Contacts of the helix formed by residues 2078 - 2087 (chain C) in PDB entry 2QRA
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 SER2078 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2073C TRP* 4.5 1.3 - - - -
2076C GLY 3.9 1.2 + - - -
2077C ASP* 1.3 73.8 - - - +
2079C ALA* 1.3 65.0 + - - +
2080C VAL* 3.5 5.4 + - - +
2081C GLY* 2.8 24.5 + - - -
2082C ARG* 2.9 25.5 + - - +
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Residues in contact with ALA2079 (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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2042C VAL* 4.6 2.7 - - + +
2046C THR* 3.8 32.2 - - + +
2047C LEU* 4.0 18.6 - - + -
2050C ALA* 3.6 21.3 - - + -
2052C PHE* 3.7 5.3 - - + -
2073C TRP* 3.9 15.1 - - + -
2077C ASP 4.0 2.2 + - - -
2078C SER* 1.3 72.3 + - - +
2080C VAL* 1.3 62.2 + - - +
2082C ARG* 4.2 0.3 - - - -
2083C HIS* 3.1 24.4 + - - +
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Residues in contact with VAL2080 (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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2049C ARG* 5.2 2.2 - - + +
2050C ALA* 3.7 24.0 - - + -
2078C SER* 3.3 4.8 + - - +
2079C ALA* 1.3 76.1 - - + +
2081C GLY* 1.3 55.4 + - - +
2083C HIS* 3.2 6.2 + - - +
2084C ARG* 2.7 55.1 + - - +
2092C PHE* 6.0 1.1 - - + -
2093C ILE* 4.2 18.4 - - + -
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Residues in contact with GLY2081 (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* 2.8 23.3 + - - -
2080C VAL* 1.3 80.3 - - - +
2082C ARG* 1.3 60.5 + - - +
2084C ARG* 3.3 7.9 + - - +
2085C LYS* 3.0 21.0 + - - +
5005C EOH 4.9 5.5 - - - +
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Residues in contact with ARG2082 (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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71A ASP* 3.0 31.3 + - - -
72A ARG* 3.3 25.6 - - - +
2070C VAL* 3.3 21.7 - - + +
2071C ASP 2.8 29.7 + - - +
2072C ARG 3.7 0.8 + - - -
2073C TRP* 3.3 43.8 - - + -
2077C ASP* 3.6 17.0 - - + -
2078C SER 2.9 19.0 + - - +
2081C GLY* 1.3 72.1 - - - -
2083C HIS* 1.3 63.7 + - - +
2085C LYS* 2.9 25.1 + - - +
2086C VAL* 3.1 12.4 + - - +
5005C EOH 3.3 33.6 + - + +
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Residues in contact with HIS2083 (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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2050C ALA 2.8 29.4 + - - -
2051C GLY* 4.6 0.2 - - - -
2052C PHE* 3.5 25.9 - + + -
2063C CYS* 3.4 18.9 - - + +
2066C CYS* 4.4 5.8 - - - -
2068C ALA* 5.5 0.4 - - + -
2070C VAL* 4.9 0.2 - - - -
2079C ALA 3.1 20.4 + - - +
2080C VAL* 3.4 7.0 - - - +
2082C ARG* 1.3 79.3 - - - +
2084C ARG* 1.3 62.1 + - - +
2085C LYS 3.2 0.2 + - - -
2086C VAL* 3.3 8.7 - - + +
2087C SER* 3.1 21.1 + - - -
2090C CYS* 3.6 2.3 - - - -
2092C PHE* 4.3 2.5 - + - -
2093C ILE* 3.5 21.6 - - + +
2100C ZN 2.2 36.0 - - - -
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Residues in contact with ARG2084 (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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2080C VAL* 2.7 36.2 + - - +
2081C GLY* 3.7 7.4 - - - +
2083C HIS* 1.3 72.9 - - - +
2085C LYS* 1.3 63.2 + - - +
2087C SER 4.0 6.7 - - - -
2088C PRO* 3.0 40.6 + - + +
2093C ILE* 3.6 37.9 + - + +
2094C ASN* 5.1 4.9 + - - -
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Residues in contact with LYS2085 (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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57A GLU* 3.7 34.9 - - - +
60A THR* 3.2 36.9 + - + +
62A ARG* 4.1 6.9 + - - -
71A ASP* 3.2 15.6 + - - -
2081C GLY 3.0 12.2 + - - +
2082C ARG* 2.9 17.7 + - - +
2084C ARG* 1.3 80.4 - - - +
2086C VAL* 1.3 66.4 + - + +
2088C PRO* 4.2 7.1 - - - +
5005C EOH 3.2 39.7 + - + -
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Residues in contact with VAL2086 (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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60A THR* 5.1 1.8 - - + -
62A ARG* 3.2 29.2 + - - +
69A ALA* 3.8 30.5 - - + +
71A ASP* 5.8 2.7 - - - +
5002A EOH 4.8 2.6 + - - -
2068C ALA* 4.0 23.6 - - + +
2069C ALA 5.3 2.7 - - - +
2070C VAL* 4.3 17.3 - - + -
2082C ARG 3.6 10.1 - - - +
2083C HIS* 3.3 18.6 - - + +
2085C LYS* 1.3 92.5 - - + +
2087C SER* 1.3 62.7 + - - +
2088C PRO* 3.9 1.8 - - - +
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Residues in contact with SER2087 (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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5002A EOH 4.0 6.9 + - - -
2066C CYS* 3.1 34.9 - - - -
2068C ALA* 3.5 10.4 - - - +
2083C HIS* 3.1 13.1 + - - +
2084C ARG* 3.4 7.5 - - - +
2086C VAL* 1.3 83.9 + - - +
2088C PRO* 1.3 67.0 - - - +
2089C ASN 3.0 6.6 + - - +
2090C CYS* 3.1 22.3 + - - +
2093C ILE* 4.4 2.1 - - - +
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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