Contacts of the helix formed by residues 63 - 70 (chain E) in PDB entry 3Q2K
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 SER 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E CYS* 3.6 12.5 - - - -
44E THR* 5.3 4.0 - - - -
61E PHE* 3.3 7.2 + - - +
62E SER* 1.3 83.5 + - - +
64E LEU* 1.3 62.1 + - - +
65E SER* 3.0 10.9 + - - -
66E ASP* 2.9 36.1 + - - +
67E MET* 3.4 15.1 + - - +
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E VAL* 4.3 18.4 - - + -
42E CYS* 3.8 10.4 - - - -
63E SER* 1.3 73.2 - - - +
65E SER* 1.3 64.9 + - - +
67E MET* 4.0 7.2 - - - -
68E LEU* 3.2 38.9 + - + +
76E LEU* 4.1 19.3 - - + -
78E LEU* 5.4 0.2 - - + -
88E GLN* 3.7 48.5 - - + +
91E GLU* 3.4 26.2 - - - +
92E VAL* 4.3 6.5 - - + -
500E NAI 5.5 3.6 + - - +
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E SER* 3.0 8.5 + - - -
64E LEU* 1.3 81.2 - - - +
66E ASP* 1.3 65.9 + - - +
68E LEU* 4.2 3.4 - - - +
69E ALA* 3.3 20.4 + - - +
91E GLU* 2.8 24.4 + - - -
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Residues in contact with ASP 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E PHE* 3.7 13.0 - - + +
62E SER* 4.1 11.6 + - - -
63E SER* 2.9 35.4 + - - +
65E SER* 1.3 76.2 - - - +
67E MET* 1.3 57.4 + - - +
68E LEU 3.1 1.3 - - - -
69E ALA* 2.9 9.2 + - - +
70E GLN* 2.8 54.7 + - - +
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Residues in contact with MET 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLY* 4.0 5.6 - - - -
15E LEU 3.2 31.6 - - - +
16E VAL* 4.5 1.3 - - - -
40E GLU* 3.4 21.6 - - + +
41E ILE 3.4 28.0 - - - +
42E CYS* 3.7 12.3 - - - -
61E PHE* 3.3 34.7 - - + -
63E SER 3.4 11.0 + - - +
64E LEU* 3.7 9.4 + - - +
66E ASP* 1.3 78.9 - - - +
68E LEU* 1.3 56.3 + - - +
71E GLY* 2.9 29.2 + - - -
76E LEU* 3.5 25.1 - - + +
97E ARG* 4.8 1.6 + - - -
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Residues in contact with LEU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E LEU* 3.2 30.9 + - + +
65E SER* 4.2 3.1 - - - +
66E ASP 3.1 1.0 - - - -
67E MET* 1.3 78.1 - - - +
69E ALA* 1.3 61.5 + - - +
71E GLY 3.4 1.6 - - - +
76E LEU* 3.6 33.7 - - + -
91E GLU* 3.8 44.9 - - + +
92E VAL* 4.0 12.1 - - + +
95E ALA* 3.7 24.7 - - + +
97E ARG* 2.5 32.8 + - + +
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E SER 3.3 13.0 + - - +
66E ASP* 2.9 9.4 + - - +
68E LEU* 1.3 79.1 - - - +
70E GLN* 1.3 66.2 + - + +
71E GLY 4.1 1.7 - - - +
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Residues in contact with GLN 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 2.8 38.9 + - - +
61E PHE* 2.6 33.1 - - + -
66E ASP* 2.8 37.2 + - - +
69E ALA* 1.3 75.2 - - + +
71E GLY* 1.3 63.0 + - - +
72E ASN* 5.1 1.9 + - - +
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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