Contacts of the helix formed by residues 53 - 65 (chain T) in PDB entry 2KFX
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 THR 53 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52T PRO* 1.3 76.7 - - - +
54T PRO* 1.3 73.1 - - - +
55T GLU* 2.9 26.5 + - + +
56T GLU* 2.9 44.0 + - + +
57T LEU* 3.4 12.4 + - - +
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Residues in contact with PRO 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T THR* 3.2 42.2 - - - +
52T PRO 4.4 1.6 - - - +
53T THR* 1.3 90.6 - - - +
55T GLU* 1.3 59.8 + - + +
56T GLU 3.4 0.2 - - - -
57T LEU* 4.1 9.8 - - + -
58T GLN* 3.4 22.2 + - - +
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Residues in contact with GLU 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53T THR* 2.9 16.6 + - + +
54T PRO* 1.3 81.2 - - + +
56T GLU* 1.3 65.2 - - + +
58T GLN* 3.7 12.8 - - - +
59T GLU* 3.9 10.8 - - - +
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Residues in contact with GLU 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T PRO* 3.6 19.9 - - + +
53T THR* 2.9 33.3 + - + +
55T GLU* 1.3 79.2 - - + +
57T LEU* 1.3 65.7 + - + +
59T GLU* 2.9 39.3 + - - +
60T MET* 4.0 2.1 + - - +
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Residues in contact with LEU 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T THR* 4.8 7.6 - - - +
41T LEU* 4.2 28.7 - - + -
42T GLY* 4.2 26.0 - - - +
45T MET* 4.9 8.3 - - + -
52T PRO* 3.7 34.1 - - + +
53T THR 3.4 16.3 + - - +
54T PRO* 4.3 11.0 - - + +
56T GLU* 1.3 75.3 - - - +
58T GLN* 1.3 53.6 + - - +
60T MET* 2.5 46.1 + - + +
61T ILE* 3.2 8.5 - - + +
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Residues in contact with GLN 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T THR* 3.8 20.6 - - + +
54T PRO 3.4 18.4 + - - +
55T GLU* 3.7 10.5 - - - +
56T GLU 3.2 0.2 - - - -
57T LEU* 1.3 78.5 - - - +
59T GLU* 1.3 51.9 + - + +
61T ILE* 3.0 19.6 + - - +
62T ASP* 2.6 48.2 + - + +
65T ASP* 4.7 1.6 - - - +
70T GLY* 4.3 13.5 - - - -
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Residues in contact with GLU 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55T GLU* 3.9 9.8 - - - +
56T GLU* 3.0 34.3 - - - +
57T LEU 2.9 0.4 - - - -
58T GLN* 1.3 79.5 - - + +
60T MET* 1.3 61.5 + - + +
62T ASP* 3.9 7.7 - - - +
63T GLU* 3.4 24.2 + - - +
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Residues in contact with MET 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56T GLU 5.0 1.8 - - - +
57T LEU* 2.5 29.9 + - + +
59T GLU* 1.3 75.5 - - + +
61T ILE* 1.3 62.7 + - + +
63T GLU* 2.7 45.7 - - - +
64T VAL* 3.5 9.0 - - - +
80T MET* 4.6 5.9 - - - +
91T WW7 3.3 39.9 - - + +
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Residues in contact with ILE 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T ILE* 5.8 1.3 - - + +
37T SER* 5.9 4.7 - - - -
38T THR* 5.6 7.4 - - + +
41T LEU* 4.5 26.5 - - + -
57T LEU* 3.2 21.5 - - + +
58T GLN* 3.0 20.3 + - - +
60T MET* 1.3 83.5 - - + +
62T ASP* 1.3 56.7 + - - +
63T GLU 3.2 2.5 - - - -
64T VAL* 3.7 5.6 - - - -
65T ASP* 2.6 64.6 + - - +
70T GLY* 4.1 4.5 - - - -
71T THR* 3.7 16.4 - - - +
72T VAL* 3.8 17.0 - - + -
80T MET* 6.3 1.6 - - + -
91T WW7 5.1 4.7 - - + +
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Residues in contact with ASP 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T GLN* 2.6 34.5 + - + +
59T GLU* 3.9 8.7 - - - +
60T MET 3.4 0.2 - - - -
61T ILE* 1.3 74.9 - - - +
63T GLU* 1.3 63.3 + - - +
65T ASP* 4.0 16.4 + - - +
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Residues in contact with GLU 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T GLU 3.4 8.9 + - - +
60T MET* 2.7 58.7 - - - +
62T ASP* 1.3 81.3 - - - +
64T VAL* 1.3 70.1 + - + +
65T ASP 4.9 0.2 - - - -
66T GLU* 3.8 15.9 - - - +
80T MET* 4.9 7.4 - - - +
83T ARG* 4.1 25.8 + - - +
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Residues in contact with VAL 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60T MET 3.5 11.2 - - - +
61T ILE* 3.3 15.7 - - - +
63T GLU* 1.3 84.5 - - - +
65T ASP* 1.3 63.6 + - - +
66T GLU* 2.4 31.5 + - - +
72T VAL* 4.3 8.1 - - + -
76T GLU* 3.5 29.8 - - + +
79T VAL* 6.1 0.7 - - + -
80T MET* 3.8 48.9 - - + +
83T ARG* 4.1 14.8 - - - +
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Residues in contact with ASP 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T GLN* 4.7 1.0 - - - +
61T ILE* 2.6 30.3 + - - +
62T ASP* 4.1 13.9 - - - +
63T GLU 3.5 1.0 - - - -
64T VAL* 1.3 72.7 - - - +
66T GLU* 1.3 57.5 + - - +
67T ASP* 2.8 13.5 + - - +
68T GLY* 3.3 14.6 + - - +
69T SER 4.5 1.1 - - - +
70T GLY* 2.8 31.9 + - - +
71T THR 2.4 27.6 + - - +
76T GLU* 2.7 16.2 - - - +
90T CA 2.8 13.0 - - - -
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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