Contacts of the helix formed by residues 63 - 71 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42G CYS* 3.5 13.5 - - - -
44G THR* 4.5 8.7 - - - -
61G PHE* 3.6 4.2 - - - +
62G SER* 1.3 79.7 + - - +
64G LEU* 1.3 61.2 + - - +
65G SER* 3.5 6.7 + - - -
66G ASP* 3.1 34.0 + - - +
67G MET 3.2 14.7 + - - -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G VAL* 4.1 15.0 - - + -
42G CYS* 3.7 12.2 - - - -
44G THR* 5.6 0.2 - - - +
63G SER* 1.3 71.6 - - - +
65G SER* 1.3 63.3 + - - +
67G MET* 3.2 22.9 + - + +
68G LEU* 2.8 46.6 + - + +
76G LEU* 4.1 8.1 - - + -
88G GLN* 3.5 47.1 - - + +
91G GLU* 3.4 25.4 - - + +
92G VAL* 4.2 3.4 - - + -
500G NAI 5.2 4.8 + - - +
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Residues in contact with SER 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G SER* 3.3 6.7 + - - -
64G LEU* 1.3 79.9 - - - +
66G ASP* 1.3 59.5 + - - +
68G LEU* 3.3 3.8 + - - +
69G ALA* 2.8 30.4 + - - +
91G GLU* 3.4 22.1 + - - -
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Residues in contact with ASP 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G PHE* 4.0 9.9 - - + -
62G SER* 4.3 12.0 + - - -
63G SER* 3.1 21.7 + - - +
65G SER* 1.3 76.6 + - - +
67G MET* 1.3 66.3 + - - +
69G ALA* 4.3 2.8 - - - +
70G GLN* 2.9 52.9 + - - +
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Residues in contact with MET 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLY* 4.9 0.2 - - - -
15G LEU 4.3 5.8 - - - +
16G VAL* 3.1 35.0 - - + -
40G GLU* 3.9 22.6 - - - +
41G ILE 4.3 1.3 - - - -
42G CYS* 3.5 22.4 - - + -
61G PHE* 3.2 38.7 - - + -
63G SER 3.2 10.9 + - - +
64G LEU* 3.2 16.3 + - + +
66G ASP* 1.3 78.6 - - - +
68G LEU* 1.3 55.3 + - - +
71G GLY* 2.7 34.3 + - - -
76G LEU* 3.5 24.2 - - + -
97G ARG* 4.7 0.5 + - - -
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Residues in contact with LEU 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G LEU* 2.8 36.3 + - + +
65G SER* 3.8 4.0 - - - +
67G MET* 1.3 76.8 - - - +
69G ALA* 1.3 65.0 + - - +
70G GLN 3.3 0.2 - - - -
76G LEU* 3.2 28.5 - - + -
91G GLU* 3.8 17.7 - - + +
92G VAL* 3.7 27.6 - - - +
95G ALA* 4.0 23.9 - - + +
97G ARG* 3.4 36.6 + - + +
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G SER* 2.8 21.3 + - - +
66G ASP* 3.3 6.3 + - - +
68G LEU* 1.3 75.8 - - - +
70G GLN* 1.3 68.8 + - + +
71G GLY 4.6 2.1 - - - +
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Residues in contact with GLN 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ARG* 3.3 24.6 + - - +
61G PHE* 3.6 24.6 - - + -
66G ASP* 2.9 36.5 + - - +
69G ALA* 1.3 82.6 - - + +
71G GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G GLU* 2.8 18.4 - - - -
59G ARG* 4.3 1.8 - - - -
61G PHE* 4.1 5.6 - - - -
67G MET 2.7 23.4 + - - -
68G LEU 4.4 1.0 - - - +
69G ALA 3.7 1.8 - - - +
70G GLN* 1.3 78.8 - - - +
72G ASN* 1.3 63.4 + - - +
73G ALA 3.9 0.4 - - - -
97G ARG* 2.9 20.6 + - - -
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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