Contacts of the helix formed by residues 63 - 71 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42H CYS* 3.4 16.1 - - - -
44H THR* 4.9 11.2 - - - -
61H PHE* 3.3 4.4 + - - +
62H SER* 1.3 81.7 - - - +
64H LEU* 1.3 63.1 + - - +
65H SER* 3.7 7.6 + - - -
66H ASP* 3.6 26.9 + - - +
67H MET* 3.2 17.7 + - - +
500H NAI 5.7 0.7 - - - -
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Residues in contact with LEU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H VAL* 4.5 14.4 - - + -
42H CYS* 3.7 9.6 - - - -
63H SER* 1.3 73.4 - - - +
65H SER* 1.3 67.2 + - - +
67H MET* 3.2 14.4 + - + +
68H LEU* 2.9 34.3 + - + +
76H LEU* 3.7 29.4 - - + -
78H LEU* 5.2 0.4 - - + -
88H GLN* 3.6 52.0 - - + +
91H GLU* 4.0 18.2 - - - +
92H VAL* 4.2 4.7 - - + -
500H NAI 5.5 3.2 + - - +
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Residues in contact with SER 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H SER* 3.3 8.6 + - - -
64H LEU* 1.3 79.5 - - - +
66H ASP* 1.3 69.4 + - - +
68H LEU* 3.0 4.9 + - - +
69H ALA* 2.9 26.2 + - - +
91H GLU* 3.2 20.0 + - - -
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Residues in contact with ASP 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H PHE* 3.8 14.5 - - + -
62H SER* 4.9 9.1 + - - +
63H SER* 3.6 21.6 + - - +
64H LEU 3.3 0.4 - - - -
65H SER* 1.3 81.8 + - - +
67H MET* 1.3 64.7 + - - +
69H ALA* 3.4 5.9 + - - +
70H GLN* 3.0 41.0 + - - +
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Residues in contact with MET 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU 4.0 12.1 - - - +
16H VAL* 4.3 6.3 - - + -
40H GLU* 4.2 22.8 - - - +
41H ILE 4.3 4.3 - - - -
42H CYS* 3.6 26.9 - - + -
61H PHE* 3.5 37.2 - - + -
63H SER 3.2 13.5 + - - +
64H LEU* 3.6 17.3 - - + +
65H SER 3.2 0.6 - - - -
66H ASP* 1.3 81.3 - - - +
68H LEU* 1.3 54.6 + - - +
71H GLY* 2.8 29.3 + - - -
76H LEU* 3.4 38.1 - - + -
97H ARG* 4.9 1.4 + - - -
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Residues in contact with LEU 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H LEU* 2.9 28.8 + - + +
65H SER* 3.7 4.0 - - - +
67H MET* 1.3 74.1 - - - +
69H ALA* 1.3 66.3 + - - +
70H GLN 3.3 0.2 - - - -
71H GLY 4.1 0.3 - - - +
76H LEU* 3.6 23.8 - - + -
91H GLU* 3.3 52.0 - - + +
92H VAL* 3.9 9.2 - - - +
95H ALA* 3.7 26.8 - - + +
97H ARG* 2.9 39.8 + - + +
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Residues in contact with ALA 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H SER 2.9 15.8 + - - +
66H ASP* 3.8 5.2 - - - +
68H LEU* 1.3 80.2 - - - +
70H GLN* 1.3 73.7 + - + +
71H GLY 4.5 0.9 - - - +
97H ARG* 5.2 0.2 + - - -
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Residues in contact with GLN 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ARG* 3.5 35.3 + - - +
61H PHE* 3.8 10.6 - - + -
66H ASP* 3.0 33.3 + - - +
69H ALA* 1.3 90.9 - - + +
71H GLY* 1.3 65.7 + - - +
72H ASN* 5.2 0.5 - - - +
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Residues in contact with GLY 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H GLU* 3.0 15.9 - - - -
59H ARG* 4.6 4.3 - - - -
61H PHE* 4.0 8.9 - - - -
67H MET 2.8 22.4 + - - -
68H LEU 4.1 0.7 - - - +
69H ALA 3.8 1.1 - - - +
70H GLN* 1.3 78.7 - - - +
72H ASN* 1.3 62.9 + - - +
73H ALA 3.8 0.9 - - - -
97H ARG* 3.3 21.5 + - - -
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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