 - - + +
2104C LEU* 3.8 27.6 - - + +
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Residues in contact with LEU2090 (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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2086C ILE* 2.9 24.0 + - + +
2087C ASN* 3.6 5.6 - - - +
2088C GLY 3.3 0.2 - - - -
2089C LYS* 1.3 78.0 - - - +
2091C ARG* 1.3 57.3 + - - +
2093C ASN* 5.1 0.2 - - - -
2094C LYS 3.0 8.7 + - - -
2095C GLY* 2.9 32.0 + - - +
2097C ILE* 3.9 6.3 - - + -
2100C PHE* 3.8 25.6 - - + -
2108C VAL* 5.0 3.4 - - + -
2170C TYR* 3.5 26.5 - - - +
2171C GLY* 3.8 9.9 - - - -
2172C TYR* 3.7 32.3 - - + -
2219C ARG* 3.7 30.7 - - - +
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Residues in contact with ARG2091 (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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2084C SER 5.1 0.8 + - - -
2087C ASN* 2.9 59.2 + - - +
2088C GLY* 3.8 10.0 - - - +
2090C LEU* 1.3 77.3 - - - +
2092C GLN* 1.3 61.6 + - - +
2094C LYS* 3.2 27.4 + - - +
2169C GLU* 2.8 36.0 + - - +
2170C TYR* 3.8 21.0 - - + -
2171C GLY 4.3 1.1 - - - +
2172C TYR 4.8 4.4 + - - -
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Residues in contact with GLN2092 (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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2088C GLY 3.0 19.4 + - - +
2089C LYS* 4.1 4.5 - - - +
2091C ARG* 1.3 76.0 - - - +
2093C ASN* 1.3 68.3 + - - +
2094C LYS* 3.8 11.4 + - - +
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Residues in contact with ASN2093 (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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2089C LYS* 2.9 31.9 + - - +
2090C LEU 4.4 0.7 - - - +
2092C GLN* 1.3 87.7 - - - +
2094C LYS* 1.3 70.9 + - - +
2095C GLY 3.3 1.3 - - - -
2096C VAL* 3.1 37.1 + - + +
2100C PHE* 3.5 18.3 - - + -
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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