Contacts of the helix formed by residues 48 - 59 (chain O) in PDB entry 4HOK
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 GLN 48 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40O GLU* 2.8 12.1 + - - +
46O HIS* 3.0 28.0 + - - +
47O PRO* 1.3 83.2 - - - +
49O LEU* 1.3 65.2 + - - +
50O HIS 3.0 4.8 + - - +
51O ILE* 3.0 16.7 + - + +
52O GLU* 3.0 20.6 + - - +
151O GLY* 6.1 6.6 - - - -
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Residues in contact with LEU 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O LYS* 3.6 47.6 - - + +
39O LEU 4.6 0.2 - - - -
40O GLU* 2.6 38.8 + - + +
48O GLN* 1.3 71.7 - - - +
50O HIS* 1.3 60.2 + - - +
52O GLU* 3.3 6.8 + - - +
53O SER* 3.0 21.6 + - - -
78O ASN* 3.9 21.3 - - + +
79O VAL* 4.0 3.1 - - - +
80O MET* 3.7 44.0 - - + +
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Residues in contact with HIS 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O GLU* 4.4 3.8 + - - +
48O GLN 3.1 1.0 - - - +
49O LEU* 1.3 73.2 - - - +
51O ILE* 1.3 61.9 + - + +
52O GLU 2.5 16.9 + - - -
53O SER* 2.4 33.3 + - - -
54O LYS* 3.1 14.0 + - + +
71O CYS* 5.1 10.1 - - - -
78O ASN* 6.0 6.2 - - - +
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Residues in contact with ILE 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O PRO* 4.3 21.3 - - + +
48O GLN* 3.0 11.1 + - + +
50O HIS* 1.3 82.6 - - + +
52O GLU* 1.3 58.4 + - - +
54O LYS* 3.7 7.9 - - + +
55O PHE* 3.0 34.4 - - + -
150O PHE 5.4 0.6 - - - +
151O GLY* 5.4 12.8 - - - -
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Residues in contact with GLU 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O LYS* 3.9 20.8 + - - -
48O GLN 3.0 9.0 + - - +
49O LEU* 3.5 14.3 - - + +
50O HIS 2.5 5.9 + - - -
51O ILE* 1.3 74.4 - - - +
53O SER* 1.3 53.2 - - - +
54O LYS* 2.2 20.8 + - - -
55O PHE* 2.4 24.6 + - - -
56O TYR* 2.6 44.7 + - + -
80O MET* 4.2 8.2 - - - +
82O MET* 4.9 1.3 - - - +
149O ASP* 3.6 20.7 + - - -
150O PHE* 3.9 17.7 + - + +
151O GLY* 4.7 7.4 - - - +
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Residues in contact with SER 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O LEU* 3.0 6.9 + - - -
50O HIS* 2.4 46.5 + - - -
52O GLU* 1.3 73.3 - - - +
54O LYS* 1.3 60.3 + - - -
55O PHE 3.4 0.2 - - - -
56O TYR* 3.3 2.5 + - - +
57O LYS* 2.8 30.9 + - - +
68O ILE* 4.4 6.5 - - - -
71O CYS* 4.2 24.2 - - - -
80O MET* 3.9 23.9 - - - -
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Residues in contact with LYS 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O HIS* 3.1 19.4 + - + +
51O ILE* 3.7 7.0 - - + +
52O GLU 2.2 12.2 + - - +
53O SER* 1.3 67.3 + - - +
55O PHE* 1.3 89.3 + - + +
57O LYS* 2.6 14.3 + - - +
58O MET* 2.5 65.0 + - + +
124O PHE* 3.5 13.8 - - - -
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Residues in contact with PHE 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O ILE* 3.0 38.6 - - + -
52O GLU* 2.4 18.7 + - - +
54O LYS* 1.3 90.1 - - + +
56O TYR* 1.3 56.6 + - - +
58O MET* 4.2 5.6 - - - +
59O MET* 2.8 47.0 + - + +
124O PHE* 3.5 43.7 - + - -
150O PHE* 3.5 50.0 - + + -
153O ALA* 3.4 26.5 - - + -
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Residues in contact with TYR 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O GLU* 2.6 43.9 + - + -
53O SER 3.3 4.3 + - - +
54O LYS 3.2 1.0 - - - -
55O PHE* 1.3 77.4 - - - +
57O LYS* 1.3 57.6 + - - +
59O MET* 3.7 3.5 - - - -
60O GLN* 3.1 23.6 + - - +
65O ILE* 4.5 5.5 - - + +
66O PRO* 3.0 53.3 - - + +
67O SER* 5.7 0.5 - - - -
68O ILE* 2.7 40.0 + - + +
80O MET* 3.8 19.1 - - + -
82O MET* 3.9 14.5 - - + +
148O ILE* 3.1 28.2 - - + +
149O ASP 3.4 1.4 + - - -
150O PHE* 4.1 14.8 - + - -
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Residues in contact with LYS 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O SER* 2.8 14.6 + - - +
54O LYS* 2.6 21.4 + - - +
56O TYR* 1.3 70.0 - - - +
58O MET* 1.3 56.2 + - - +
59O MET 3.1 1.3 - - - -
60O GLN* 2.6 45.1 + - - +
68O ILE* 3.5 37.6 - - + +
71O CYS* 5.1 12.5 - - - +
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Residues in contact with MET 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O LYS* 2.5 42.7 + - + +
55O PHE* 4.1 4.5 - - - +
57O LYS* 1.3 74.9 - - - +
59O MET* 1.3 84.3 - - + +
60O GLN 3.3 4.9 + - - +
122O LYS* 2.6 52.3 + - + +
124O PHE* 3.0 29.8 - - + -
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Residues in contact with MET 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55O PHE* 2.8 32.3 + - + +
56O TYR 3.7 3.1 - - - -
58O MET* 1.3 105.9 - - + +
60O GLN* 1.3 70.6 + - - +
61O GLY 3.4 0.2 + - - -
62O GLY 3.1 10.9 + - - -
65O ILE* 3.5 32.3 - - + +
118O TYR* 3.5 25.6 + - + -
119O ILE* 4.0 37.5 - - + +
122O LYS* 3.7 15.7 - - + -
124O PHE* 4.1 8.5 - - + -
150O PHE* 4.6 7.0 - - + -
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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